title: Bull X001, Sample 17

status: Public on Dec 10 2014

city: Clemson

middle: L

last: Pratt

state: SC

address: 138 Poole Ag Center

institute: Clemson University

description: microRNA

hyb_protocol: standard LC Sciences protocol

scan_protocol: standard LC Sciences protocol

data_processing: standard LC Sciences protocol

organism: Bos taurus

source_name: Mature, ejaculated spermatozoa

label_protocol: standard LC Sciences protocol

extract_protocol: A modified procedure for Ambion's mirVana microRNA isolation kit was used to isolate total RNA enriched for miRNA.

tag: breed

value: Angus

tag: treatment

value: Endophyte-free, tall fescue seed

tag: cell type

value: spermatozoa


title: Bull X904, Sample 26

type: RNA

first: Scott

country: USA

description: microRNA

molecule: total RNA

value: Endophyte-infected, tall fescue seed


title: Bull X907, Sample 18

description: microRNA


title: cKO mouse_2

status: Public on Dec 11 2014

city: Washington

first: Yang

last: Liu

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology Research

institute: Childrens' National Medical Center

hyb_protocol: Hybridization of biotin-labeled cDNA was carried out on a miRNA microarray chip (MD Anderson Cancer Center Version 5.0). The labeled targets of first-strand biotin-cDNA are used to hybridize miRNA arrays in 6 X SSPE/30% formamide at 25°C for 18 h.

scan_protocol: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4000B (Axon Instruments, Union City, CA). The images were quantified by GENEPIX 6.0 software (Axon Instruments, Union City, CA).

data_processing: The raw intensity for each probe is the median feature pixel intensity with the median background subtracted. Quantitation of raw intensity is based on global median. First, Median and STDEV are caculated for all blank/buffer banground controls. The threshold value is defined as backgound Median plus 3 times of STDEV. The relative value for each probe is caculated by using the threshold value to divide the F635 median of each probe. The global mdedian is caculated from those have relative values >1. The final output of namalized intensity is caculated by using the global median to divide the relative value of each probe. Signals from probes measuring the same miRNA were averaged.

organism: Mus musculus

source_name: mouse BM HSPCs

label_protocol: 5 µg of total RNA from each sample was biotin-labeled by reverse transcription using 5' biotin end-labeled random octamer oligo primer.

growth_protocol: Mice were maintained in the animal facility at the University of Michigan with standard housing conditions and protocols.  All procedures involving experimental animals were approved by the University Committee on the Use and Care of Animals at the University of Michigan.

extract_protocol: Total RNA isolation was performed with TRIzol (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Mice were treated with 400 µg polyinosinic:polycytidylic acid (pIpC, 2mg/ml in 1xDPBS, Sigma-Aldrich) 7 times every other day by intraperitoneal injection (i.p.) to induce targeted gene deletion.  At 10 days after the last pIpC injection, Lin-cKit+ HSPCs were isolated from mouse bone marrow.

tag: strain

tag: gender

value: Female

tag: genotype

value: Rprtf/f, Mx1-Cre+


title: Bull X703, Sample 15

description: microRNA


title: Ctrl mouse_2

description: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4000B (Axon Instruments, Union City, CA)

value: Rprtf/f, Mx1-Cre-


title: Bull X709, Sample 13

description: microRNA


title: cKO mouse_1


title: cKO mouse_3


title: IgM+IgD-CD27+ B cells donor4

city: Essen

first: Marc

last: Seifert

state: NRW

address: Virchowstrasse 173

department: Institute of Cell Biology (Cancer Research)

country: Germany

institute: University of Duisburg Essen

description: Gene expression data from sort-purified PB B cell subsets

hyb_protocol: Following fragmentation, 1 ug of cRNA was hybridized to HG U133 2.0 Plus Arrays.

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

data_processing: The data were analyzed with GeneSpring GX software after vsn normalization and ComBat correction.

label: biotin

organism: Homo sapiens

source_name: IgM+IgD-CD27+ B cells donor4 peripheral blood

label_protocol: Affymetrix enhanced biotinylation protocol

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

treatment_protocol: sort purification according to surface Ig and CD27 expression patterns

tag: tissue

value: peripheral blood

value: caucasian

tag: age


title: Bull X910, Sample 27

description: microRNA


title: KG1

type: genomic

city: Nanjing

first: zhang

middle: kao

last: ping

address: 71 East Beijing Road

country: China

institute: Chinese Academy of Sciences

description: GeoChip data for soil sample collected at the KG, replicate 1

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45℃ for 45 minutes. The hybridization was carried out at 42℃ for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

molecule: genomic DNA

organism: Bacteria

source_name: Soil microbes in 24 arctic sites

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: Surface soil organic samples were collected from 24 heath tundra sites (at least 190 km apart from each other) across the Canadian, Alaskan and European Arctic in the summer of 2007 and 2008 as described by Chu et al. (2010). At each site, soil samples were taken close to the top of exposed ridges at three similar locations (20–100 m apart) from below dry heath vegetation in which at least one of the following plant species was common: Empetrum spp., Cassiope spp. or Dryas spp.. Each sample (~12 cm ×12 cm in area, and 2-5 cm depth) of dark brown/black organic soil was cut out with a clean serrated knife and placed in a separate plastic bag. All the samples were shipped to Kingston, Canada as soon as possible where they were stored at -20°C until processing.

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20℃. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 ul of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: sample id

value: KG1,tundra soil


title: KG2

description: GeoChip data for soil sample collected at the KG, replicate 2

treatment_protocol: Surface soil organic samples were collected from 24 heath tundra sites (at least 190 km apart from each other) across the Canadian, Alaskan and European Arctic in the summer of 2007 and 2008 as described by Chu et al. (2010). At each site, soil samples were taken close to the top of exposed ridges at three similar locations (20–100 m apart) from below dry heath vegetation in which at least one of the following plant species was common: Empetrum spp., Cassiope spp. or Dryas spp.. Each sample (~12 cm ×12 cm in area, and 2-5 cm depth) of dark brown/black organic soil was cut out with a clean serrated knife and placed in a separate plastic bag. All the samples were shipped to Kingston, Canada as soon as possible where they were stored at -20°C until processing.

value: KG2,tundra soil


title: DH2

description: GeoChip data for soil sample collected at the DH, replicate 2

value: DH2,tundra soil


title: KG3

description: GeoChip data for soil sample collected at the KG, replicate 3

value: KG3,tundra soil


title: DH3

description: GeoChip data for soil sample collected at the DH, replicate 3

value: DH3,tundra soil


title: DH1

description: GeoChip data for soil sample collected at the DH, replicate 1

value: DH1,tundra soil


title: CP3

description: GeoChip data for soil sample collected at the CP, replicate 3

value: CP3,tundra soil


title: Zac3

description: GeoChip data for soil sample collected at the Zac, replicate 3

value: Zac3,tundra soil


title: Tru1

description: GeoChip data for soil sample collected at the Tru, replicate 1

value: Tru1,tundra soil


title: Abi3

description: GeoChip data for soil sample collected at the Abi, replicate 3

value: Abi3,tundra soil


title: Tru2

description: GeoChip data for soil sample collected at the Tru, replicate 2

value: Tru2,tundra soil


title: Tru3

description: GeoChip data for soil sample collected at the Tru, replicate 3

value: Tru3,tundra soil


title: TM3

description: GeoChip data for soil sample collected at the TM, replicate 3

value: TM3,tundra soil


title: Noa2

description: GeoChip data for soil sample collected at the Noa, replicate 2

value: Noa2,tundra soil


title: Abi1

description: GeoChip data for soil sample collected at the Abi, replicate 1

value: Abi1,tundra soil


title: Zac1

description: GeoChip data for soil sample collected at the Zac, replicate 1

value: Zac1,tundra soil


title: CT3

description: GeoChip data for soil sample collected at the CT, replicate 3

value: CT3,tundra soil


title: Abi2

description: GeoChip data for soil sample collected at the Abi, replicate 2

value: Abi2,tundra soil


title: Zac2

description: GeoChip data for soil sample collected at the Zac, replicate 2

value: Zac2,tundra soil


title: Noa3

description: GeoChip data for soil sample collected at the Noa, replicate 3

value: Noa3,tundra soil


title: CP2

description: GeoChip data for soil sample collected at the CP, replicate 2

value: CP2,tundra soil


title: TM2

description: GeoChip data for soil sample collected at the TM, replicate 2

value: TM2,tundra soil


title: CP1

description: GeoChip data for soil sample collected at the CP, replicate 1

value: CP1,tundra soil


title: CT1

description: GeoChip data for soil sample collected at the CT, replicate 1

value: CT1,tundra soil


title: CT2

description: GeoChip data for soil sample collected at the CT, replicate 2

value: CT2,tundra soil


title: Noa1

description: GeoChip data for soil sample collected at the Noa, replicate 1

value: Noa1,tundra soil


title: 6749.Q2.Mtb.wk8.2

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: Sample 10

hyb_protocol: 55 C overnight for no longer than 16 hrs as described in PMID: 25322074

scan_protocol: GenePix 4000B as described in PMID: 25322074

data_processing: DData from stored TIFF files was extracted using GenePix Pro 6.1 and the resulting .gpr files were loaded on to Spotfire DecisionSite for Microarray Analysis. Data was essentially notmalized using locally weighted linear regression based intensity normalization (LOWESS) and statistical significance derived using a one way ANOVA with false discovery rate correction within R, using Log2 fold change values computed by Spotfire.

source_name: Mtb infection day 1

label_protocol: Agilent kit as described in PMID: 25322074

growth_protocol: We used euthanized mice to extract RNA (Kramnik, C3HeB/FeJ) obtained from Jackson Laboratories.

