title: ixr1 hypoxic shift A

city: A Coruña

first: M Esperanza

last: Cerdan

state: A Coruña

address: Campus de A Zapateira

department: Biología Celular y Molecular

institute: Universidad de A Coruña

hyb_protocol: Filters were pre-hybridised for 1 hour at 65C in the hybridisation mix (750 mM NaCl, 75 mM Sodium acetate, 0.1% w/v Bovine Serum Albumine, 0.1% w/v Ficoll, 0.1% w/v Polyvinylpyrrolidone and 0.5% w/v Sodium dodecylsulphate, pH 7). The probe was then denatured for 5 minutes at 100C, cooled quickly on ice, and hybridized with the arrays over night at 65C. The following day, two washes were performed at 65C, for 5 and 20 minutes respectively, in 300 mM NaCl, 30 mM Sodium acetate, 0.1% (w/v) Sodium dodecylsulphate, pH 7.

scan_protocol: The filters were exposed for 24 hours to a phosphor screen and the data were collected using a Phosphor Imager Scanning Instrument 425 (Molecular Dynamics-Amersham Biosciences, Buckinghamshire, UK). Signal quantification was performed with Array Vision software (Molecular Dynamics-Amersham Biosciences).

data_processing: Normalisation of data from each membrane was carried out by dividing the measurement for each gene by the media of all spots in the filter. Media and standard deviations were calculated for the expression of each single gene in the total number of replica. To find those genes which were expressed at higher levels in the wild type than in the mutant strain the ratio wt/ixr1null was calculated (activation ratio). To find those genes which were expressed at higher levels in the mutant than in the wt strain the ratio ixr1null/wt was calculated (repression ratio). A t-test was applied to evaluate the differences between means. Genes were considered to be differentially expressed in the two strains (wild type and ixr1 null mutant) or in response to different culture conditions (normoxia, hypoxia or shift from normoxia to hypoxia) if they satisfied both a p-value lower than 0.05 in the t-test statistical evaluation of differences between means and at least a two-fold change in expression levels. The data were processed, clustered and analysed using the bio-informatic tool Genespring (Agilent Technologies. Palo Alto, California, USA).

organism: Saccharomyces cerevisiae

label_protocol: RNA was annealed to oligonucleotide dT18 and used as a template to synthesize and radiolabel the corresponding first strand cDNA with 50 uCi of [32P]-dATP (Amersham Biosciences, Buckinghamshire, UK) and SuperScript II (GIBCO BRL Life Technologies, Gaithersburg, Maryland, USA). The reactions were carried out at 43C for 1 h, after which the RNA was eliminated with NaOH at 65C for 30 minutes. The probe was purified by isopropanol precipitation and the incorporation of 32P was measured to check the efficiency of the reaction.

growth_protocol: Yeast cells were grown at 30C in synthetic complete medium (CM) containing 2% glucose (w/v) and prepared as previously described (Zitomer and Hall 1976). During hypoxic growth, cells well cultured over night in anaerobic jars with the GasPack EZAnaerobe system (Becton, Dickinson and Company) and under these conditions (oxygen concentration <1%) the medium was supplemented with 20 mg/l ergosterol and 0.5% Tween 80. In experiments analyzing the consequences of a shift  from aerobic to hypoxic conditions, cells were grown first in aerobiosis until OD600 = 0.8 and then the hypoxia was generated by bubbling nitrogen in the flasks at constant pressure during 3 hours.

extract_protocol: For RNA isolations, cells were harvested, immediately frozen in liquid nitrogen, disrupted using a Micro-Dismembrator (B. Braun Biotech International, Allentown, Pennsylvania, USA). The resulting powder was mixed with TRIZOL Reagent (GIBCO BRL- Life Technologies, Gaithersburg, Maryland, USA) and total RNA was extracted by the method previously described (Chomczynski and Sacchi,1987)

treatment_protocol: Comparison of wild type versus ixr1 null

tag: background strain

value: BY4741 EUROSCARF

value: ixr1 null

tag: growth condition

value: hypoxic shift


title: ixr1 hypoxic shift B

status: Public on Sep 13 2012

type: RNA

country: Spain

molecule: total RNA

tag: genotype/variation


title: Tumor from TRP mouse model, 163488, tamoxifen induced, 21w

city: Seattle

first: Burak

last: Kutlu

state: WA

address: 1441 North 34th Street

country: USA

institute: Institute for Systems Biology

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

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

data_processing: The data were analyzed with R/Bioconductor rma package.

label: biotin

organism: Mus musculus

source_name: Solid tumor cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Mice were induced with 5 Tamoxifen injections

tag: strain

tag: gender

value: m

tag: genotype

tag: genotype abbreviation

value: TRPhet

tag: agent

value: tamoxifen

tag: time

value: 21w post induction


title: Tumor from TRP mouse model, 190949, tamoxifen induced, 15w

value: TRPnull

value: 15w post induction


title: Tumor from TRP mouse model, 164237, tamoxifen induced, 9w

value: f

value: 9w post induction


title: Tumor from TRP mouse model, 125988, uninduced

treatment_protocol: Uninduced.

value: TR

value: control (uninduced)


title: Tumor from TRP mouse model, 1953, tamoxifen induced, 10w

value: 10w post induction


title: SM019_1.3_B6_MA15_d4_3

first: Michael

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

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

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

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.
platform: x86_64-redhat-linux-gnu
arch: x86_64
os: linux-gnu
system: x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package: 'limma'
limma version: 3.6.9
limma date: 2010/12/01version
For the generation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

source_name: lung, wild-type, infected with SARS MA15 virus, day 4

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.

extract_protocol: Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation. All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol:
Ten-week-old mice were infected by intranasal instillation of 10^5 PFU of SARS MA15 in 50 µl of PBS or mock-infected with PBS alone. At days 4 and 7 days post-infection, lungs were harvested.
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing.

tag: strain/background

value: wild-type

value: female

tag: age

value: 10 weeks

tag: tissue

value: lung

tag: treatment

value: infected with 10^5 PFU of SARS MA15 virus

tag: time of sample collection

value: day 4 post-infection


title: lin- cells, technical rep 1

city: Toronto

first: Wenlian

last: Qiao

state: Ontario

address: Room 1110, 160 College Street

country: Canada

institute: University of Toronto

description: developmental stage; progenitors

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 machine

data_processing: Background noise in gene expression data was corrected using the justRMA function (function parameters: normalize=FALSE,background=TRUE) of the affy package (version 1.34.0)  from BioConductor

organism: Homo sapiens

source_name: umbilical cord blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

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

treatment_protocol: Mono-nucleated cells were obtained by lysing the erythrocytes. Lineage-depleted cells (Lin−) were isolated from mono-nucleated cells using the EasySep® system (Stemcell Technologies, Vancouver, Canada).

tag: cell type

value: lin- cell


title: ixr1 hypoxia B

value: BY4741 EUROSCARF

value: ixr1 null

value: hypoxia


title: wt hypoxic shift A

value: WT

value: hypoxic shift


title: Tumor from TRP mouse model, 131711, tamoxifen induced, 11w

value: m

value: TRPhet

value: tamoxifen

value: 11w post induction


title: Tumor from TRP mouse model, 751, tamoxifen induced, 18w

value: 18w post induction


title: Tumor from TRP mouse model, 601, tamoxifen induced, 20w

value: 20w post induction


title: wt hypoxic shift B


title: mononucleated cells, technical rep 2

description: developmental stage; progenitors and differentiated cells

value: mononucleated cell


title: lin- cells, technical rep 2

description: developmental stage; progenitors


title: wt hypoxia B


title: ixr1 hypoxia A


title: ixr1 O2 B

value: normoxia


title: mononucleated cells, technical rep 1


title: ixr1 O2 A


title: wt hypoxia A


title: wt O2 B


title: wt O2 A


title: Uninfected HFF #1

city: St Louis

middle: Sean

last: Behnke

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology

institute: Washington University School of Medicine

hyb_protocol: Standard Affymetrix protocol with 10ug fragmented labeled cRNA.

scan_protocol: Standard Affymetrix protocol

data_processing: GeneSpring 7.2 RMA, Data transformation: Set measurements less than 0.01 to 0.01, Per Chip and Per Gene: Median Polishing

source_name: Uninfected HFF

label_protocol: Standard Ambion Message Amp Premier protocol starting with 500ng of total RNA.