extract_protocol: Trizol based extraction followed by on column DNAse treatment as described in Gautam US et al PMID: 25322074

tag: timepoint

tag: mouse strain

value: Kramnik, C3HeB/FeJ

tag: pathogen

value: M. tuberculosis H37Rv

source_name: Mtb infection week 8

value: week 8


title: TM1

description: GeoChip data for soil sample collected at the TM, replicate 1

value: TM1,tundra soil


title: RL2

description: GeoChip data for soil sample collected at the RL, replicate 2

value: RL2,tundra soil


title: Too1

description: GeoChip data for soil sample collected at the Too, replicate 1

value: Too1,tundra soil


title: Sva2

description: GeoChip data for soil sample collected at the Sva, replicate 2

value: Sva2,tundra soil


title: Sva1

description: GeoChip data for soil sample collected at the Sva, replicate 1

value: Sva1,tundra soil


title: Byl2

description: GeoChip data for soil sample collected at the Byl, replicate 2

value: Byl2,tundra soil


title: Sva3

description: GeoChip data for soil sample collected at the Sva, replicate 3

value: Sva3,tundra soil


title: Too2

description: GeoChip data for soil sample collected at the Too, replicate 2

value: Too2,tundra soil


title: Byl1

description: GeoChip data for soil sample collected at the Byl, replicate 1

value: Byl1,tundra soil


title: Byl3

description: GeoChip data for soil sample collected at the Byl, replicate 3

value: Byl3,tundra soil


title: BI3

description: GeoChip data for soil sample collected at the BI, replicate 3

value: BI3,tundra soil


title: RL1

description: GeoChip data for soil sample collected at the RL, replicate 1

value: RL1,tundra soil


title: RL3

description: GeoChip data for soil sample collected at the RL, replicate 3

value: RL3,tundra soil


title: Too3

description: GeoChip data for soil sample collected at the Too, replicate 3

value: Too3,tundra soil


title: CB1

description: GeoChip data for soil sample collected at the CB, replicate 1

value: CB1,tundra soil


title: CB3

description: GeoChip data for soil sample collected at the CB, replicate 3

value: CB3,tundra soil


title: Lax2

description: GeoChip data for soil sample collected at the Lax, replicate 2

value: Lax2,tundra soil


title: BI2

description: GeoChip data for soil sample collected at the BI, replicate 2

value: BI2,tundra soil


title: Thu1

description: GeoChip data for soil sample collected at the Thu, replicate 1

value: Thu1,tundra soil


title: Lax1

description: GeoChip data for soil sample collected at the Lax, replicate 1

value: Lax1,tundra soil


title: CB2

description: GeoChip data for soil sample collected at the CB, replicate 2

value: CB2,tundra soil


title: Tag1

description: GeoChip data for soil sample collected at the Tag, replicate 1

value: Tag1,tundra soil


title: Lax3

description: GeoChip data for soil sample collected at the Lax, replicate 3

value: Lax3,tundra soil


title: Thu2

description: GeoChip data for soil sample collected at the Thu, replicate 2

value: Thu2,tundra soil


title: BI1

description: GeoChip data for soil sample collected at the BI, replicate 1

value: BI1,tundra soil


title: Thu3

description: GeoChip data for soil sample collected at the Thu, replicate 3

value: Thu3,tundra soil


title: Tag3

description: GeoChip data for soil sample collected at the Tag, replicate 3

value: Tag3,tundra soil


title: Tag2

description: GeoChip data for soil sample collected at the Tag, replicate 2

value: Tag2,tundra soil


title: Ska3

description: GeoChip data for soil sample collected at the Ska, replicate 3

value: Ska3,tundra soil


title: Ska1

description: GeoChip data for soil sample collected at the Ska, replicate 1

value: Ska1,tundra soil


title: Kuu3

description: GeoChip data for soil sample collected at the Kuu, replicate 3

value: Kuu3,tundra soil


title: Ska2

description: GeoChip data for soil sample collected at the Ska, replicate 2

value: Ska2,tundra soil


title: DL3

description: GeoChip data for soil sample collected at the DL, replicate 3

value: DL3,tundra soil


title: Kuu2

description: GeoChip data for soil sample collected at the Kuu, replicate 2

value: Kuu2,tundra soil


title: LR2

description: GeoChip data for soil sample collected at the LR, replicate 2

value: LR2,tundra soil


title: DL2

description: GeoChip data for soil sample collected at the DL, replicate 2

value: DL2,tundra soil


title: Fai2

description: GeoChip data for soil sample collected at the Fai, replicate 2

value: Fai2,tundra soil


title: Fai1

description: GeoChip data for soil sample collected at the Fai, replicate 1

value: Fai1,tundra soil


title: LR1

description: GeoChip data for soil sample collected at the LR, replicate 1

value: LR1,tundra soil


title: LR3

description: GeoChip data for soil sample collected at the LR, replicate 3

value: LR3,tundra soil


title: Kuu1

description: GeoChip data for soil sample collected at the Kuu, replicate 1

value: Kuu1,tundra soil


title: DL1

description: GeoChip data for soil sample collected at the DL, replicate 1

value: DL1,tundra soil


title: AF2

description: GeoChip data for soil sample collected at the AF, replicate 2

value: AF2,tundra soil


title: AF1

description: GeoChip data for soil sample collected at the AF, replicate 1

value: AF1,tundra soil


title: Fai3

description: GeoChip data for soil sample collected at the Fai, replicate 3

value: Fai3,tundra soil


title: HighDose_72

city: Göteborg

first: Bethanie

last: Carney Almroth

address: Medicinaregatan 38

department: Biological and Environmental Sciences

country: Sweden

institute: University of Gothenburg

hyb_protocol: Samples were hybridized one chip at the time using the Maui hybridization 4-bay system for 17 hours at 42°C

scan_protocol: Samples were scanned using the Agilent High-Resolution C Microarray Scanner at 2μm resolution.

data_processing: Subsequent image processing and reporting was performed in Nimble Scan version 2.6. The raw data (.pair file) were normalized by quantile–quantile normalization (Bolstad, Irizarry et al. 2003) and then log2 transformed.

organism: Oncorhynchus mykiss

source_name: liver

label_protocol: Labeling was performed by  NimbleGen One-Color DNA Labeling Kit (Roche), following the manufacturer’s instructions.

growth_protocol: Fish were maintained in a fresh water flow through aquarium system with aeration, 12:12 light:dark cycle, temp 10-12 C. They were fed commercial pellets prior to but not during the exposure.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis using Nanodrop 2000c spectrophotometer (Thermo Scientific) and ExperionTM automated electrophoresis system (Bio-Rad).

treatment_protocol: Fish in treatment groups were exposed to waterbourne beclomethasone diproprionate (nominal concentration 1 µg/L)

tag: treatment group

value: beclomethasone diproprionate exposure

tag: carrier solution

value: DMSO


title: HighDose_71


title: HighDose_50


title: NG14_2 T6vsT0

city: Rueil Malmaison

first: Frederique

last: Bidard

address: 1-4 avenue de Bois Préau

department: Biotechnology

country: France

institute: IFPEN

description: NG14 T6h vs T0h - Replicate 2 - Dye

hyb_protocol: 1.5µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scaning.

scan_protocol: Microarrays of the GPL9076 plateform were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature. Microarrays of the GPL19095 plateform were scanned using Genepix 4000B (Molecular Devices, Sunnyvale, CA, USA) and the resulting image files analyzed by GenePix Pro 6.1 software (Axon).

data_processing: For Microarray GPL9076, spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software normalized data (Local background was subtracted and LOWESS normalization). For Microarray GPL19095, For each GenePix output file, two filters were applied, one to clear out flagged spots and another one to discard saturating spots where the median foreground intensity was greater than 60,000 in one of the two channels. The resulting median foreground intensities were normalized, without background signal subtraction, using a global Lowess correction followed by a print-tip median normalization step (Lemoine et al., 2006).

organism: Trichoderma reesei

label_protocol: 1 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.

growth_protocol: Frozen spores were used to inoculate a Fernbach flask containing 250 ml of the culture medium described previously (Gilbert HJ (2010) The biochemistry and structural biology of plant cell wall deconstruction. Plant physiology 153: 444–455). Cultivation was carried out at 30°C with stirring at 150 rpm. After 72 h, the medium containing mycelia was used as an inoculum for bioreactor culture.Cellulase was produced in a 4-liter bioreactor with a two-step cultivation procedure. Strains were first grown at 28°C in 2 liters of a medium containing 30 g·liter−1 of glucose as a carbon source and pH regulated at 4.8 with 5.5 M NH3. The airflow was adjusted at 0.5 volume per volume per min (VVM), and initial stirring was set at 400 rpm. This parameter was gradually increased to maintain partial O2 pressure (pO2) above 40% oxygen saturation. When the initial glucose was close to depletion (<20% of initial glucose content), the fed-batch phase was initiated. During this second step, a 250-g·liter−1carbon source solution (lactose) was injected at a rate of 0.98 g·h−1. Samples were collected periodically to determine the biomass, carbon, and protein concentrations

extract_protocol: Fungal mycelia were harvested by filtration, washed with distilled cold water, frozen and ground under liquid nitrogen. For extraction of total RNA purification kits (SV Total RNA Isolation System, Promega) were used according to the manufacturer’s protocol.

tag: time


title: NG14_2 T0vsT24

description: NG14 T0h vs T24h - Replicate 2


title: NG14_2 T24vsT0

description: NG14 T24h vs T0h - Replicate 2 - Dye


title: HighDose_69


title: HighDose_52


title: DMSO_67

value: control


title: HighDose_29


title: DMSO_68


title: DMSO_8


title: NG14_2 T0vsT6

description: NG14 T0h vs T6h - Replicate 2


title: control_76

value: water


title: NG14_2 T3vsT0

description: NG14 T3h vs T0h - Replicate 2 - Dye


title: Control_15


title: HIghDose_10


title: AF3

description: GeoChip data for soil sample collected at the AF, replicate 3

value: AF3,tundra soil


title: NG14_2 T1vsT0

description: NG14 T1h vs T0h - Replicate 2 - Dye


title: control_75


title: HighDose_32


title: control_56


title: NG14_2 T0vsT3

description: NG14 T0h vs T3h - Replicate 2


title: NG14_2 T0vsT1

description: NG14 T0h vs T1h - Replicate 2


title: DMSO_28


title: Control_35


title: HighDose_30


title: HIghDose_9


title: NG14_1 T24vsT0

description: NG14 T24h vs T0h - Replicate 1 - Dye


title: HIghDose_12


title: NG14_1 T0vsT24

description: NG14 T0h vs T24h - Replicate 1


title: NG14_1 T0vsT6

description: NG14 T0h vs T6h - Replicate 1


title: Control_16


title: NG14_1 T3vsT0

description: NG14 T3h vs T0h - Replicate 1 - Dye


title: NG14_1 T6vsT0

description: NG14 T6h vs T0h - Replicate 1 - Dye


title: NG14_1 T0vsT3

description: NG14 T0h vs T3h - Replicate 1


title: NG14_1 T1vsT0

description: NG14 T1h vs T0h - Replicate 1 - Dye


title: NG14_1 T0vsT1

description: NG14 T0h vs T1h - Replicate 1


title: DMSO_48


title: NSCLC, sty [Q4-07-14]

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. Copy number from the parffin embedded tumor DNA was calculated after filtration of the PCR fragments above 800 Bp to account for DNA degradation
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from cell lines, and fresh frozen lung tumors using  the Qiagen AllPrep kit. DNA from lung paraffin embedded tumors was obtained using the RecoverAll kit from Ambion. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Lung tumor


title: SCLC, sty [Q045-07-A4]

description: Hybridized to 250K_Nsp


title: NSCLC cell line SK-1 sty [SK-14]

description: Hybridized to 250K_Nsp

value: lung carcinoma cell line

tag: cell line


title: AD-PD, sty [Q1488-06-24]

description: Hybridized to 250K_Nsp


title: SCLC, sty [OTB0702084]

description: Hybridized to 250K_Nsp


title: RutC30_2 T24vsT0

description: RutC30 T24h vs T0h - Replicate 2 - Dye


title: RutC30_2 T0vsT24

description: RutC30 T0h vs T24h - Replicate 2


title: HighDose_31


title: 3D corpus -Wnt vs 3D corpus +Wnt

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: cell culture

hyb_protocol: Whole human genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: gastric cells

label_protocol: RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Gastric glands were extracted from human gastric tissue samples and seeded in Matrigel. The culture medium (expansion medium; EM) contained ADF, 50% conditioned human Wnt3A-medium , 25 % conditioned human R-spondin-1 medium supplemented with 10 mM HEPES, 1% Glutamax, 2% B27, 1% N2, 100 ng/ml human EGF (all from Invitrogen), 150 ng/ml human noggin, 150 ng/ml human FGF-10 (both from Peprotech), 1.25 mM N-acetyl-L-cystein, 1 mM nicotinamide, 10 µM human gastrin, 5 µM SB202190 (all from Sigma) and 50 nM A83-01 (Calbiochem). 25 µM Y-27632 (Sigma) was added for the first 3 days. Cultures were kept at 37°C, 5% CO2 in a humidified incubator.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Treatment 1 (Corpus EM vs Corpus EM/DM): Culture were grown in EM for five days. Sample Corpus EM was kept in EM for further five days; sample Corpus EM/DM was differentiated towards organoids by withdrawing of Wnt3A and R-spondin 1 for five days (differentiation medium; DM). Treatment 2 (3D vs. 2D): Established spheroids (sample 3D) cultured in EM were sheared, collected in 2-D medium (ADF, 10% FCS, 2% B27, 1% N2, 1 mM nicotinamide, 300 ng/ml human EGF, 25 µM Y-27632 and 50 nM A83-01) and seeded in collagen-coated wells. 2-D cells (sample 2D) were harvested three days after seeding.

value: gastric cells

value: stomach

tag: sample type

value: corpus EM/DM

value: corpus EM


title: SCLC, sty [OTB070208N_4]

description: Hybridized to 250K_Nsp


title: 3D corpus +Wnt vs 3D corpus -Wnt

description: cell culture


title: SCC, nsp [Q1235-06-A4]

description: Hybridized to 250K_Sty


title: SCLC, sty [Q177-084]

description: Hybridized to 250K_Nsp


title: NSCLC, sty   [NRJ270508_T1_4]

description: Hybridized to 250K_Nsp


title: NSCLC, sty [NRJ270508_N1_4]

description: Hybridized to 250K_Nsp


title: RutC30_2 T6vsT0

description: RutC30 T6h vs T0h - Replicate 2 - Dye


title: AD-PD, sty [INER_254]

description: Hybridized to 250K_Nsp


title: Lung precursor Metaplasia,  sty [293-06-4]

description: Hybridized to 250K_Nsp

value: Lung metaplasia


title: RutC30_2 T0vsT6

description: RutC30 T0h vs T6h - Replicate 2


title: RutC30_2 T1vsT0

description: RutC30 T1h vs T0h - Replicate 2 - Dye


title: NSCLC AD (Mexican Mestizo) cell line, sty [INER-37_4]

description: Hybridized to 250K_Nsp


title: RutC30_2 T0vsT3

description: RutC30 T0h vs T3h - Replicate 2


title: RutC30_2 T0vsT1

description: RutC30 T0h vs T1h - Replicate 2


title: NSCLC SCC-PD, sty [708-06-104]

description: Hybridized to 250K_Nsp


title: RutC30_1 T6vsT0

description: RutC30 T6h vs T0h - Replicate 1 - Dye


title: SCLC, sty [GOA290508_T_4]

description: Hybridized to 250K_Nsp


title: RutC30_1 T0vsT24

description: RutC30 T0h vs T24h - Replicate 1


title: RutC30_1 T0vsT6

description: RutC30 T0h vs T6h - Replicate 1


title: RutC30_1 T3vsT0

description: RutC30 T3h vs T0h - Replicate 1 - Dye


title: Lung Epithelium without cellular atypias, and metaplasia, sty [1278-05-24]

description: Hybridized to 250K_Nsp

value: Normal lung


title: SCLC, sty [INER_84]

description: Hybridized to 250K_Nsp


title: RutC30_1 T0vsT3

description: RutC30 T0h vs T3h - Replicate 1


title: RutC30_2 T3vsT0

description: RutC30 T3h vs T0h - Replicate 2 - Dye


title: Lung precursor metaplasia-displasia, sty [834-06-2-4]

description: Hybridized to 250K_Nsp


title: NSCLC SCC-BD, sty [897-06-24]

description: Hybridized to 250K_Nsp


title: AD, sty [INER_224]

description: Hybridized to 250K_Nsp


title: NSCLC, sty [INER_34]

description: Hybridized to 250K_Nsp


title: AD-MD, sty [INER_74]

description: Hybridized to 250K_Nsp


title: A427 lung adenocarcinoma cell line, sty [A427_4]

description: Hybridized to 250K_Nsp


title: NSCLC SCC-MD (IV), tumor sty [1551-064]

description: Hybridized to 250K_Nsp


title: NSCLC SCC-PD, tumor sty [1479-06-14]

description: Hybridized to 250K_Nsp


title: SCLC, sty [INER_54]

description: Hybridized to 250K_Nsp


title: Lung precursor metaplasia, sty [1032-05-1-4]

description: Hybridized to 250K_Nsp


title: SCLC, sty  [GOA290508_N_4]

description: Hybridized to 250K_Nsp


title: RutC30_1 T24vsT0

description: RutC30 T24h vs T0h - Replicate 1 - Dye


title: RutC30_1 T1vsT0

description: RutC30 T1h vs T0h - Replicate 1 - Dye


title: RutC30_1 T0vsT1

description: RutC30 T0h vs T1h - Replicate 1


title: NSCLC SCC-MD, tumor sty [1352-06-14]

description: Hybridized to 250K_Nsp


title: NSCLC, sty [INER_14]

description: Hybridized to 250K_Nsp


title: genomic DNA from HCC_60T.AVG_Beta

city: Singapore

first: Lee

middle: Guat Lay

last: Caroline

address: 11 Hospital Drive

department: Department of Biochemistry, National University of Singapore

country: Singapore

institute: National Cancer Centre Singapore

description: tumor

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

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

data_processing: BeadStudio software

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from HCC samples using phenol-chloroform method.

value: liver tissue

tag: disease state

value: hepatocellular carcinoma tumor


title: genomic DNA from HCC_59T.AVG_Beta

description: tumor


title: Female, hyperoxia, biological rep3

city: Houston

first: Krithika

last: Lingappan

address: 6621 Fannin

institute: Baylor College of Medicine

description: female,8-10 week,lung

hyb_protocol: 80 uL hybridization cocktails containing Affymetrix spike-in controls and the fragmented, labeled cDNA were loaded onto the GeneChip® Mouse Gene 1.0 ST arrays. The arrays were hybridized for 17 hours at 45°C, with rotation at 60 rpm on the GeneChip® Hybridization Oven 640.

scan_protocol: The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000. The images were analyzed and quality control metrics recorded using Affymetrix Command Console software version 3.0.

data_processing:
Raw gene expression data was preprocessed using ‘Robust Multichip Average’ methodology. This strategy allows background subtraction, quantile normalization and summarization (via median-polish). Preprocessed gene expression data was analyzed by fitting a linear model, using a moderated t-statistic for significance analysis of pair-wise comparisons and interaction terms. Benjamini and Hochberg’s method was applied to control the false discovery rate (FDR). A combination of fold-change (FC) ≥ 1.4 and FDR < 5% was used to define differentially expressed genes (DEGs).
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: wild-type, female,lung,hyperoxia

label_protocol: As per the Ambion WT Expression Kit protocol, samples of 100ng of total RNA were added to T7 primers and used as a template to synthesize antisense-stranded cDNA. The cDNA was then in vitro transcribed to create a cRNA template. Per sample, 10ug of cRNA was combined with random primers and synthesized to produce sense-stranded cDNA. The resulting 5.5ug of cDNA per sample was fragmented and biotin-labeled following the Affymetrix GeneChip® WT Terminal Labeling kit protocol. The cRNA, sense-stranded cDNA and fragmented cDNA were each tested for integrity on the Agilent Bioanalyzer and quantified using the NanoDrop® ND-1000 spectrophotometer to ensure successful reactions.

growth_protocol: 8-10 wk old fed standard mice food and water ad libitum. Animals were maintained in a12-h day/night cycle.

extract_protocol: Lungs from male and female C56BL/6J mice either maintained in room air or exposed to hyperoxia (FiO2>95%) were snap frozen in liquid N2 We had 3 biological replicates in each group. The groups were: 1) Room air-Male, 2) Room air-Female, 3) Hyperoxia-Male and 4) Hyperoxia-Female. To minimize the impact of individual mouse to mouse variability on the microarray data, each biological replicate was comprised of a randomized pool of lung RNA prepared from n = 4 mice.Total RNA from lung samples was isolated using the miRNeasy kit as per the manufacturer’s standard protocols (Qiagen, Valencia, CA, USA). Following total RNA isolation, sample concentration was assayed using a Nanodrop-8000 (Thermo Scientific, Wilmington, DE, USA). Sample Quality checks were done using the NanoDrop spectrophotometer and Agilent Bioanalyzer. We used the Ambion WT Expression Kit protocol and reagents to convert total RNA into sense-strand cDNA. The cDNA was then fragmented and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit.

treatment_protocol: Exposure to hyperoxia (FiO2 > 0.95 for 48 hours).  We used pooled samples in this study to decrease the biological variability.

value: female

value: lung

tag: treatment

value: hyperoxia


title: Female, room air, biological rep2

description: female,8-10 week,lung

source_name: wild-type, female,lung,room air


title: genomic DNA from HCC_60N.AVG_Beta

description: adjacent non-tumorous

value: adjacent non-tumorous


title: genomic DNA from HCC_57N.AVG_Beta

description: adjacent non-tumorous


title: Female, hyperoxia, biological rep2

description: female,8-10 week,lung


title: genomic DNA from HCC_57T.AVG_Beta

description: tumor


title: genomic DNA from HCC_58T.AVG_Beta

description: tumor


title: Female, room air, biological rep1

description: female,8-10 week,lung

value: control


title: genomic DNA from HCC_59N.AVG_Beta

description: adjacent non-tumorous


title: Male, hyperoxia, biological rep1

description: male,8-10 week,lung

source_name: wild-type, male,lung, hyperoxia

value: male


title: genomic DNA from HCC_56N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_58N.AVG_Beta

description: adjacent non-tumorous


title: Female, room air, biological rep3

description: female,8-10 week,lung


title: genomic DNA from HCC_56T.AVG_Beta

description: tumor


title: Male, room air, biological rep3

description: male,8-10 week,lung

source_name: wild-type, male,lung, room air


title: genomic DNA from HCC_55N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_55T.AVG_Beta

description: tumor


title: Female, hyperoxia, biological rep1

description: female,8-10 week,lung


title: Male, hyperoxia, biological rep2

description: male,8-10 week,lung


title: Male, hyperoxia, biological rep3

description: male,8-10 week,lung


title: Male, room air, biological rep2

description: male,8-10 week,lung


title: genomic DNA from HCC_61N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_61T.AVG_Beta

description: tumor


title: genomic DNA from HCC_54T.AVG_Beta

description: tumor


title: genomic DNA from HCC_54N.AVG_Beta

description: adjacent non-tumorous


title: Head-salmon juvenile reared with gravel-family X35-replicate 4

city: Newport

first: Melissa

last: Evans

state: OR

address: 2030 SE Marine Science Dr.