growth_protocol: Human foreskin fibroblasts (HFF) were infected (or not) with Toxoplasma gondii (two different strains) at MOI of 4 for 24 hrs.

extract_protocol: Monolayers were washed 2X with 1 X PBS and then trypsinized. Lifted cells were collected in DMEM with FBS, spun, and the pellet frozen at -80C. RNA was extracted using a Qiagen RNeasy kit (b-mercaptoethanol and DNase I treatment).

treatment_protocol: Normal growth media: DMEM supplemented with 10% FBS

value: Human foreskin fibroblasts (HFF)

tag: infection status

value: Uninfected HFF


title: HFF + RH-deltaku80 #2

source_name: Human HFF infected with Toxoplasma gondii for 24 hrs.

value: Infected HFF with Toxoplasma gondii strain RH-deltaku80


title: HFF + RH-deltaku80 #1


title: HFF + RH-deltaku80-deltarop5 #2

value: Infected HFF with Toxoplasma gondii strain RH-deltaku80-deltarop5


title: Tumor from TRP mouse model, 15379, tamoxifen induced, 19w

hyb_protocol: Hybridized as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis protocol, version 6.5

scan_protocol: Agilent DNA Microarray Scanner at 3 micron resolution and 20-bit dynamic range

data_processing: Row median centered and standardized, after background substraction and quantile normalization using Limma and R scripts

label_protocol: Cy3 labeling was performed with 200 ng total RNA using Low Input Quick Amp Agilent kit

growth_protocol: Mice were induced with 5 Tamoxifen injections

value: 19w post induction


title: Uninfected HFF #2


title: X1A

city: Kunming

first: Cheng Gang

last: Zou

state: Yunnan

address: No. 2,North of Cuihu Road

country: China

institute: Yunnan University

description: This sample is ofC.elegans wild-type. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.

organism: Caenorhabditis elegans

source_name: C.elegans wild-type

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: C. elegans wild-type, kin-1(ok338)mutant and crh-1(tz2) mutant were grown to L4 at 20°C in NGM media. Then they infected 24 hours by fungi Drechmeria coniospora respectively.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

tag: developmental stage

value: wild-type


title: X3A

description: This sample is ofC.elegans wild-type. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures.


title: HFF + RH-deltaku80-deltarop5 #1


title: X3B

description: This sample is of C.elegans kin-1(ok338) loss of function mutant. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: C.elegans kin-1 mutant

value: kin-1 mutant


title: X2C

description: This sample is of C.elegans crh-1(tz2) loss of function mutant. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: C.elegans crh-1mutant

value: crh-1 mutant


title: X3C

description: This sample is of C.elegans crh-1(tz2) loss of function mutant. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: non-depleted 2

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: control HeLa cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: control HeLa cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Hela cells were cultured in MEM medium complemented with 10% FBS, 2 mM L-glutamine, 100 µg/ml penicillin/streptomycin, 5 µg/ml blasticidin, 200 µg/ml zeocin and non-essential amino-acids for 7 days.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) according to the manufacturer’s recommendations.

value: HeLa

value: normal cells


title: X2B

description: This sample is of C.elegans kin-1(ok338) loss of function mutant. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Tumor from TRP mouse model, 17365, tamoxifen induced, 19w

value: m

value: TRPhet


title: Tumor from TRP mouse model, 16172, tamoxifen induced, 19w

value: tamoxifen


title: Tumor from TRP mouse model, 15269, tamoxifen induced, 19w


title: NAGLU-depleted 1

description: HeLa cells depleted of NAGLU

source_name: HeLa cells depleted of NAGLU

value: MPSIIIB


title: non-depleted 1

description: control HeLa cells


title: X1C

description: This sample is of C.elegans crh-1(tz2) loss of function mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: X1B

description: This sample is of C.elegans kin-1(ok338) loss of function mutant. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: X2A

description: This sample is ofC.elegans wild-type. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures.


title: NAGLU-depleted 2

description: HeLa cells depleted of NAGLU


title: Tumor from TRP mouse model, 16438, tamoxifen induced, 15w

value: 15w post induction


title: Human breast tumor pre treatment, biological rep3

city: Lexington

first: Suleiman

last: Massarweh

state: KY

address: 800 Rose St., Cc452

institute: University of Kentucky and Markey Cancer Center

description: Gene expression data from human breast cancer

hyb_protocol: Standard Affymetrix protocol for 3' IVT design

scan_protocol: Affymetrix Genechip 7G scanner

data_processing: GCRMA, gcrma package (version 2.28.0) in R/Bioconductor

source_name: Human breast tumor, pre sorafenib treatment

label_protocol: 3' IVT express

extract_protocol: Trizol extraction

treatment_protocol: After day 1 biopsy on endocrine therapy alone, sorafenib was added and a second biopsy was obtained on day 28.

value: breast tumor

tag: er status

value: Positive

tag: pgr status

tag: endocrine agent

value: Tamoxifen

tag: status on endocrine agent

value: Progressive disease (PD)

tag: response to sorafenib


title: Human breast tumor pre treatment, biological rep4

value: Negative

value: Letrozole


title: Human breast tumor post treatment, biological rep4

source_name: Human breast tumor, post sorafenib treatment

value: Stable disease (SD)


title: Human breast tumor post treatment, biological rep3


title: Human breast tumor post treatment, biological rep2


title: Human breast tumor post treatment, biological rep1


title: megakaryocytes at day0, biological rep A

data_processing: Gene expression values were normalized using the justRMA function of the affy package from BioConductor

growth_protocol: Lineage negative cells derived from fresh human umbilical cord blood were cultured in serum free condition supplemented with SCF, THPO and FLT3LG.

treatment_protocol: CD34-CD33+CD13+ colony forming unit-monocytes (CFU-M) and CD34-CD41+CD61+CD45- megakaryocytes were sorted from pooled fresh cord blood samples on BD FACS Aria (CD34: PE; CD33: APC; CD13: PERCP; CD41: PE; CD61: FITC; CD45: APC. All antibodies were purchased from BD BioScience)

value: CD34-CD41+CD61+CD45- megakaryocytes

value: 0 day in culture


title: megakaryocytes at day0, biological rep B


title: megakaryocytes at day4, biological rep B

source_name: Lin- cell culture derived samples, day4

value: 4 days in culture


title: megakaryocytes at day4, biological rep A


title: Human breast tumor pre treatment, biological rep2


title: Human breast tumor pre treatment, biological rep1


title: Tumor from TRP mouse model, 15076, tamoxifen induced, 21w

tag: strain

tag: gender

tag: genotype

value: 21w post induction


title: S. aureus_walRc_rep2

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: S. aureus walRc strain, second biological replicate

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing: An aggregated expression value was computed for each Genbank annotated CDS as the median log2 intensity of probes lying entirely within the corresponding region. To control for possible cross-hybridization artefacts, the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008, Nucl. Acids Res. 36, 2926-2938).

organism: Staphylococcus aureus

source_name: S. aureus_pCN51_Pcad-walRc

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009, Mol. Microbiol. 73, 1043-1057).

growth_protocol: The S. aureus strains HG001/pCN51 and HG001/pSD3-12 were grown aerobically at 37°C in TSB medium added with 0.25 µM CdCl2 until OD600nm of 1.

extract_protocol: Cells were 2-fold diluted in ice-cold killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3), centrifuged and immediately frozen at -80 °C. Total RNA was isolated by mechanical disruption and Trizol extraction as previously described (Even et al., 2006, J. Bacteriol. 188, 2184–2197) followed by DNase I treatment in order to eliminate residual genomic DNA and column purification using the RNA Clean-Up kit (Norgen Biotech Corp.). RNA quality was checked by electropherogram analysis (Agilent Bioanalyzer).


title: S. aureus_wild type_rep3

description: S. aureus wild type, third biological replicate

source_name: S. aureus_pCN51_empty vector


title: S. aureus_walRc_rep1

description: S. aureus walRc strain, first biological replicate


title: SK-N-AS DAC treated

city: Ghent

first: Maté

last: Ongenaert

address: De Pintelaan 185 - MRB

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

hyb_protocol: Hybridisation was performed according to the manufacturer's protocol

scan_protocol: Scanning was performed according to the manufacturer's protocol

data_processing: Data was processed in R/Bioconductor by affy, simpleaffy packages. Quality was controlled (5'-3' degradation plots; boxplots; image scan inspection). Data was normalized using just.gcrma (GC-RMA) and P/M/A calls were determined by using MAS 5.0

source_name: SK-N-AS neuroblastoma cell line

label_protocol: Biotin labelling was performed according to manufacturer's protocol

extract_protocol: RNA was extracted using Qiagen RNEasy kit

treatment_protocol: Treatment with DAC (2'-deoxy-5'-cytydine): 3 micromolars for 3 days

value: DACtreated

tag: mycn

value: not amplified


title: SJNB-1 untreated

source_name: SJNB-1 neuroblastoma cell line

value: untreated


title: S. aureus_walRc_rep3

description: S. aureus walRc strain, third biological replicate


title: SK-N-AS untreated


title: LAN-2 untreated

source_name: LAN-2 neuroblastoma cell line

value: amplified


title: N206 DAC treated

source_name: N206 neuroblastoma cell line


title: IRF4-control_Th17_cells_42hr_rep3

city: South San Francisco

first: Smita

last: Agrawal

state: CA

address: 1 DNA Way

department: Immunology

institute: Genentech Inc.

description: IRF4+-/- rep3

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing:
The matrix data table was created by first log transforming the raw data and then filtering out all probes that showed a standard deviation of <0.25  across all samples as well as probes that do not have an associated entrez id. Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.
The normalized data was then analyzed further using Partek Genomic Suite Version 6.6 by performing a 1-way ANOVA test between the IRF4 KO vs IRF4 Het samples. Data for the probes which showed a > 2-fold change (up or down) with a p-value <0.05 is presented in the 'Analyzed_data.txt' file (available on Series records). It is presented in ascending order of differential expression (Fold-Change) between the IRF4 KO vs IRF4 Het samples. The probeset ID, Gene Symbol, p-value of differential expression and Fold-Change between the IRF4 KO and IRF4 Het samples are indicated. Negative fold changes indicate down-regulation in IRF4 KO samples and positive fold changes indicate up-regulation.

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: Naïve T- cells isolated from spleen were cultured on a-CD3 coated plates with 2.5 mg/ml a-CD28, 20 ng/ml IL-6, 20 ng/ml IL-23, 1 ng/ml hTGFb, 10 mg/ml a-IL4 and 10 mg/ml a-IFNg for 42 hrs

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol and including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.

tag: strain background

tag: genotype/variation

value: spleen

value: Naïve CD4+, CD62L hi, CD25 - T cells

tag: differentiation condition

tag: timepoint

value: 42 hrs

source_name: Stratagene's Universal Mouse Reference RNA (UMRR) cat # 740100

tag: sample type

value: Reference:pooled RNA from 11 tissues


title: CHP-902R DAC treated

source_name: CHP-902R neuroblastoma cell line

tag: treatment


title: S. aureus_wild type_rep2

description: S. aureus wild type, second biological replicate

extract_protocol: Cells were 2-fold diluted in ice-cold killing buffer (20 mM Tris-HCl pH 7.5 ,5 mM MgCl2, 20 mM NaN3), centrifuged and immediately frozen at -80 °C. Total RNA was isolated by mechanical disruption and Trizol extraction as previously described (Even et al., 2006, J. Bacteriol. 188, 2184–2197) followed by DNase I treatment in order to eliminate residual genomic DNA and column purification using the RNA Clean-Up kit (Norgen Biotech Corp.). RNA quality was checked by electropherogram analysis (Agilent Bioanalyzer).


title: SJNB-1 DAC treated


title: N206 untreated


title: SH-SY5Y DAC treated

source_name: SH-SY5Y neuroblastoma cell line


title: S. aureus_wild type_rep1

description: S. aureus wild type, first biological replicate


title: CHP-902R untreated


title: SH-SY5Y untreated


title: LAN-2 DAC treated


title: ground-control

city: Toyonaka

first: Yoshinobu

last: Ohira

state: Osaka

address: 1-17 Machikaneyama-cho

department: Applied Physiology

country: Japan

institute: Osaka University

description: 70 Negative control probes (derived from bacteria, plants, and bacteriophages) were spotted, and 326 factory QC probes were also spotted on the microarray. In addition, there were 148 empty (blank) spots available for background signal measurement.  Therefore, signal data from total of 544 control spots were included in 12,544-spot data on the custom-designed Mus musculus 12K oligo DNA microarray.

hyb_protocol: 5μg of the purified Cy5-aRNA sample was dissolved in 100μl of hybridization solution (CombiMatrix CustomArray 12K Hybridization and Imaging Protocol: PTL006), and hybridization reaction was carried out at 45ºC for 16hours.

scan_protocol: The microarrays went through post-hybridization washes according to CombiMatrix CustomArray 12K Hybridization and Imaging Protocol (PTL006), and they were scaned by Axon Instruments' GenePix 4000B scanner (5μm resolution, PMT gain at 500, Laser power at 100%).

data_processing: The raw data (Mm_B-GC_RawData_for_GEO.txt, Mm_B-LC_RawData_for_GEO.txt, and Mm_B-SF_RawData_for_GEO.txt) were obtained from the scanned images using MicroarrayImager ver.6.0.1 (CombiMatrix Corp.), and were background-subtracted and median-normalized by Microsoft Office Excel 2003 within each of the microarray.  We employed simple fold-difference calculation using Microsoft Office Excel 2003 for each of the spot intensities between GC:LC, GC:SF, and LC:SF.  Since sample number (n) was 1 for all of the condition groups, there was no application of statistical analysis for this data processing.

source_name: whole brain

label_protocol: 1μg of total RNA was reverse-transcribed using T7-oligo-dT primer and produced cDNA was double-stranded by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, cat#AM1753).  From ds-cDNA, aRNA was amplified and labeled with amino allyl UTP, and then Cy5-coupling to amino allyl modified aRNA was carried out according to the instruction of the Amino Allyl MessageAmp II aRNA Amplification Kit.

growth_protocol: Male wild type C57BL/10J mice (8 weeks old at the beginning of experiment) were utilized (n=3).  They were individually housed in mouse drawer system (MDS, 11.6 x 9.8 x 8.4 cm), which is a payload developed by Alenia-Space.  Food and water were supplied ad libitum.  These mice were launched by Space Shuttle Discovery (space transport system, STS-128) at August 28, 2009.  They were housed in Japanese Experimental Module (Kibou) on the ISS until they returned to the Earth by Space Shuttle Atlantis (STS-129) on November 27, 2009.  Only one mouse returned to the Earth alive.  Whole brain was sampled from the mouse killed by inhalation of carbon dioxide at the Life Sciences Support Facility of Kennedy Space Center within 3-4 hours after landing.  After the spaceflight experiment, the on-ground experiment was also carried out at the Advanced Biotechnology Center in Genova, Italy.  A mouse with the same species, sex, and age was housed in MDS for 3 months as the ground control (GC).  Another mouse was housed in normal vivarium cage as the laboratory control (LC).  Amount of food and water supplementation and environmental conditions were simulated as the flight group.  After 3 months, brain was sampled from one mouse in group GC and LC, respectively.

extract_protocol: Approximately 100mg of brain tissue from each of the snap-frozen mouse whole brain samples were collected, and total RNA was extracted by RNeasy Mini Kit according to the manufacturer's protocol provided in the kit (QIAGEN, cat#74903).

treatment_protocol: Since all of the space flown mice were housed in MDS, effects of housing MDS with small size (11.6 x 9.8 x 8.4 cm) were also examined by comparing the characteristics of brain with those of mice housed in normal vivarium cage in the on-ground control experiment.

tag: location

value: ground

tag: cage

value: MDS


title: laboratory-control

value: Normal


title: IMR-32 DAC treated

source_name: IMR-32 neuroblastoma cell line


title: space-flight

value: space


title: CLB-GA DAC treated

source_name: CLB-GA neuroblastoma cell line


title: IMR-32 untreated


title: CLB-GA untreated


title: Series B T6-T7

status: Public on Sep 12 2012

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: Series A - T6-T7

hyb_protocol: Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.