institute: Oregon State University

hyb_protocol: The microarrays were scanned at 5μm resolution using the ScanArray Gx Plus scanner and ScanExpress v4.0 software (Perkin-Elmer Life Sciences, Waltham, MA, USA).

scan_protocol: TIFF images for each channel (Cy5, Cy3) were exported from ScanExpress and signal intensity data extracted from the images using Imagene v9.0 (BioDiscovery, El Segundo, CA, USA). Poor quality spots on each array were manually flagged in Imagene.

data_processing: We used the Bioconductor package “mArray” as implemented in R to remove flagged spots from the dataset and log2-transform and Loess-normalize signal intensity data for each of the 44K grids on a microarray slide. Probe signal intensities that were lower (undetected signal) than the average of the median background signal ±2 SD were removed and marked as “N/A”.

organism: Salmo salar

source_name: whole head; severed from body directly behind operculum

label_protocol: Anti-sense RNA (aRNA) was amplified and fluorescently-labelled using the Amino Allyl MessageAmpTM II aRNA amplification kit (Ambion, Life Technologies Inc.) and Cy5 and Cy3 mono-reactive dyes (GE Healthcare, Mississauga, ON, Canada), according to the manufacturer’s instructions. One μg of total RNA was used as starting material for each of the amplifications. Twenty µg of each “experimental” aRNA (i.e. from each of the individual head samples) was labelled with Cy5 dye. A common “reference” sample composed of equal contributions (pooled RNA) of each of the experimental aRNA samples was also amplified, and 20 µg of reference amplified RNA was labelled with Cy3 dye.

extract_protocol: Whole heads were removed from the RNAlater, blotted dry, and then homogenized using Kontes’ disposable pestles and a hand-held homogenizer (Thermo Fisher Scientific, Wilmington, DE, USA) in 1.5mL TRI Reagent (Sigma-Aldrich). Total RNA was isolated following the manufacturer’s instructions. Isolated RNA was treated with RNAse-free DNase-I (QIAGEN, Mississauga, ON, Canada) and purified using the RNeasy MinElute kit (QIAGEN), according to the manufacturer’s instructions.

treatment_protocol: Whole heads were stored in RNAlater at 4C overnight and then moved to -80C for long-term storage.

tag: rearing

value: with gravel

tag: family

value: emergence (end of endogenous feeding)

value: whole head

source_name: Pooled juvenile salmon head tissue RNA

value: head


title: Head-salmon juvenile reared with gravel-family X35-replicate 5


title: Head-salmon juvenile reared with gravel-family X35-replicate 1


title: Head-salmon juvenile reared with gravel-family X11-replicate 5


title: Head-salmon juvenile reared with gravel-family X11-replicate 1


title: genomic DNA from HCC_53N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_50T.AVG_Beta

description: tumor


title: genomic DNA from HCC_51T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared with gravel-family X22-replicate 3


title: Head-salmon juvenile reared with gravel-family X35-replicate 3


title: Head-salmon juvenile reared with gravel-family X11-replicate 4


title: Head-salmon juvenile reared with gravel-family X11-replicate 3


title: genomic DNA from HCC_53T.AVG_Beta

description: tumor


title: genomic DNA from HCC_50N.AVG_Beta

description: adjacent non-tumorous


title: Head-salmon juvenile reared with gravel-family X35-replicate 2


title: Head-salmon juvenile reared with gravel-family X22-replicate 2


title: Head-salmon juvenile reared with gravel-family X11-replicate 2


title: Head-salmon juvenile reared without gravel-family X35-replicate 4

value: without gravel


title: genomic DNA from HCC_49N.AVG_Beta

description: adjacent non-tumorous


title: Head-salmon juvenile reared without gravel-family X35-replicate 5


title: genomic DNA from HCC_51N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_47T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared with gravel-family X22-replicate 4


title: genomic DNA from HCC_52T.AVG_Beta

description: tumor


title: genomic DNA from HCC_48T.AVG_Beta

description: tumor


title: genomic DNA from HCC_46T.AVG_Beta

description: tumor


title: genomic DNA from HCC_52N.AVG_Beta

description: adjacent non-tumorous


title: Head-salmon juvenile reared with gravel-family X22-replicate 1


title: genomic DNA from HCC_49T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared with gravel-family X22-replicate 5


title: genomic DNA from HCC_48N.AVG_Beta

description: adjacent non-tumorous


title: Head-salmon juvenile reared without gravel-family X35-replicate 3


title: genomic DNA from HCC_46N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_45N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_43_B_T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared without gravel-family X11-replicate 1


title: genomic DNA from HCC_45T.AVG_Beta

description: tumor


title: genomic DNA from HCC_40T.AVG_Beta

description: tumor


title: genomic DNA from HCC_47N.AVG_Beta

description: adjacent non-tumorous


title: Head-salmon juvenile reared without gravel-family X22-replicate 1


title: genomic DNA from HCC_42T.AVG_Beta

description: tumor


title: genomic DNA from HCC_42N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_43_A_T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared without gravel-family X22-replicate 5


title: Head-salmon juvenile reared without gravel-family X11-replicate 3


title: Head-salmon juvenile reared without gravel-family X22-replicate 4


title: genomic DNA from HCC_43_C_T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared without gravel-family X11-replicate 2


title: genomic DNA from HCC_44T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared without gravel-family X11-replicate 5


title: Head-salmon juvenile reared without gravel-family X11-replicate 4


title: genomic DNA from HCC_41T.AVG_Beta

description: tumor


title: Head-salmon juvenile reared without gravel-family X35-replicate 2


title: Head-salmon juvenile reared without gravel-family X22-replicate 2


title: Head-salmon juvenile reared without gravel-family X22-replicate 3


title: Head-salmon juvenile reared without gravel-family X35-replicate 1


title: genomic DNA from HCC_40N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_41N.AVG_Beta

description: adjacent non-tumorous


title: Male, room air, biological rep1

description: male,8-10 week,lung

tag: gender

tag: strain


title: genomic DNA from HCC_43N.AVG_Beta

description: adjacent non-tumorous

tag: tissue


title: genomic DNA from HCC_44N.AVG_Beta

description: adjacent non-tumorous


title: HBEC30-KT 92a3

first: Alexander

last: Pertsemlidis

address: 8403 Floyd Curl Drive, MC 7784

department: Pediatrics and Cellular & Structural Biology

institute: UT Health Science Center at San Antonio

description: replicate 3

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scan protocol

data_processing: The data were background subtracted and quantile-normalized using the MBCB algorithm.

source_name: Human bronchial epithelial cell (HBEC) immortalized with cdk4 and hTERT

label_protocol: Standard Illumina protocol

growth_protocol: Cells were cultured in 6-well plates in a humid environment at 5% CO2 in ACL4 medium supplemented with 2% fetal bovine serum and without antibiotics.

extract_protocol: RNA was extracted, cleaned and eluted using the Ambion mirVana total RNA kit and protocol. Quality control was performed with an Agilent Bioanalyzer.

treatment_protocol: Cells were reverse transfected with inhibitor at a final concentration of 50 nM and an appropriate amount of Lipofectamine RNAiMAX reagent.

value: wildtype TP53

tag: oligonucleotide treatment

value: miR-92a inhibitor


title: genomic DNA from HCC_38T.AVG_Beta

description: tumor


title: genomic DNA from HCC_39N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_39T.AVG_Beta

description: tumor


title: HBEC30-KT 92a2

description: replicate 2


title: HBEC30-KT 92a1

description: replicate 1


title: HBEC30-KT mm1

description: replicate 1

value: miR-92a mismatch


title: genomic DNA from HCC_35T.AVG_Beta

description: tumor


title: HBEC30-KT mm3

description: replicate 3

growth_protocol: Cells were cultured in 6-well plates a humid environment at 5% CO2 in ACL4 medium supplemented with 2% fetal bovine serum and without antibiotics.


title: genomic DNA from HCC_36N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_38N.AVG_Beta

description: adjacent non-tumorous


title: HBEC30-KT shTP53 92a2

description: replicate 2

value: constitutive shTP53


title: HBEC30-KT shTP53 mm3

description: replicate 3

data_processing: The data were background subtracted and quantile-normalized using the MBCB algorithm


title: HBEC30-KT shTP53 mm2

description: replicate 2


title: HBEC30-KT mm2

description: replicate 2


title: HBEC30-KT shTP53 92a1

description: replicate 1


title: genomic DNA from HCC_37T.AVG_Beta

description: tumor

value: liver tissue


title: genomic DNA from HCC_33T.AVG_Beta

description: tumor

value: hepatocellular carcinoma tumor


title: genomic DNA from HCC_31N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_36T.AVG_Beta

description: tumor


title: RNA from HCC_41N

description: adjacent non-tumorous

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Partek Software

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.


title: genomic DNA from HCC_33N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_40N

description: adjacent non-tumorous


title: RNA from HCC_39T

description: tumor


title: genomic DNA from HCC_34N.AVG_Beta

description: adjacent non-tumorous


title: HBEC30-KT shTP53 92a3

description: replicate 3


title: RNA from HCC_39N

description: adjacent non-tumorous


title: Spontaneously hypertensive rat (SHR) 1

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

description: mRNA and LncRNA expression

hyb_protocol: A total of 1μg of labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100μl of hybridization solution was then dispensed in the gasket slide and assembled to the custom Rat Long Non-coding RNA Array microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technologies’ guidelines.

data_processing: Raw data .txt files were extracted using Agilent Feature Extraction Software (version 10.5.1.1) and imported into the Agilent GeneSpring GX software (version11.0) for further analysis. The 9 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (Quantile normalization). Differentially expressed lncRNAs and genes with statistically significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.0). GO analysis and Pathway analysis was performed in the standard enrichment computation method.

organism: Rattus norvegicus

source_name: SHR fed with Low-salt (0.3%) diet

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA were linearly amplified and labeled with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol cy3/μg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: All rats born on the same day were selected and weaned at 30 days of age.

treatment_protocol: After weaning all rats were fed with Low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).