scan_protocol: Slides were scanned using the Genepix 4200AL DNA micro array slide scanner.  Quantification of the signal of the spots on slides was done with ArrayPro 4.5.

data_processing: Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (ref. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244.).

organism: Lactococcus cremoris subsp. cremoris MG1363

source_name: Net intensity (mean) {A}, T6 is A, T6 is 349 minutes

label_protocol: Synthesis of cDNA and indirect Cy-3/Cy-5-dUTPs labeling of 15–20 µg of total RNA was performed with the CyScribe Post labeling kit (Amersham Biosciences) according to the supplier's instructions.

growth_protocol: L. lactis strains were incubated in reconstituted skim milk at 30 ºC without shaking

extract_protocol: RNA was isolated from 50 ml of cells grown to midexponential phase of growth (A600 = 0.4). Cells were harvested by centrifugation for 1 min at 10,000 rpm at room temperature. Cell pellets were immediately frozen in liquid nitrogen and stored at –80 °C. Pellets were resuspended in 500 µl of 10 mM Tris-HCl, 1 mM EDTA (T10E1), pH 8.0, after which 50 µl of 10% SDS, 500 µl of phenol/chloroform, 500 mg of glass beads (75–150 µm), and 175 µl of Macaloid suspension (Bentone) were added. Further purification was done using the High Pure RNA isolation (Roche), using the suppliers protocol.

value: incubated in reconstituted skim milk at 30C

tag: time

value: 349 minutes

source_name: Net intensity (mean) {B}, T6 is B, T7 is 400 minutes

value: 400 minutes


title: Series B T5-T6

description: Series A - T5-T6

source_name: Net intensity (mean) {A}, T5 is A, T5 is 300 minutes

value: 300 minutes

source_name: Net intensity (mean) {B}, T5 is B, T6 is 349 minutes


title: Loop back sample T1-T4

description: Loop back sample T1-T4

source_name: Net intensity (mean) {A}, T1 is A, T1 is 103 minutes

value: 103 minutes

source_name: Net intensity (mean) {B}, T4 is B, T4 is 250 minutes

value: 250 minutes


title: Loop back sample T1-T7

description: Loop back sample T1-T7

source_name: Net intensity (mean) {B}, T7 is B, T7 is 400 minutes


title: Series B T7-T8

description: Series A - T7-T8

source_name: Net intensity (mean) {A}, T7 is A, T7 is 400 minutes

source_name: Net intensity (mean) {B}, T7 is B, T8 is 500 minutes

value: 500 minutes


title: Loop back sample T8-T12

description: Loop back sample T8-T12

source_name: Net intensity (mean) {A}, T8 is A, T8 is 500 minutes

source_name: Net intensity (mean) {B}, T12 is B, T12 is 1110 minutes

value: 1110 minutes


title: Series B T9-T10

description: Series A - T9-T10

source_name: Net intensity (mean) {A}, T9 is A, T9 is 600 minutes

value: 600 minutes

source_name: Net intensity (mean) {B}, T9 is B, T10 is 800 minutes

value: 800 minutes


title: Series B T8-T9

description: Series A - T8-T9

source_name: Net intensity (mean) {B}, T8 is B, T9 is 600 minutes


title: Series A T11-T12

description: Series A - T11-T12

source_name: Net intensity (mean) {A}, T11 is A, T11 is 999 minutes

value: 999 minutes


title: Series B T1-T2

description: Series B - T1-T2

source_name: Net intensity (mean) {B}, T1 is B, T2 is 154 minutes

value: 154 minutes


title: Series B T11-T12

description: Series A - T11-T12

source_name: Net intensity (mean) {B}, T11 is B, T12 is 1110 minutes


title: Series B T10-T11

description: Series A - T10-T11

source_name: Net intensity (mean) {A}, T10 is A, T10 is 800 minutes

source_name: Net intensity (mean) {B}, T10 is B, T11 is 999 minutes


title: Series A T10-T11

description: Series A - T10-T11

source_name: Net intensity (mean) {B}, T11 is B, T11 is 999 minutes


title: Series B T4-T5

description: Series A - T4-T5

source_name: Net intensity (mean) {A}, T4 is A, T4 is 250 minutes

source_name: Net intensity (mean) {B}, T4 is B, T5 is 300 minutes


title: Series B T3-T4

description: Series A - T3-T4

source_name: Net intensity (mean) {A}, T3 is A, T3 is 200 minutes

value: 200 minutes

source_name: Net intensity (mean) {B}, T3 is B, T4 is 250 minutes


title: Series B T2-T3

description: Series B - T2-T3

source_name: Net intensity (mean) {A}, T2 is A, T2 is 154 minutes

source_name: Net intensity (mean) {B}, T2 is B, T3 is 200 minutes


title: Series A T9-T10

description: Series A - T9-T10

source_name: Net intensity (mean) {B}, T10 is B, T10 is 800 minutes


title: Series A T7-T8

description: Series A - T7-T8

source_name: Net intensity (mean) {A}, T7 is A, T7 is 400 minutes

source_name: Net intensity (mean) {B}, T8 is B, T8 is 500 minutes


title: Series A T6-T7

description: Series A - T6-T7

source_name: Net intensity (mean) {A}, T6 is A, T6 is 349 minutes

source_name: Net intensity (mean) {B}, T7 is B, T7 is 400 minutes


title: Series A T5-T6

description: Series A - T5-T6

source_name: Net intensity (mean) {A}, T5 is A, T5 is 300 minutes

source_name: Net intensity (mean) {B}, T6 is B, T6 is 349 minutes


title: Series A T8-T9

description: Series A - T8-T9

source_name: Net intensity (mean) {A}, T8 is A, T8 is 500 minutes

source_name: Net intensity (mean) {B}, T9 is B, T9 is 600 minutes


title: Series A T4-T5

description: Series A - T4-T5

source_name: Net intensity (mean) {B}, T5 is B, T5 is 300 minutes


title: Series A T3-T4

description: Series A - T3-T4

source_name: Net intensity (mean) {B}, T4 is B, T4 is 250 minutes


title: Series A T1-T2

description: Series A - T1-T2

source_name: Net intensity (mean) {A}, T1 is A, T1 is 103 minutes

source_name: Net intensity (mean) {B}, T2 is B, T2 is 154 minutes


title: Series A T2-T3

description: Series A - T2-T3

source_name: Net intensity (mean) {B}, T3 is B, T3 is 200 minutes


title: normal_PBMCS_8

type: genomic

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, biotinylated PCR fragments were hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix MAS5 summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100. Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.

molecule: genomic DNA

source_name: normal control

label_protocol: PCR products were labeled with a single biotin according to the Affymetrix protocol.

extract_protocol: For total RNA, frozen tissue sections were homogenized in Trizol and RNA was extracted according to standard protocols. For high molecular weight genomic DNA,  frozen tissue sections were homogenized in 1 ml of G2-buffer supplemented with 2 ml RNase (Qiagen). Subsequently, DNA was extracted  using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.

treatment_protocol: 10-20 x 20mm sections from frozen tumor specimens from newly diagnosed previously untreated diffuse large B-cell lymphomas and peripheral blood lymphocytes from normal donors were directly transferred to extraction buffers.

tag: type

value: normal control


title: c_P_44


title: c_P_51


title: c_P_50


title: normal_PBMCS_18


title: normal_PBMCS_7


title: normal_PBMCS_20


title: normal_PBMCS_6


title: normal_PBMCS_4


title: normal_PBMCS_3


title: normal_PBMCS_1


title: c_P_46


title: c_P_45


title: c_P_47


title: normal_PBMCS_9


title: normal_PBMCS_17


title: normal_PBMCS_12


title: normal_PBMCS_11


title: normal_PBMCS_10


title: c_P_4


title: normal_PBMCS_16


title: normal_PBMCS_2


title: c_P_7


title: c_P_6


title: c_P_5


title: normal_PBMCS_13


title: normal_PBMCS_19


title: normal_PBMCS_21


title: c_P_48


title: normal_PBMCS_5


title: LOGIA_Hapmap_11


title: c_P_3


title: LOGIA_Hapmap_8


title: c_P_1


title: LOGIA_Hapmap_10


title: LOGIA_Hapmap_16


title: c_P_2


title: LOGIA_Hapmap_14


title: LOGIA_Hapmap_3


title: LOGIA_Hapmap_6


title: HAMES_Hapmap_20


title: LOGIA_Hapmap_1


title: LOGIA_Hapmap_15


title: HAMES_Hapmap_3


title: HAMES_Hapmap_8


title: HAMES_Hapmap_13


title: LOGIA_Hapmap_7


title: LOGIA_Hapmap_2


title: HAMES_Hapmap_1


title: HAMES_Hapmap_17


title: LOGIA_Hapmap_13


title: HAMES_Hapmap_7


title: LOGIA_Hapmap_9


title: HAMES_Hapmap_9


title: LOGIA_Hapmap_4


title: HAMES_Hapmap_2


title: HAMES_Hapmap_6


title: HAMES_Hapmap_5


title: HAMES_Hapmap_18


title: Shef1, FGF3+10

city: Sheffield

first: Marcelo

middle: Nicolas

last: Rivolta

state: Yorkshire

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

hyb_protocol: 12.5µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

data_processing: Normalization and initial analysis were done using puma (www.bioconductor.org) that estimates gene expression levels using probabilistic models

source_name: hESCs differentiating in the presence of FGF3 and 10

label_protocol: 200ng of total RNA was amplified using the 3' IVT method  and biotinylation of antisense RNA carried out according to Affymetrix protocol

growth_protocol: hESC lines H14, Shef1 and Shef3 were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in medium comprised of knockout Dulbecco’s modified Eagle’s medium supplemented with 20% knockout serum replacement (KOSR), 1% nonessential amino acids, 2mM L-glutamine, (all from Invitrogen), 0.1mM ß-mercaptoethanol (Sigma), and 4ng/ml of basic fibroblast growth factor (bFGF; R&D systems).

extract_protocol: Total RNA was extracted using the RNAeasy Kit (Qiagen) following the manufacturer's instructions

treatment_protocol: Undifferentiated hESCs were dissociated with Trypsin -EDTA (Sigma) and the cell suspension passed through a 100-micrometer cell strainer (BD Labware). Cells were plated onto laminin-coated plastic and incubated with DFNB medium (DMEM/high glucose: F12 mixed as 1:1, with N2 and B27) supplemented with FGF3 (50ng/ml) and FGF10 (50ng/ml) or with DFNB alone, without FGFs. Cells were allowed to differentiate for 14 days.

value: Day 14

tag: cell line


title: Shef3, FGF3+10


title: H14, DFNB

source_name: hESCs differentiating with basal DFNB medium

value: DFNB


title: H14, FGF3+10


title: Shef1, DFNB


title: H14, hESC

source_name: Undifferentiated hESCs

value: Day 0


title: Shef3, DFNB


title: Shef1, hESC


title: Shef3, hESC


title: c_D_1048

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

source_name: fresh frozen tumor sample

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

value: primary DLBCL


title: c_D_1158


title: HAMES_Hapmap_11


title: c_D_1052


title: HAMES_Hapmap_10


title: HAMES_Hapmap_16


title: c_D_1103


title: c_D_1054


title: LOGIA_Hapmap_5


title: IM010_WT C57BL6J_VN203_2d_2

source_name: lung, wild-type, infected with A/VN/1203/04 virus, day 2

treatment_protocol:
Six-week-old mice were infected by intranasal instillation of 10^3 PFU of A/Vietnam/1203/04 H5N1 influenza virus in 50 µl of PBS or mock-infected with PBS alone. At days 2 and 6 days post-infection, lungs were harvested.
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing.

tag: strain/background

value: wild-type

value: female

tag: age

value: 6 weeks

tag: tissue

value: lung

value: infected with 10^3 PFU of A/Vietnam/1203/04 virus

tag: time of sample collection

value: day 2 post-infection


title: HAMES_Hapmap_14


title: ALLEE_Hapmap_10


title: c_D_1004


title: c_D_1049


title: IM010_WT C57BL6J_VN203_2d_3

tag: genotype

tag: gender


title: c_D_1151


title: c_D_1130


title: ALLEE_Hapmap_1


title: ALLEE_Hapmap_16


title: c_D_1108


title: c_D_1129


title: ALLEE_Hapmap_7


title: HAMES_Hapmap_19


title: HAMES_Hapmap_4


title: c_D_1109


title: memory Treg

city: Dresden

first: Anke

last: Theil

address: Fetscherstr. 105

institute: CRTD

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization the following four housekeeping genes were selected: B2M, HPRT1 , RPL13A, GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBER Green

source_name: MACS enriched and FACS sorted CD4+CD25+CD127lowCD45RA- Treg from human PBMC

label_protocol: PCR arrays were performed using the T cell anergy and immune tolerance RT2 profiler PCR array from SABiosciences/Qiagen (PAHS-074)

extract_protocol: RNA from cell lysates was extracted using the RNeasy mini kit (Qiagen) with on-column DNase treatment. cDNA synthesis was performed following manufacturer’s instructions (SABiosciences, RT2 first strand Kit)

tag: cell type

value: memory Treg

tag: activation

value: anti-CD3/anti-CD28 beads


title: HAMES_Hapmap_21


title: c_D_1135


title: naive Treg + IL-7

source_name: MACS enriched and FACS sorted CD4+CD25+CD127lowCD45RA+ Treg from human PBMC

value: naive Treg

value: anti-CD3/anti-CD28 beads + 10 ng/ml IL-7


title: ALLEE_Hapmap_15


title: IM010_WT C57BL6J_Mock_2d_2

source_name: lung, wild-type, mock infected, day 2

value: mock infected


title: IM010_WT C57BL6J_VN203_2d_1


title: ALLEE_Hapmap_8


title: IM010_WT C57BL6J_Mock_2d_3


title: c_D_1046


title: IM010_WT C57BL6J_Mock_2d_1


title: naive Treg


title: ALLEE_Hapmap_3


title: IM010_TNFRSF1B KO_VN203_6d_2

source_name: lung, TNFRSF1B KO, infected with A/VN/1203/04 virus, day 6

value: TNFRSF1B KO

value: day 6 post-infection


title: c_D_1124


title: ALLEE_Hapmap_13

value: normal control


title: c_D_1127


title: memory Treg + IL-7


title: ALLEE_Hapmap_11


title: ALLEE_Hapmap_14


title: c_D_1106


title: ALLEE_Hapmap_2


title: IM010_TNFRSF1B KO_VN203_6d_1


title: c_D_1043


title: c_D_1118


title: c_D_1153


title: IM010_TNFRSF1B KO_VN203_2d_3

source_name: lung, TNFRSF1B KO, infected with A/VN/1203/04 virus, day 2


title: RPE1_H2B GFP_Chr21_R2

city: Martinsried

first: Gabriele

last: Stoehr

address: Am Klopferspitz 18

department: Proteomics ans Signaltransduction

institute: MPI of Biochemistry

description: Gene expression of RPE-1 cell lines incl. 3x Chr21

hyb_protocol: Following cRNA clean-up and quantification (NanoDrop ND-1000 Spectrophotometer, peqlab) 1.65 µg (HCT116) or 0.60 µg (RPE-1) of each Cyanin-3-labeled cRNA sample was fragmented and prepared for One-Color based hybridization (Gene Expression Hybridization Kit, Agilent). Each cRNA sample was hybridized at 65 °C for 17 hrs on separate Whole Human Genome Oligo Microarrays (4x44K format) (for HCT116) or SurePrint G3 Human Gene Expression Arrays (8x60K).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.1.3. Software (Agilent Technologies) (HCT116) or Scan Control A.8.4.1 Software (Agilent Technologie) (RPE-1) on the Agilent DNA Microarray Scanner.

data_processing: Signal intensities were extracted from the image using Feature Extraction 10.5.1 Software (Agilent Technologies) and the design file 014850_D_F_20090416.xml (HCT116) or 10.7.3.1 Software  and the design file 028004_D_F_20120130.xml (RPE-1). Data was background subtracted; log2 ratios calculated and normalized. Medians of replicates were calculated and a ratio of the aneuploid cell line (median) vs the corresponding WT cell line (median) was used for further analysis (indicated in the column header).

source_name: RPE-1 cell line, triploid for Chr21, replicate 2

label_protocol: 500 ng (HCT116) or 100 ng (RPE-1) total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (HCT116: Quick-Amp Labeling Kit One-Color, Agilent Technologies; RPE-1: Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP according to the manufacturer´s instructions.