value: Spontaneously hypertensive rat (SHR)

value: Kidney

value: Male

tag: age

value: 53 days


title: RNA from HCC_41T

description: tumor


title: Spontaneously hypertensive rat (SHR) 3

description: mRNA and LncRNA expression


title: genomic DNA from HCC_32N.AVG_Beta

description: adjacent non-tumorous

value: adjacent non-tumorous


title: genomic DNA from HCC_35N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_40T

description: tumor


title: RNA from HCC_38T

description: tumor


title: Spontaneously hypertensive rat (SHR) 2

description: mRNA and LncRNA expression


title: genomic DNA from HCC_37N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_30T.AVG_Beta

description: tumor


title: HBEC30-KT shTP53 mm1

description: replicate 1


title: genomic DNA from HCC_31T.AVG_Beta

description: tumor


title: HL-60-GFP + 4-OHT replicate 3

city: Bern

first: Christina

last: Stoeckle

address: Friedbuehlstrasse 49

department: Institute of Pharmacology

country: Switzerland

institute: University of Bern

description: HL-60-GFP + 4-OHT

hyb_protocol: Affymetrix Human Gene 2.0 ST arrays were hybridised at  45°C for 17 hours, washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix). Raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: Raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software . All statistical analyses were performed using the free high-level interpreted statistical language R and various Bioconductor packages (http://www.Bioconductor.org). Normalized expression signals were calculated from Affymetrix CEL files using RMA normalization methods. Differential hybridized features were identified using Bioconductor package “limma” that implements linear models for microarray data

source_name: 4-OHT-treated HL-60-GFP

label_protocol: biotin-labelling using the GeneChip WT terminal labelling kit (Affymetrix)

growth_protocol: cells were grown in ATCC recommended medium (RPMI 10% FCS, P/S, 2mM L-glutamine, 10mM HEPES, 1mM sodium pyruvate, 4500mg/l glucose, pH 7.5 at 37°C, 5% CO2

extract_protocol: SV Total RNA Isolation System (Promega) according to manufacturer's instructions

treatment_protocol: cells were or were not treated with 100nM 4-OHT (4-hydroxytamoxifen) to induce lentiviral gene expression

value: HL-60 clone 15

tag: transduced

value: GFP


title: HL-60-GFP + 4-OHT replicate 2

description: HL-60-GFP + 4-OHT


title: HL-60-GFP + 4-OHT replicate 1

description: HL-60-GFP + 4-OHT


title: HL-60-RhoH + 4-OHT replicate 3

description: HL-60-RhoH + 4-OHT

source_name: 4-OHT-treated HL-60-RhoH

value: RhoH


title: RNA from HCC_38N

description: adjacent non-tumorous


title: Dahl Salt Resistant rats (Dahl R) 2

description: mRNA and LncRNA expression

source_name: Dahl R Rat fed with Low-salt (0.3%) diet

value: Dahl Salt Resistant rats (Dahl R)


title: genomic DNA from HCC_30N.AVG_Beta

description: adjacent non-tumorous


title: HL-60-RhoH + 4-OHT replicate 1

description: HL-60-RhoH + 4-OHT


title: RNA from HCC_37N

description: adjacent non-tumorous


title: genomic DNA from HCC_29N.AVG_Beta

description: adjacent non-tumorous


title: HL-60-RhoH + 4-OHT replicate 2

description: HL-60-RhoH + 4-OHT


title: RNA from HCC_37T

description: tumor


title: Dahl Salt Resistant rats (Dahl R) 1

description: mRNA and LncRNA expression


title: HL-60-RhoH no 4-OHT replicate 2

description: HL-60-RhoH no 4-OHT

source_name: untreated HL-60-RhoH

value: no 4-OHT


title: RNA from HCC_36T

description: tumor


title: HL-60-RhoH no 4-OHT replicate 3

description: HL-60-RhoH no 4-OHT


title: Dahl Salt Sensitive rats (Dahl S) 3

description: mRNA and LncRNA expression

source_name: Dahl S Rat fed with Low-salt (0.3%) diet

value: Dahl Salt Sensitive rats (Dahl S)


title: genomic DNA from HCC_28T.AVG_Beta

description: tumor


title: genomic DNA from HCC_27T.AVG_Beta

description: tumor


title: genomic DNA from HCC_29T.AVG_Beta

description: tumor


title: genomic DNA from HCC_27N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_26T.AVG_Beta

description: tumor


title: Dahl Salt Sensitive rats (Dahl S) 1

description: mRNA and LncRNA expression


title: RNA from HCC_35N

description: adjacent non-tumorous


title: HL-60-RhoH no 4-OHT replicate 1

description: HL-60-RhoH no 4-OHT


title: RNA from HCC_33T

description: tumor


title: RNA from HCC_36N

description: adjacent non-tumorous


title: RNA from HCC_34N

description: adjacent non-tumorous


title: genomic DNA from HCC_26N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_28N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_25T.AVG_Beta

description: tumor


title: Dahl Salt Resistant rats (Dahl R) 3

description: mRNA and LncRNA expression


title: RNA from HCC_33N

description: adjacent non-tumorous


title: genomic DNA from HCC_24T.AVG_Beta

description: tumor


title: RNA from HCC_31T

description: tumor


title: RNA from HCC_32N

description: adjacent non-tumorous


title: Dahl Salt Sensitive rats (Dahl S) 2

description: mRNA and LncRNA expression


title: RNA from HCC_35T

description: tumor


title: genomic DNA from HCC_24N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_31N

description: adjacent non-tumorous


title: genomic DNA from HCC_23N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_22T.AVG_Beta

description: tumor


title: RNA from HCC_30T

description: tumor


title: RNA from HCC_29T

description: tumor


title: genomic DNA from HCC_21N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_28T

description: tumor


title: genomic DNA from HCC_22N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_20N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_29N

description: adjacent non-tumorous


title: RNA from HCC_30N

description: adjacent non-tumorous


title: genomic DNA from HCC_20T.AVG_Beta

description: tumor


title: genomic DNA from HCC_21T.AVG_Beta

description: tumor


title: RNA from HCC_27T

description: tumor


title: genomic DNA from HCC_23T.AVG_Beta

description: tumor


title: genomic DNA from HCC_19T.AVG_Beta

description: tumor


title: SH-SY5Y_TRPM7shRNA_rep2

city: Nijmegen

first: Jeroen

last: Middelbeek

address: POBOX 9101

department: Pediatric Oncology

country: Netherlands

institute: Radboudumc

description: Replicate 2

hyb_protocol: Hybridized to Illumina HumanHT-12 v4 array according to the Illumina Manual Direct Hybridization Assay Guide.

scan_protocol: Illumina iScan.

data_processing: Illumina GenomeStudio v2011.1 Gene Expression Software.

source_name: SH-SY5Y neuroblastoma cells, transduced with TRPM7 shRNA

label_protocol: According to manufacturer's instructions.

growth_protocol: Cultured in DMEM supplemented with Glutamax, 10% fetal bovine serum, 1% non-essential amino acids and 1% pen/strep.

extract_protocol: RNA was extracted with RNeasy Mini Kit (Qiagen), followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Lentivirally transduced with scrambled or TRPM7 shRNA.

value: SH-SY5Y (American Type Culture Collection)

tag: tumour type

value: neuroblastic neuroblastoma

tag: transduced shrna

value: TRPM7 shRNA


title: genomic DNA from HCC_19N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_28N

description: adjacent non-tumorous


title: RNA from HCC_27N

description: adjacent non-tumorous


title: RNA from HCC_26T

description: tumor


title: HDACi2_24h

city: Toronto

first: Andras

last: Nagy

address: 25 Orde street

department: Mount Sinai Hospital

country: Canada

institute: Lunenfeld Tanenbaum Research Institute

description: HDACi 24h replicate 2

data_processing: The data were normalised using quantile normalisation with Lumi in R, no background correction.

source_name: F-class HDACi 24h replicate 2

label_protocol: Not provided

extract_protocol: RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: rtTA Mouse