growth_protocol: Both HCT116 and RPE-1 cell lines were cultured in DMEM (supplemented with 10% FBS) at 5% CO2, 37°C

extract_protocol: mRNA was purified using the Qiagen mRNeasy mini kit.

treatment_protocol: no treatment

tag: multisomy/variation

value: 3x Chr21 H2B GFP


title: HAMES_Hapmap_15


title: c_D_1134


title: ALLEE_Hapmap_4


title: c_D_1050


title: c_D_1025


title: RPE1_H2B GFP_Chr21_R1

source_name: RPE-1 cell line, triploid for Chr21, replicate 1


title: RPE1_H2B GFP_Chr21_R3

source_name: RPE-1 cell line, triploid for Chr21, replicate 3


title: ALLEE_Hapmap_6


title: c_D_1047


title: c_D_1042


title: c_D_1029


title: IM010_TNFRSF1B KO_VN203_2d_2

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.
platform: x86_64-redhat-linux-gnu
arch: x86_64
os: linux-gnu
system: x86_64, linux-gnu
R version 2.12.2 (2011-02-25)
bioconductor packages: limma
Information on package: 'limma'
limma version: 3.6.9
limma date: 2010/12/01version
For the generation of the normalized data, the limma package was used. Background correction was performed (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation.


title: RPE1_hTERT_Chr5Chr12_R3

description: Gene expression of RPE-1 cell lines incl. 3x Chr5 and 3x Chr12

source_name: RPE-1 cell line, triploid for Chr5 and Chr12, replicate 3

value: 3x Chr5 3x Chr12


title: IM010_TNFRSF1B KO_VN203_2d_1


title: ALLEE_Hapmap_5


title: IM010_TNFRSF1B KO_Mock_6d_3

source_name: lung, TNFRSF1B KO, mock infected, day 6


title: c_D_1053

value: primary DLBCL


title: c_D_1027


title: RPE1_hTERT_Chr5Chr12_R2

source_name: RPE-1 cell line, triploid for Chr5 and Chr12, replicate 2


title: c_D_1020


title: RPE1_H2B GFP WT_R3

description: Gene expression of RPE-1 cell lines

source_name: RPE-1 cell line including H2B GFP, diploid cell line, replicate 3

value: WT H2B GFP


title: c_D_1036


title: c_D_1005


title: c_D_1010


title: c_D_1112


title: IM010_TNFRSF1B KO_Mock_2d_3

source_name: lung, TNFRSF1B KO, mock infected, day 2

value: female


title: c_D_1019


title: IM010_TNFRSF1B KO_Mock_6d_1

value: 6 weeks


title: IM010_TNFRSF1B KO_Mock_2d_2

value: lung


title: RPE1_hTERT_Chr5Chr12_R1

source_name: RPE-1 cell line, triploid for Chr5 and Chr12, replicate 1


title: RPE1_H2B GFP WT_R1

description: Gene expression of RPE-1 cell lines

source_name: RPE-1 cell line including H2B GFP, diploid cell line, replicate 1


title: RPE1_H2B GFP WT_R2

description: Gene expression of RPE-1 cell lines

source_name: RPE-1 cell line including H2B GFP, diploid cell line, replicate 2


title: IM010_TNFRSF1B KO_Mock_2d_1


title: c_D_1012

source_name: fresh frozen tumor sample


title: ALLEE_Hapmap_9

source_name: normal control


title: RPE1_hTERT_WT_R2

description: Gene expression of RPE-1 cell lines

source_name: RPE-1 cell line, diploid cell line, replicate 2

value: WT


title: c_D_1008


title: c_D_1002


title: c_D_1023


title: c_D_1031


title: c_D_1034


title: IM010_ID01 KO_VN203_6d_2

source_name: lung, IDO1 KO, infected with A/VN/1203/04 virus, day 6

value: IDO1 KO

value: infected with 10^3 PFU of A/Vietnam/1203/04 virus


title: IM010_ID01 KO_VN203_2d_3

source_name: lung, IDO1 KO, infected with A/VN/1203/04 virus, day 2

value: day 2 post-infection


title: c_D_1028


title: RPE1_hTERT_WT_R1

description: Gene expression of RPE-1 cell lines

source_name: RPE-1 cell line, diploid cell line, replicate 1


title: IM010_ID01 KO_VN203_6d_1


title: c_D_1003


title: old_c506


title: old_c514


title: c_D_1039


title: old_c504


title: c_D_1016


title: old_c503


title: IM010_ID01 KO_VN203_2d_2


title: c_D_1035


title: c_D_1006


title: IM010_ID01 KO_Mock_6d_3

source_name: lung, IDO1 KO, mock infected, day 6


title: c_D_1037


title: c_D_1022


title: c_D_1001


title: c_D_1032


title: IM010_ID01 KO_VN203_2d_1


title: IM010_ID01 KO_Mock_6d_1


title: old_c502


title: IM010_ID01 KO_Mock_6d_2


title: c_D_1024


title: c_D_1166


title: IM010_ID01 KO_Mock_2d_2

source_name: lung, IDO1 KO, mock infected, day 2


title: old_c501


title: old_c498


title: RPE1_hTERT_WT_R3

description: Gene expression of RPE-1 cell lines

source_name: RPE-1 cell line, diploid cell line, replicate 3


title: c_D_1164


title: old_c496


title: IM010_ID01 KO_Mock_2d_3


title: old_c495


title: old_c497


title: Chicken_54_LB [Chicken_58]

city: Hannover

first: Ottmar

last: Distl

address: Buenteweg 17p

department: Institute for Animal Breeding and Genetics

institute: University of Veterinary Medicine Hannover

description: Gene expression data from two different strains of laying hens from a small group housing system

hyb_protocol: A total of 10 μg of the labelled cRNAs were fragmented and hybridized for 16 hours at +45 °C on Affymetrix GeneChip® Chicken Genome Arrays. Microarrays were washed and stained with Streptavidin Phycoerythrin using the Fluidics Station FS 400 (Affymetrix).

scan_protocol: Microarrays were scanned using the Affymetrix GCS3000 Scanner.

data_processing: Image analysis was processed with GCOS1.2 Software Suite (Affymetrix). Normalization of the raw microarray data was performed with the Robust Multi array Average method (RMA) and GeneSpring GX 11.5 Software was used for statistical analysis.

organism: Gallus gallus

source_name: posterior right site of the cerebrum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (3’ IVT Express Kit User Manual, 2008-2009, Affymetrix).

extract_protocol: Samples were extracted without meninges and separately stored in reaction tubes filled with 1.5 ml RNAlater™. Isolation of total RNA was made using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.

value: brain

tag: tissue region

value: posterior right site of the cerebrum

tag: layer line

value: Lohmann Brown

value: 65-67 weeks


title: ileum.BDL_GW4064_rep-2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: bile duct ligation mice pre-treated with GW4064

hyb_protocol: Fragmented  biotinylated cRNA (15 μg) was hybridized at 45°C for 16 hours to Affymetrix® high density oligonucleotide array mouse genome 430A 2.0 chips. The arrays were washed and stained with streptavidin-phycoerythrin (10 μg/ml). Signal amplification was performed using a biotinylated anti-streptavidin antibody.

scan_protocol: The array was scanned according to the manufacturer's instructions (Affymetrix Genechip Technical Manual,  2004).

data_processing: Scanned images were inspected for obvious defects (artifacts or scratches) on the  array to exclude defective chips. To minimize discrepancies due to variables, the raw expression data was scaled using Affymetrix Microarray Suite 5.0 software and pair-wise comparisons were performed.  The trimmed mean signal of all probe sets on the MG430A chip was adjusted to a user-specified target signal value (200) for each array for global scaling.  No specific exclusion criteria were applied.

source_name: ileum

label_protocol: In brief, 5 μg of total RNA from each sample and T7-linked oligo-dT primers were used for first-strand cDNA synthesis.  IVT reactions were performed in batches to generate biotinylated cRNA targets, which were chemically fragmented at 94°C for 35 minutes.

growth_protocol: Mice were maintained on a mixed-strain background  (C57BL/6:129Sv) and housed in a temperature-controlled environment with 12 hr light/dark cycles.  Mice were fed ad-libitum standard rodent chow.

extract_protocol: Total RNA was extracted from tissues using RNA  STAT-60 (Tel-Test, Inc., Friendswood, TX)

treatment_protocol: All experiments were performed on age-matched, male  mice. For bile duct ligation experiments, 8-10 month old wild type mice were treated daily with GW4064 (100 mg/kg/day, in 1% Tween80, 1%  methylcellulose) or vehicle by gavage for 2 days prior to surgery and for 5 days after.  Animals treated with GW4064 or vehicle for 2 days were randomly assigned to one of two groups: bile duct ligation or sham operated.  The abdomen was shaved and the skin  was sprayed with 70% ethanol and wiped.  Surgery was performed under aseptic conditions and general anesthesia through an upper midline abdominal incision.  The common bile duct was mobilized and ligated using 4/0 silk for the bile duct ligated group.  Sham operated mice had the same incision followed by mobilization of the common bile duct without ligation.

value: male

tag: strain

value: 8-10 months

tag: protocol

value: bile duct ligation

tag: treatment


title: c_D_1163

tag: sample type


title: Chicken_36_LB [Chicken_59]


title: c_D_1017


title: IM010_ID01 KO_Mock_2d_1

city: Seattle

last: Katze

address: Rosen Building 960 Republican St.

institute: University of Washington

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

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

extract_protocol: Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation. All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

value: mock infected


title: ileum.BDL_Vehicle_rep-2

description: bile duct ligation mice treated with vehicle

value: vehicle


title: old_c494

value: primary DLBCL


title: c_D_1156


title: c_D_1155


title: Chicken_54_LB [Chicken_57]


title: IM010_TNFRSF1B KO_Mock_6d_2

source_name: lung, TNFRSF1B KO, mock infected, day 6

value: TNFRSF1B KO

value: female

value: day 6 post-infection


title: Chicken_54_LSL [Chicken_60]

value: Lohmann Selected Leghorn


title: old_c491


title: ileum.BDL_GW4064_rep-1


title: c_D_1162


title: c_D_1159


title: Chicken_36_LB [Chicken_54]


title: old_c490


title: old_c486


title: old_c492


title: Chicken_54_LSL [Chicken_56]


title: Chicken_36_LSL [Chicken_55]


title: Chicken_54_LB [Chicken_53]


title: ileum.BDL_Vehicle_rep-1


title: Chicken_54_LSL [Chicken_52]


title: c_D_1132


title: c_D_1154


title: c_D_1149


title: old_c484


title: ileum.Sham_Vehicle_rep-1

description: sham operated mice treated with vehicle

value: sham operation


title: c_D_1146


title: c_D_1150


title: ileum.Sham_Vehicle_rep-2

description: sham operated mice treated with vehicle


title: old_c482


title: Chicken_54_LB [Chicken_50]


title: old_c479


title: SHP-/-_rep1

description: SAMPLE 7

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: Data were normalized and modeled in R 2.15.0 using Affy 1.8.0

label_protocol: Standard Affymetrix labeling protocol.

growth_protocol: Mice were fed a standard rodent chow (Test Diet No. 5001) and water ad libitum in temperature-controlled (23°C) and virus-free facilities.

extract_protocol: Total RNA was isolated using Tri-reagent (Invitrogen).

tag: strain background

tag: genotype/variation

value: SHP knockout; SHP-/-

value: liver


title: wild-type_rep2

description: SAMPLE 6

value: wild-type


title: SHP-/-_rep2

description: SAMPLE 8


title: Chicken_54_LSL [Chicken_51]

source_name: posterior left site of the cerebrum

value: brain

value: posterior left site of the cerebrum


title: c_D_1147


title: Chicken_36_LB [Chicken_48]

value: posterior right site of the cerebrum

value: Lohmann Brown

value: 65-67 weeks


title: old_c481


title: old_c476


title: OB-/-/SHP-/-_rep1

description: SAMPLE 3

value: leptin/SHP double knockout; OB-/-/SHP-/-


title: Chicken_54_LB [Chicken_46]


title: wild-type_rep1

description: SAMPLE 5


title: old_c478


title: Chicken_54_LSL [Chicken_47]


title: c_D_1145


title: old_c477


title: Chicken_36_LSL [Chicken_49]


title: old_c474


title: OB-/-_rep2

description: SAMPLE 2

value: leptin knockout; OB-/-


title: old_c460


title: c_D_1142


title: old_c514


title: OB-/-/SHP-/-_rep2

description: SAMPLE 4


title: Chicken_54_LB [Chicken_44]


title: Chicken_54_LB [Chicken_45]


title: old_c506


title: c_D_1139


title: OB-/-_rep1

description: SAMPLE 1


title: c_D_1141


title: old_c475


title: c_D_1144


title: Chicken_54_LB [Chicken_42]


title: c_D_1138


title: old_c470


title: old_c471


title: c_D_1140


title: Chicken_54_LB [Chicken_43]


title: c_D_1136


title: old_c504


title: old_c472


title: c_D_1131


title: old_c468


title: old_c469


title: c_D_1133


title: c_D_1128


title: old_c467


title: c_D_1125


title: old_c498


title: old_c501


title: old_c502


title: old_c503


title: Chicken_36_LSL [Chicken_40]


title: Chicken_54_LSL [Chicken_38]


title: old_c497


title: old_c466


title: Chicken_36_LB [Chicken_36]


title: Chicken_36_LB [Chicken_39]


title: old_c465


title: old_c496


title: Chicken_36_LB [Chicken_35]


title: c_D_1123


title: Chicken_54_LB [Chicken_41]


title: Chicken_54_LSL [Chicken_37]


title: Chicken_36_LB [Chicken_34]


title: old_c464


title: old_c495


title: c_D_1121


title: c_D_1114


title: c_D_1119


title: c_D_1120


title: old_c494


title: old_c462


title: old_c473


title: Chicken_36_LSL [Chicken_32]


title: old_c492


title: old_c458


title: c_D_1111


title: old_c491


title: old_c486


title: Chicken_54_LB [Chicken_29]


title: old_c461


title: old_c453


title: Chicken_36_LSL [Chicken_33]


title: c_D_1113


title: c_D_1110


title: old_c484


title: Chicken_36_LSL [Chicken_31]


title: Chicken_54_LSL [Chicken_30]


title: old_c451


title: old_c450


title: old_c482


title: Chicken_36_LSL [Chicken_27]


title: c_D_1107


title: c_D_1105


title: old_c490


title: Chicken_36_LB [Chicken_26]


title: c_D_1104


title: old_c449


title: Chicken_36_LSL [Chicken_28]


title: old_c481


title: c_D_1026


title: old_c479


title: old_c478


title: old_c477


title: old_c448


title: c_D_1044


title: old_c445


title: c_D_1045


title: Chicken_54_LB [Chicken_25]


title: old_c443


title: Chicken_54_LSL [Chicken_24]


title: Chicken_54_LB [Chicken_23]


title: Chicken_36_LSL [Chicken_21]


title: old_c447


title: old_c438


title: old_c437


title: Chicken_36_LSL [Chicken_20]


title: old_c460


title: DNA_muscle_high-fat_22

city: Copenhagen N

first: Stine

last: Jacobsen

address: Tagensvej 20, sec. 7652

department: Diabetes and Metabolism

country: Denmark

institute: Rigshospitalet

description: SAMPLE 43

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

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

data_processing: BeadStudio software v3.2 as recommended by Illumina

label: Cy5 and Cy3

source_name: Vastus lateralis muscle

label_protocol: Standard Illumina Protocol

extract_protocol: Skeletal muscle biopsies were excised from Vastus lateralis and snap frozen in liquid nitrogen at -80°C. DNA was extracted using the Dneasy kit from Qiagen according to standard instructions.

treatment_protocol: A total of 24 individuals recieved both a short-term high-fat overfeeding and control diet in a randomized cross-over setting. The high-fat overfeeding diet contained 50% extra calories comparred to the control diet and had a macronutrient distribution of: 60% fat, 32.5% carbohydrate and 7.5% protein. The control diet consisted of 35% fat, 50% carbohydrate and 15% protein.