title: HDACi2_48h

description: HDACi 48h replicate 2

source_name: F-class HDACi 48h replicate 2


title: genomic DNA from HCC_18T.AVG_Beta

description: tumor

value: liver tissue


title: SH-SY5Y_control_rep2

description: Replicate 2

source_name: SH-SY5Y neuroblastoma cells, transduced with scrambled shRNA

value: scrambled shRNA


title: RNA from HCC_25T

description: tumor

value: hepatocellular carcinoma tumor


title: RNA from HCC_26N

description: adjacent non-tumorous


title: HDACi1_48h

description: HDACi 48h replicate 1

source_name: F-class HDACi 48h replicate 1


title: HDACi2_0h

description: HDACi 0h replicate 2

source_name: F-class HDACi 0h replicate 2


title: genomic DNA from HCC_18N.AVG_Beta

description: adjacent non-tumorous


title: SH-SY5Y_control_rep1

description: Replicate 1


title: HDACi1_24h

description: HDACi 24h replicate 1

source_name: F-class HDACi 24h replicate 1


title: RNA from HCC_24T

description: tumor


title: SH-EP2_TRPM7shRNA_rep1

description: Replicate 1

source_name: SH-EP2 neuroblastoma cells, transduced with TRPM7 shRNA

value: epithelial-like neuroblastoma


title: RNA from HCC_23T

description: tumor


title: RNA from HCC_24N

description: adjacent non-tumorous


title: genomic DNA from HCC_16T.AVG_Beta

description: tumor


title: HDACi1_0h

description: HDACi 0h replicate 1

source_name: F-class HDACi 0h replicate 1


title: genomic DNA from HCC_17N.AVG_Beta

description: adjacent non-tumorous


title: Myc2_48h

description: Tet-Myc line2 48h no dox

source_name: Tet-Myc line2


title: SH-EP2_TRPM7shRNA_rep2

description: Replicate 2


title: SH-EP2_control_rep2

description: Replicate 2

source_name: SH-EP2 neuroblastoma cells, transduced with scrambled shRNA


title: genomic DNA from HCC_17T.AVG_Beta

description: tumor


title: RNA from HCC_23N

description: adjacent non-tumorous


title: genomic DNA from HCC_16N.AVG_Beta

description: adjacent non-tumorous


title: Myc2_0h

description: Tet-Myc line2 plus dox


title: SH-EP2_control_rep1

description: Replicate 1


title: RNA from HCC_22T

description: tumor


title: genomic DNA from HCC_15N.AVG_Beta

description: adjacent non-tumorous


title: 2D corpus H.pylori P12 infected vs 2D corpus not infected

description: +/- infection with H.pylori P12 wildtype

source_name: gastric cells

value: P12 wildtype infected

value: stomach

value: 2D monolayer

value: not infected

tag: tag


title: ESC2

description: ESC control

source_name: ESCs replicate 2


title: Myc1_0h

description: Tet-Myc line1 plus dox

source_name: Tet-Myc line1


title: RNA from HCC_21T

description: tumor


title: genomic DNA from HCC_14T.AVG_Beta

description: tumor


title: RNA from HCC_22N

description: adjacent non-tumorous

value: adjacent non-tumorous


title: RNA from HCC_20T

description: tumor


title: genomic DNA from HCC_14N.AVG_Beta

description: adjacent non-tumorous


title: SH-SY5Y_TRPM7shRNA_rep1

description: Replicate 1


title: RNA from HCC_19T

description: tumor


title: RNA from HCC_21N

description: adjacent non-tumorous


title: 3D corpus +Wnt +DBZ vs 3D corpus +Wnt

description: +/- inhibition NOTCH signalling

value: Corpus +Wnt +DBZ

value: 3D Corpus

value: Corpus +Wnt


title: ESC1

description: ESC control

source_name: ESCs replicate 1


title: genomic DNA from HCC_13N.AVG_Beta

description: adjacent non-tumorous


title: 2D corpus not infected vs 2D corpus H.pylori P12 infected


title: 1B 2° iPSC

description: Dox independent iPSCs

source_name: No Dox secondary iPSC


title: genomic DNA from HCC_15T.AVG_Beta

description: tumor


title: genomic DNA from HCC_13T.AVG_Beta

description: tumor


title: 3D antrum +Wnt +DBZ vs 3D antrum +Wnt

description: +/- inhibition NOTCH signalling

value: Antrum +Wnt +DBZ

value: 3D Antrum

value: Antrum +Wnt


title: 1B 1° iPSC

description: Dox independent iPSCs

source_name: No Dox primary iPSC


title: RNA from HCC_20N

description: adjacent non-tumorous


title: 1B 2° D18

description: F-class cells

source_name: D18 secondary reprogramming


title: genomic DNA from HCC_12T.AVG_Beta

description: tumor


title: 3D corpus -Wnt vs 3D antrum -Wnt

description: +/- depletion Wnt signalling

value: Corpus -Wnt

value: Antrum -Wnt


title: 3D antrum +Wnt vs 3D antrum +Wnt +DBZ

description: +/- inhibition NOTCH signalling


title: 1B 2° D16

description: F-class cells

source_name: D16 secondary reprogramming

value: rtTA Mouse


title: 1B 2° D11

description: Reprogramming cells

source_name: D11 secondary reprogramming


title: Myc1_48h

description: Tet-Myc line1 48h no dox


title: genomic DNA from HCC_11T.AVG_Beta

description: tumor

value: liver tissue


title: 3D antrum -Wnt vs 3D antrum +Wnt

description: +/- depletion Wnt signalling


title: SKMES-1  [SK-1-6]

description: Hibridized to SNP 6.0

tag: cell type

value: lung carcinoma cell line


title: RNA from HCC_18N

description: adjacent non-tumorous


title: RNA from HCC_19N

description: adjacent non-tumorous


title: 3D antrum -Wnt vs 3D corpus -Wnt

description: +/- depletion Wnt signalling


title: Lung Epithelium without Cellular Atypias, and metaplasia [1278-05-6]

description: Hibridized to SNP 6.0

value: Normal lung


title: RNA from HCC_18T

description: tumor

value: hepatocellular carcinoma tumor


title: 3D corpus +Wnt vs 3D corpus +Wnt +DBZ

description: +/- inhibition NOTCH signalling

value: stomach


title: genomic DNA from HCC_11N.AVG_Beta

description: adjacent non-tumorous


title: corpus 2D vs corpus 3D

description: cell culture

value: gastric cells


title: NSCLC  [897-06-6]

description: Hibridized to SNP 6.0

value: Lung tumor


title: genomic DNA from HCC_10T.AVG_Beta

description: tumor


title: 1B 2° D5

description: Reprogramming cells

source_name: D5 secondary reprogramming


title: RNA from HCC_17T

description: tumor


title: 3D antrum +Wnt vs 3D antrum -Wnt

description: +/- depletion Wnt signalling


title: genomic DNA from HCC_10N.AVG_Beta

description: adjacent non-tumorous

value: adjacent non-tumorous


title: NSCLC  [1551-06-6]

description: Hibridized to SNP 6.0


title: genomic DNA from HCC_12N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_16T

description: tumor


title: 1B 2° D0

description: Secondary fibroblasts (2MEF)

source_name: D0 secondary reprogramming


title: 1B 2° D2

description: Reprogramming cells

source_name: D2 secondary reprogramming


title: genomic DNA from HCC_9T.AVG_Beta

description: tumor


title: 1B 2° D8

description: Reprogramming cells

source_name: D8 secondary reprogramming


title: NSCLC [1479-06-6]

description: Hibridized to SNP 6.0


title: Lung Precursor Metaplasia [834-06-6]

description: Hibridized to SNP 6.0

value: Lung metaplasia


title: corpus 3D vs corpus 2D

description: cell culture


title: Pri clone 1-D30

description: F-class cells

source_name: D30 primary reprogramming


title: RNA from HCC_15T

description: tumor


title: genomic DNA from HCC_8N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_16N

description: adjacent non-tumorous


title: RNA from HCC_14N

description: adjacent non-tumorous


title: Pri clone 25

description: C-class cells

source_name: D16 primary reprogramming


title: RNA from HCC_14T

description: tumor


title: Pri clone 27

description: F-class cells


title: RNA from HCC_15N

description: adjacent non-tumorous


title: genomic DNA from HCC_9N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_7T.AVG_Beta

description: tumor


title: Pri clone 26

description: C-class cells


title: genomic DNA from HCC_8T.AVG_Beta

description: tumor


title: Pri clone 28

description: C-class cells


title: genomic DNA from HCC_7N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_13N

description: adjacent non-tumorous


title: Pri clone 24

description: C-class cells


title: genomic DNA from HCC_6N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_13T

description: tumor


title: RNA from HCC_12N

description: adjacent non-tumorous


title: genomic DNA from HCC_5T.AVG_Beta

description: tumor


title: genomic DNA from HCC_5N.AVG_Beta

description: adjacent non-tumorous


title: RNA from HCC_11N

description: adjacent non-tumorous


title: RNA from HCC_11T

description: tumor


title: genomic DNA from HCC_4T.AVG_Beta

description: tumor


title: AD-PD, nsp [Q1488-06-23_2]

description: Hybridized to 250K_Sty


title: genomic DNA from HCC_4N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_6T.AVG_Beta

description: tumor


title: NSCLC, nsp [Q4-07-13]

description: Hybridized to 250K_Sty


title: Pri clone 21

description: C-class cells


title: Pri clone 23

description: C-class cells


title: RNA from HCC_10T

description: tumor


title: SCLC, nsp [Q177-083]

description: Hybridized to 250K_Sty


title: Pri clone 19

description: C-class cells


title: Pri clone 22

description: C-class cells


title: Pri clone 20

description: C-class cells


title: SCC, sty [Q1235-06-23]

description: Hybridized to 250K_Nsp


title: SCLC nsp [Q045-07-A3]

description: Hybridized to 250K_Sty


title: RNA from HCC_17N

description: adjacent non-tumorous


title: RNA from HCC_10N

description: adjacent non-tumorous


title: RNA from HCC_9N

description: adjacent non-tumorous


title: Pri clone 18

description: C-class cells


title: SCLC, nsp [OTB0702083]

description: Hybridized to 250K_Sty


title: RNA from HCC_9T

description: tumor


title: NSCLC, nsp [NRJ270508_T1_3]

description: Hybridized to 250K_Sty


title: RNA from HCC_8T

description: tumor


title: Pri clone 16

description: C-class cells


title: Pri clone 13

description: F-class cells


title: Pri clone 17

description: C-class cells


title: genomic DNA from HCC_3T.AVG_Beta

description: tumor


title: SCLC, nsp [OTB070208N_3]

description: Hybridized to 250K_Sty


title: genomic DNA from HCC_2N.AVG_Beta

description: adjacent non-tumorous


title: genomic DNA from HCC_3N.AVG_Beta

description: adjacent non-tumorous


title: BvlR mutant complemented replicate 3

city: Cork

first: Fergal

last: O'Gara

address: University College Cork

department: Microbiology

country: Ireland

institute: BIOMERIT Research Centre

description: PA14bvlR pMEbvlR rep3

hyb_protocol: Carried out at DNAVISION, Belgium, according to manufacturer's (Affymetrix) guidelines.

data_processing: The probe set data were generated using Microarray suite 5.0. The raw data was normalised using the MAS5 algorithm. Pairwise comparison (t-test, P < 0.05) was carried out using GeneSpringGX to generate a list of genes with significantly altered expression between the test strains (PA14::bvlR pme6032,PA14::bvlR pMEbvlR ) greater than 2 fold.

organism: Pseudomonas aeruginosa PA14

source_name: BvlR mutant complemented

label_protocol: standard Affymetrix protocol

growth_protocol: Cultures grown to logarithmic-phase (OD 600nm 0.7-0.8)  PA14::bvlR pME6032 and PA14::bvlR pMEbvlR

extract_protocol: Total RNA was extracted using the Qiagen  RNeasy® Mini RNA extraction kit in accordance with the manufacturers guidelines. The RNA was treated with Ambion® TURBO DNase at 37°C for 20 minutes and the RNA pellet was then resuspended in sterile nuclease free water to a final volume of 25 µl.

treatment_protocol: RNA was extracted from logarithmic-phase cultures (OD 600nm 0.7-0.8)  PA14::bvlR pME6032 and PA14::bvlR pMEbvlR

tag: genotype/variation

value: BvlR mutant complemented

value: logarithmic-phase cultures


title: Pri clone 15

description: C-class cells


title: NSCLC, nsp [NRJ270508_N1_3]

description: Hybridized to 250K_Sty


title: genomic DNA from HCC_2T.AVG_Beta

description: tumor


title: RNA from HCC_8N

description: adjacent non-tumorous


title: RNA from HCC_12T

description: tumor


title: Pri clone 14

description: C-class cells


title: genomic DNA from HCC_1T.AVG_Beta

description: tumor


title: RNA from HCC_7T

description: tumor


title: BvlR mutant complemented replicate 2

description: PA14bvlR pMEbvlR rep2

scan_protocol: Carried out at DNAVISION, Belgium, according to manufacturer's (Affymetrix) guidelines.


title: SCLC, nsp [INER_53]

description: Hybridized to 250K_Sty


title: Pri clone 12

description: C-class cells


title: SCLC, nsp [INER_83]

description: Hybridized to 250K_Sty


title: AD-MD, nsp [INER_73]

description: Hybridized to 250K_Sty


title: NSCLC, nsp [INER_33]

description: Hybridized to 250K_Sty


title: RNA from HCC_7N

description: adjacent non-tumorous


title: AD-PD, nsp [INER_253]

description: Hybridized to 250K_Sty


title: Pri clone 9

description: C-class cells


title: BvlR mutant replicate 2

description: PA14bvlR pME6032 rep2

source_name: BvlR mutant

value: BvlR mutant


title: AD, nsp [INER_223]

description: Hybridized to 250K_Sty


title: BvlR mutant replicate 3

description: PA14bvlR pME6032 rep3


title: RNA from HCC_4T

description: tumor


title: Pri clone 11

description: C-class cells


title: RNA from HCC_6T

description: tumor


title: BvlR mutant replicate 1

description: PA14bvlR pME6032 rep1


title: RNA from HCC_5T

description: tumor


title: RNA from HCC_6N

description: adjacent non-tumorous


title: RNA from HCC_5N

description: adjacent non-tumorous


title: Pri clone 8

description: C-class cells


title: RA-FLS_sample4_TL1A-stimulated

city: Kobe

first: Toshihisa

last: Maeda

state: Hyogo

address: 7-5-1, Kusunokicho, Chuo-ku

department: Department of Orthopaedic Surgery

country: Japan

institute: Kobe University Graduate School of Medicine

description: Gene expression data from TL1A-stimulated RA-FLS sample4

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 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, TL1A-stimulated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: RA-FLS were cultured in DMEM supplemented with 10% fetal bovine serum (FBS; BioWhittaker, Walkersville, MD, USA) and 100 units/ml of penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the QIAshredder and RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacture’s protocol.

treatment_protocol: RA-FLS were incubated with either 1.0 μg/ml recombinant human TL1A protein (TL1A; R&D Systems, Minneapolis, MN, USA) or phosphate buffered saline (PBS) diluted with serum-free Opti-MEM medium as non-stimulated control for 12 hours at 37°C with 5% CO2.

value: Fibroblast like synoviocytes

tag: ethnicity

value: Asian


title: Pri clone 10

description: C-class cells


title: Pri clone 7

description: F-class cells


title: BvlR mutant complemented replicate 1

description: PA14bvlR pMEbvlR rep1

tag: sample type


title: RNA from HCC_4N

description: adjacent non-tumorous

tag: disease state


title: SCLC, nsp [GOA290508_T_3]

description: Hybridized to 250K_Sty


title: RA-FLS_sample4_control

description: Gene expression data from non-stimulated RA-FLS sample4

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4

tag: treatment

value: untreated


title: Lung precursor metaplasia-displasia, nsp [834-06-2-3]

description: Hybridized to 250K_Sty


title: RNA from HCC_3N

description: adjacent non-tumorous


title: RA-FLS_sample2_TL1A-stimulated

description: Gene expression data from TL1A-stimulated RA-FLS sample2

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, TL1A-stimulated


title: RNA from HCC_3T

description: tumor


title: Pri clone 3

description: C-class cells


title: RNA from HCC_2N

description: adjacent non-tumorous


title: Pri clone 6

description: F-class cells


title: Pri clone 2

description: F-class cells


title: RNA from HCC_2T

description: tumor


title: Pri clone 5

description: C-class cells


title: Pri clone 4

description: C-class cells


title: RA-FLS_sample3_control

description: Gene expression data from non-stimulated RA-FLS sample3

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3


title: NSCLC SCC-BD, nsp [897-06-23]

description: Hybridized to 250K_Sty


title: RNA from HCC_1T

description: tumor


title: Primary MEF

description: Parental fibroblasts

source_name: E15.5 embryo


title: NSCLC, nsp [INER_13]

description: Hybridized to 250K_Sty


title: NSCLC SCC-PD, nsp [708-06-103]

description: Hybridized to 250K_Sty


title: RA-FLS_sample2_control

description: Gene expression data from non-stimulated RA-FLS sample2

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2


title: Pri clone 1

description: F-class cells


title: Lung precursor Metaplasia, nsp [293-06-3]

description: Hybridized to 250K_Sty


title: NSCLC SCC-MD, tumor nsp [1352-06-13]

description: Hybridized to 250K_Sty


title: SEJ_10008_V0

status: Public on Dec 09 2014

city: Nantes

first: Richard

last: Danger

address: 30 Boulevard Jean Monnet

institute: CHU Nantes - INSERM- Nantes Universite

description:
SEJ_10008_V0_13295_2_1

This Sample represents one channel of a dual-channel array.

hyb_protocol: cRNA samples were hybridized to an Agilent Technologies Human Gene Expression 8x60K Microarray during 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies). The hybridization slides were washed, stabilized, dried, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Microarray Scanner using default parameters (protocol GE2_107_Sep09 and Grid: 028004_D_F_20110325). Each sample represents one channel of a dual-channel array.

data_processing: Data extraction of median feature intensity without background subtraction was peformed with Feature Extraction software v10.7.1.1 (gMedianSignal or rMedianSignal column) (Agilent Technologies). In order to remove systemic signal intensity bias between each array, median feature intensity were normalized with the function lowess (Locally weighted scatterplot smoothing) method, and then spots with half of the samples exhibiting signal less than the mean of all median signals were removed (threshold: 90.83). 30,146 spots were kept out of 58,717.

source_name: Whole blood sample, PAH

label_protocol: The cRNA labeling was performed according to Protocol from Agilent Technologies Inc. (Santa Clara, CA) using the Agilent Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, CA) following the two-colour manufacturer's protocol. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted from whole blood using the PAXgeneTM Blood RNA System Kit (PreAnalytix, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop ND-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Blood was collected in a PAXgene® tube, incubated at room temperature for 4h for RNA stabilization and then stored at -80°C.

value: pulmonary arterial hypertension (PAH)

value: whole blood

value: female


title: SIS_3068

description:
SIS_3068_13296_1_2

This Sample represents one channel of a dual-channel array.

source_name: Whole blood sample, CF

value: cystic fibrosis (CF)

value: male


title: SCLC, nsp [GOA290508_N_3]

description: Hybridized to 250K_Sty


title: PES_6003

description:
PES_6003_13297_1_2

This Sample represents one channel of a dual-channel array.


title: RA-FLS_sample1_control

description: Gene expression data from non-stimulated RA-FLS sample1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1


title: SUXA__1028

description:
SUXA__1028_13297_1_4

This Sample represents one channel of a dual-channel array.


title: SIV_10007_V0

description:
SIV_10007_V0_13296_2_4

This Sample represents one channel of a dual-channel array.


title: SZF_10046_V1R

description:
SZF_10046_V1R_13297_2_4

This Sample represents one channel of a dual-channel array.


title: SAA_8007_B

description:
SAA_8007_B_13295_1_1

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_WNV_24h_e

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

institute: University of Washington

description: Gene expression after 24 hours in WNV treated neurons

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B).

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

source_name: Mouse Granule cell neuron WNV 100  IU/mL treated for 24h hours, replicate e

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Cortical neurons and granule cell neurons were generated from embryonic day 15 (E15) mouse embryos and 6-day-old neonatal mice, respectively. Cells were seeded onto poly-D-lysine/laminin-coated plates and cultured in serum-free Neurobasal/B27 medium (Invitrogen). The purity of neuron cultures (>95%) was determined after staining with anti-MAP-2 (Sigma), anti-glial fibrillary acidic protein (Dako), and anti-CD11b (BD Biosciences) antibodies.

extract_protocol: Total RNA was isolated according to the manufacturer’s protocol with an RNeasy kit (Qiagen)

treatment_protocol: IFN-β treatment or virus infection was performed on neurons cultured for 3 to 4 days. The cultures were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: Granule cell neuron

value: WNV

tag: timepoint (hours)

tag: replicate

value: e


title: PAM_10029_V1R

description:
PAM_10029_V1R_13297_2_2

This Sample represents one channel of a dual-channel array.

tag: gender


title: WNV-M2011-01_WT_GC_WNV_24h_a

source_name: Mouse Granule cell neuron WNV 100  IU/mL treated for 24h hours, replicate a

value: a

tag: strain


title: WNV-M2011-01_WT_GC_WNV_24h_d

source_name: Mouse Granule cell neuron WNV 100  IU/mL treated for 24h hours, replicate d

value: d


title: RAE_3024

description:
RAE_3024_13295_1_3

This Sample represents one channel of a dual-channel array.

tag: tissue


title: RA-FLS_sample1_TL1A-stimulated

description: Gene expression data from TL1A-stimulated RA-FLS sample1

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, TL1A-stimulated


title: TASE_2016

description:
TASE_2016_13295_2_3

This Sample represents one channel of a dual-channel array.


title: PAF_3035

description:
PAF_3035_13297_2_2

This Sample represents one channel of a dual-channel array.


title: NSCLC SCC-PD, tumor nsp [1479-06-13]

description: Hybridized to 250K_Sty

value: Lung tumor


title: NSCLC SCC-MD (IV), tumor nsp [1551-063]

description: Hybridized to 250K_Sty


title: WNV-M2011-01_WT_GC_WNV_24h_b

source_name: Mouse Granule cell neuron WNV 100  IU/mL treated for 24h hours, replicate b

value: b


title: P71111019918_9

description:
P71111019918_9_13295_1_3

This Sample represents one channel of a dual-channel array.

source_name: Whole blood sample, HV

value: healthy


title: WNV-M2011-01_WT_GC_Mock_12h_b

description: Gene expression after 12 hours in Mock treated neurons

source_name: Mouse Granule cell neuron Mock 100  IU/mL treated for 12h hours, replicate b

value: Mock


title: Lung Epithelium without cellular atypias, and metaplasia, nsp [1278-05-23]

description: Hybridized to 250K_Sty

value: Normal lung


title: P71111019555_8

description:
P71111019555_8_13297_2_3

This Sample represents one channel of a dual-channel array.


title: P71111019686_3

description:
P71111019686_3_13295_1_4

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_WNV_24h_c

source_name: Mouse Granule cell neuron WNV 100  IU/mL treated for 24h hours, replicate c

value: c


title: P71111019782_4

description:
P71111019782_4_13295_2_4

This Sample represents one channel of a dual-channel array.


title: P7111101990_10

description:
P7111101990_10_13292_2_3

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_IFNb_12h_b

description: Gene expression after 12 hours in IFNb treated neurons

source_name: Mouse Granule cell neuron IFNb 100  IU/mL treated for 12h hours, replicate b

value: IFNb


title: P71111019723_12

description:
P71111019723_12_13295_1_1

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_Mock_12h_a

source_name: Mouse Granule cell neuron Mock 100  IU/mL treated for 12h hours, replicate a


title: P71111019467_11

description:
P71111019467_11_13296_2_1

This Sample represents one channel of a dual-channel array.


title: Lung precursor metaplasia, nsp [1032-05-1-3]

description: Hybridized to 250K_Sty


title: P71111019512_1

description:
P71111019512_1_13297_1_1

This Sample represents one channel of a dual-channel array.


title: P7110155898_5_82

description:
P7110155898_5_82_13292_2_1

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_mock_12h_d

description: Gene expression after 12 hours in mock treated neurons

source_name: Mouse Granule cell neuron mock 100  IU/mL treated for 12h hours, replicate e

value: mock


title: RA-FLS_sample3_TL1A-stimulated

description: Gene expression data from TL1A-stimulated RA-FLS sample3

source_name: Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, TL1A-stimulated

value: Fibroblast like synoviocytes

value: Asian


title: WNV-M2011-01_WT_GC_IFNb_12h_a

source_name: Mouse Granule cell neuron IFNb 100  IU/mL treated for 12h hours, replicate a


title: WNV-M2011-01_WT_GC_IFNb_12h_d

source_name: Mouse Granule cell neuron IFNb 100  IU/mL treated for 12h hours, replicate d


title: WNV-M2011-01_WT_GC_mock_12h_e


title: P7110155897_7_73

description:
P7110155897_7_73_13295_2_3

This Sample represents one channel of a dual-channel array.

value: whole blood

value: female


title: P71111019504_6

description:
P71111019504_6_13296_1_1

This Sample represents one channel of a dual-channel array.


title: siTERC-BMSCs, biological rep3

city: Bethesda

first: Prasun

middle: J.

last: Mishra

state: MD

address: 37 Convent Drive

department: United States Department of Health and Human Services

institute: National Cancer Institute, National Institutes of Health

description: Gene expression data from N-BMSCs were transfected with siTERC-RNA (siTERC) construct

hyb_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing: Genes that were under/over-represented by >2-fold were analyzed using GeneSpring software.  Signal intensity values were normalized using RMA (Robust Multi-array Analysis) summarization and baseline transformation to median of all samples was performed.  Entities were filtered based on their signal intensity values.  Hierarchical clustering was performed on filtered signal intensity (>20.0), non-averaged, fold change >2.  A fold change analysis (>10-fold) was performed to generate a list of top genes under/over represented between the groups.

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

growth_protocol: Cell lines were cultured and maintained in growth medium (alpha-MEM, 2 mM glutamine, 100 U/ml penicillin, 100ug/ml streptomycin sulfate, 20% lot-selected fetal bovine, non-heat inactivated serum, 10-8 M dexamethasone and 10-4 M ascorbic acid-2-phosphate)

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

treatment_protocol: To mimic the defect found in TBD-BMSCs, TERC expression was reduced in N-BMSCs in two different ways.  Initially, TERC short hairpin (sh) RNA lentiviral particles were used to generate cells with stably-reduced expression of TERC.  However, these cells were unable to grow.  Thus, transient knockdown of TERC was performed using siTERC-RNA (SilencerTM Select, pre-designed and validated, AM 16706, Ambion) and a negative control siRNA [(siNC), SilencerTM negative control No. 2 siRNA, AM4637, Ambion].  Constructs were transfected into N-BMSCs using Lipofectamine RNAiMAX (#13778-075, Life Technologies), according to the manufacturer’s instructions.

tag: cell line

value: non-clonal BMSC cultures

tag: transfection

value: siTERC-RNA (siTERC) construct


title: siTERC-BMSCs, biological rep2

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

source_name: N-BMSCs were transfected with siTERC-RNA (siTERC) construct


title: P7110155935_5_54

description:
P7110155935_5_54_13292_2_4

This Sample represents one channel of a dual-channel array.


title: siTERC-BMSCs, biological rep1


title: P7110155914_4_75

description:
P7110155914_4_75_13292_1_1

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_Mock_12h_c

description: Gene expression after 12 hours in Mock treated neurons

source_name: Mouse Granule cell neuron Mock 100  IU/mL treated for 12h hours, replicate c

value: Granule cell neuron


title: WNV-M2011-01_WT_GC_IFNb_12h_c

source_name: Mouse Granule cell neuron IFNb 100  IU/mL treated for 12h hours, replicate c


title: P7110155890_89

description:
P7110155890_89_13297_2_1

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_GC_IFNb_12h_e

source_name: Mouse Granule cell neuron IFNb 100  IU/mL treated for 12h hours, replicate e

value: e


title: siNC-BMSCs , biological rep3

description: Gene expression data from N-BMSCs were transfected with negative control (siNC) construct.

value: negative control (siNC) construct


title: siNC-BMSCs , biological rep1

source_name: N-BMSCs were transfected with negative control (siNC) construct


title: P7110155850_4_80

description:
P7110155850_4_80_13295_2_2

This Sample represents one channel of a dual-channel array.

value: male


title: P7110155880_3_88

description:
P7110155880_3_88_13296_2_2

This Sample represents one channel of a dual-channel array.


title: siNC-BMSCs , biological rep2


title: WNV-M2011-01_WT_CN_WNV_24h_e

description: Gene expression after 24 hours in WNV treated neurons

source_name: Mouse cortical neuron WNV 100  IU/mL treated for 24h hours, replicate e

value: Cortical neuron

value: WNV


title: N-BMSCs, biological rep2

description: Gene expression data from non-clonal BMSC cultures from normal donors.

source_name: BM single-cell suspensions from bone fragments and aspirates were used to establish non-clonal BMSC cultures from normal donors (N-BMSCs)


title: P71111019635_7

description:
P71111019635_7_13297_2_1

This Sample represents one channel of a dual-channel array.

value: healthy


title: WNV-M2011-01_WT_CN_WNV_24h_b

source_name: Mouse cortical neuron WNV 100  IU/mL treated for 24h hours, replicate b

value: b


title: P7110155851_2_80

description:
P7110155851_2_80_13292_1_4

This Sample represents one channel of a dual-channel array.

source_name: Whole blood sample, HV


title: P7110155852_64

description:
P7110155852_64_13296_2_2

This Sample represents one channel of a dual-channel array.


title: N-BMSCs, biological rep3


title: P7110155831_52

description:
P7110155831_52_13295_2_1

This Sample represents one channel of a dual-channel array.


title: N-BMSCs, biological rep1


title: P71101558432_86

description:
P71101558432_86_13296_1_3

This Sample represents one channel of a dual-channel array.


title: P7110155818_4_81

description:
P7110155818_4_81_13296_1_4

This Sample represents one channel of a dual-channel array.


title: P7110155835_2_64

description:
P7110155835_2_64_13292_1_2

This Sample represents one channel of a dual-channel array.


title: P7110155822_1_65

description:
P7110155822_1_65_13292_2_2

This Sample represents one channel of a dual-channel array.


title: P7110155865_1_51

description:
P7110155865_1_51_13296_1_2

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_CN_WNV_24h_d

source_name: Mouse cortical neuron WNV 100  IU/mL treated for 24h hours, replicate d

value: d


title: WNV-M2011-01_WT_CN_WNV_24h_a

source_name: Mouse cortical neuron WNV 100  IU/mL treated for 24h hours, replicate a

value: a


title: WNV-M2011-01_WT_CN_WNV_24h_c

source_name: Mouse cortical neuron WNV 100  IU/mL treated for 24h hours, replicate c

value: c


title: P7110155875_8_61

description:
P7110155875_8_61_13297_1_3

This Sample represents one channel of a dual-channel array.


title: P7110155824_8_81

description:
P7110155824_8_81_13296_2_4

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_CN_mock_12h_d

description: Gene expression after 12 hours in mock treated neurons

source_name: Mouse cortical neuron mock 100  IU/mL treated for 12h hours, replicate d

value: mock


title: MCG_4017

description:
MCG_4017_13297_2_4

This Sample represents one channel of a dual-channel array.

source_name: Whole blood sample, CF

value: cystic fibrosis (CF)


title: MOD_10027_V0

description:
MOD_10027_V0_13295_2_2

This Sample represents one channel of a dual-channel array.

source_name: Whole blood sample, PAH

value: pulmonary arterial hypertension (PAH)

value: whole blood


title: MAM_3008

description:
MAM_3008_13296_2_3

This Sample represents one channel of a dual-channel array.

value: female


title: MOA_3006

description:
MOA_3006_13295_2_4

This Sample represents one channel of a dual-channel array.


title: P7110155830_1_58

description:
P7110155830_1_58_13297_1_2

This Sample represents one channel of a dual-channel array.


title: fibroblast cultured from normal esophageal tissue_HEF_1173

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

address: 3311-1 Yakushiji

department: Department of Integrative Pathology

institute: Jichi Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: Cells were cultured in RPMI(cancer cell) or DMEM(fibroblast) supplemented with 10% FBS, antibiotics, and glutamine at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was isolated after the third passage of cells.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No specific treatments were done.

tag: tissue type

value: normal esophageal tissue of surgically resected human esophagus

value: fibroblast


title: fibroblast cultured from normal esophageal tissue_HEF_2111


title: WNV-M2011-01_WT_CN_Mock_12h_b

description: Gene expression after 12 hours in Mock treated neurons

source_name: Mouse cortical neuron Mock 100  IU/mL treated for 12h hours, replicate b

value: Mock


title: NAK_8005_B

description:
NAK_8005_B_13297_1_1

This Sample represents one channel of a dual-channel array.


title: MAP_8033_V0

description:
MAP_8033_V0_13295_1_2

This Sample represents one channel of a dual-channel array.


title: fibroblast cultured from esophageal squamous cell carcinoma tissue_HECaF_2111

value: surgically resected esophageal squamous cell carcinoma tissue


title: human esophageal squamous cell carcinoma cell line_EC-GI-10

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

value: squamous cell carcinoma


title: LAA_10026_V0

description:
LAA_10026_V0_13292_1_3

This Sample represents one channel of a dual-channel array.


title: fibroblast cultured from normal esophageal tissue_HEF_75


title: MAD_4006

description:
MAD_4006_13296_1_1

This Sample represents one channel of a dual-channel array.

value: male


title: WNV-M2011-01_WT_CN_mock_12h_e

source_name: Mouse cortical neuron mock 100  IU/mL treated for 12h hours, replicate e

value: Cortical neuron

value: e


title: HOM_4002

description:
HOM_4002_13297_2_3

This Sample represents one channel of a dual-channel array.


title: GRS_3037

description:
GRS_3037_13292_1_3

This Sample represents one channel of a dual-channel array.


title: MAF_3007

description:
MAF_3007_13292_2_3

This Sample represents one channel of a dual-channel array.


title: LOG_1037_V0

description:
LOG_1037_V0_13296_2_1

This Sample represents one channel of a dual-channel array.


title: human esophageal squamous cell carcinoma cell line_TE-14


title: WNV-M2011-01_WT_CN_Mock_12h_c

source_name: Mouse cortical neuron Mock 100  IU/mL treated for 12h hours, replicate c


title: WNV-M2011-01_WT_CN_Mock_12h_a

source_name: Mouse cortical neuron Mock 100  IU/mL treated for 12h hours, replicate a


title: GID_2004

description:
GID_2004_13296_1_4

This Sample represents one channel of a dual-channel array.


title: WNV-M2011-01_WT_CN_IFNb_12h_b

description: Gene expression after 12 hours in IFNb treated neurons

source_name: Mouse cortical neuron IFNb 100  IU/mL treated for 12h hours, replicate b

value: IFNb

value: b


title: WNV-M2011-01_WT_CN_IFNb_12h_e

source_name: Mouse cortical neuron IFNb 100  IU/mL treated for 12h hours, replicate e