tag: diet

value: High-fat overfeeding

tag: from same subject

tag: order of treatment

value: Vastus lateralis muscle


title: Chicken_54_LSL [Chicken_22]

tag: tissue

tag: age


title: DNA_muscle_high-fat_24

description: SAMPLE 44


title: old_c475

value: primary DLBCL


title: old_c474


title: DNA_muscle_high-fat_23

description: SAMPLE 42


title: old_c436


title: DNA_muscle_high-fat_18

description: SAMPLE 39


title: old_c432


title: old_c476


title: DNA_muscle_high-fat_20

description: SAMPLE 41


title: Chicken_36_LSL [Chicken_19]


title: old_c469


title: DNA_muscle_high-fat_17

description: SAMPLE 38


title: Chicken_54_LB [Chicken_16]


title: DNA_muscle_high-fat_19

description: SAMPLE 40


title: Chicken_36_LB [Chicken_18]


title: old_c430


title: old_c433


title: DNA_muscle_high-fat_16

description: SAMPLE 37


title: old_c429


title: DNA_muscle_high-fat_15

description: SAMPLE 36


title: old_c472


title: old_c468


title: old_c428


title: Chicken_54_LSL [Chicken_15]


title: DNA_muscle_high-fat_14

description: SAMPLE 35


title: old_c426


title: Chicken_54_LSL [Chicken_17]


title: Chicken_36_LSL [Chicken_12]


title: Chicken_54_LSL [Chicken_14]


title: old_c425


title: old_c422


title: old_c408


title: old_c465


title: DNA_muscle_high-fat_10

description: SAMPLE 31


title: DNA_muscle_high-fat_11

description: SAMPLE 32


title: old_c462


title: old_c464


title: Chicken_36_LB [Chicken_11]


title: old_c466


title: old_c407


title: Chicken_54_LSL [Chicken_9]


title: Chicken_54_LB [Chicken_8]


title: old_c461


title: DNA_muscle_high-fat_12

description: SAMPLE 33


title: old_c467


title: old_c473


title: old_c404


title: DNA_muscle_high-fat_13

description: SAMPLE 34


title: DNA_muscle_high-fat_7

description: SAMPLE 29


title: Chicken_36_LB [Chicken_6]


title: Chicken_54_LB [Chicken_7]


title: old_c411


title: old_c453


title: old_c307


title: DNA_muscle_high-fat_6

description: SAMPLE 28


title: old_c451


title: old_c304


title: old_c300


title: old_c295


title: DNA_muscle_high-fat_4

description: SAMPLE 26


title: DNA_muscle_high-fat_5

description: SAMPLE 27


title: DNA_muscle_high-fat_3

description: SAMPLE 25


title: old_c449


title: DNA_muscle_high-fat_1

description: SAMPLE 23


title: old_c448


title: Chicken_36_LB [Chicken_3]


title: old_c287


title: Chicken_36_LB [Chicken_2]


title: Chicken_54_LB [Chicken_13]


title: old_c450


title: HCT116_Chr5_R3

description: Gene expression of HCT116 cell lines incl. 4x Chr5

source_name: HCT116 cell line, tetraploid for Chr5, replicate 3

tag: cell line

value: 4x Chr5


title: Chicken_54_LSL [Chicken_5]


title: old_c447


title: DNA_muscle_control_21

description: SAMPLE 21

value: Control


title: old_c445


title: old_c277


title: DNA_muscle_control_22

description: SAMPLE 22


title: Chicken_36_LSL [Chicken_1]

value: Lohmann Selected Leghorn


title: Chicken_36_LB [Chicken_4]


title: old_c274


title: old_c443


title: old_c268


title: DNA_muscle_control_20

description: SAMPLE 20


title: DNA_muscle_control_19

description: SAMPLE 19


title: HCT116_Chr5_R2

source_name: HCT116 cell line, tetraploid for Chr5, replicate 2


title: old_c471


title: old_c438


title: old_c470


title: HCT116_Chr5_R1

source_name: HCT116 cell line, tetraploid for Chr5, replicate 1


title: DNA_muscle_control_18

description: SAMPLE 18


title: old_c267

source_name: fresh frozen tumor sample


title: old_c261


title: HCT116_WT_R2

description: Gene expression of HCT116 cell lines

source_name: HCT116 cell line, diploid cell line, replicate 2

value: WT


title: old_c437


title: old_c254


title: HCT116_WT_R3

description: Gene expression of HCT116 cell lines

source_name: HCT116 cell line, diploid cell line, replicate 3


title: old_c436


title: old_c433


title: DNA_muscle_control_16

description: SAMPLE 16


title: old_c432


title: HCT116_WT_R1

description: Gene expression of HCT116 cell lines

source_name: HCT116 cell line, diploid cell line, replicate 1


title: DNA_muscle_control_17

description: SAMPLE 17


title: old_c251


title: DNA_muscle_control_15

description: SAMPLE 15


title: old_c250


title: FusX_rep3

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

institute: National Food Rsearch Institute

description:
pdr5_FusX_3
Gene expression data from PDR5 mutant yeast treated with fusarenone-X (FusX).

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Signals were calculated by MAS5.0 using Affymetrix GeneChip Operating Software Version 1.4.

source_name: PDR5 mutant strain, FusX

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets using the Affymetrix 3' IVT Express Kit.

growth_protocol: S. cerevisiae BY4743 (BY4743; MATa/α his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 lys2Δ0) derivative pdr5 (PDR5 (YOR153W) knock-out strain) was grown in YPD medium at 25C for 2 days.

extract_protocol: Each sample of total RNA was extracted using the FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: The yeast strain was grown in YPD medium with 25 ppm of each type B trichothecene mycotoxin for 2 hours.

tag: background/strain

value: PDR5 knockout mutant

value: fusarenone-X


title: FusX_rep2

description:
pdr5_FusX_2
Gene expression data from PDR5 mutant yeast treated with fusarenone-X (FusX).


title: old_c430


title: old_c429


title: NIV_rep3

description:
pdr5_NIV_3
Gene expression data from PDR5 mutant yeast treated with nivalenol (NIV).

source_name: PDR5 mutant strain, NIV

value: nivalenol


title: old_c458


title: old_c239


title: DNA_muscle_control_14

description: SAMPLE 14


title: DNA_muscle_high-fat_8

description: SAMPLE 30


title: old_c428


title: old_c242


title: old_c230


title: old_c426


title: FusX_rep1

description:
pdr5_FusX_1
Gene expression data from PDR5 mutant yeast treated with fusarenone-X (FusX).


title: DNA_muscle_control_13

description: SAMPLE 13


title: DNA_muscle_control_12

description: SAMPLE 12


title: DNA_muscle_control_11

description: SAMPLE 11


title: Chicken_36_LB [Chicken_10]

value: brain


title: NIV_rep2

description:
pdr5_NIV_2
Gene expression data from PDR5 mutant yeast treated with nivalenol (NIV).


title: NIV_rep1

description:
pdr5_NIV_1
Gene expression data from PDR5 mutant yeast treated with nivalenol (NIV).


title: old_c425


title: DNA_muscle_control_9

description: SAMPLE 9


title: old_c422


title: DNA_muscle_control_10

description: SAMPLE 10


title: 15ADON_rep1

description:
pdr5_15ADON_1
Gene expression data from PDR5 mutant yeast treated with 15-acetyldeoxynivalenol (15ADON).

source_name: PDR5 mutant strain, 15ADON


title: DNA_muscle_control_7

description: SAMPLE 7


title: 3ADON_rep3

description:
pdr5_3ADON_3
Gene expression data from PDR5 mutant yeast treated with 3-acetyldeoxynivalenol (3ADON).

source_name: PDR5 mutant strain, 3ADON


title: DNA_muscle_control_8

description: SAMPLE 8


title: old_c407


title: old_c411


title: 15ADON_rep2

description:
pdr5_15ADON_2
Gene expression data from PDR5 mutant yeast treated with 15-acetyldeoxynivalenol (15ADON).


title: old_c291


title: old_c404


title: DNA_muscle_control_6

description: SAMPLE 6


title: old_c408


title: 3ADON_rep2

description:
pdr5_3ADON_2
Gene expression data from PDR5 mutant yeast treated with 3-acetyldeoxynivalenol (3ADON).


title: DNA_muscle_control_3

description: SAMPLE 3


title: 15ADON_rep3

description:
pdr5_15ADON_3
Gene expression data from PDR5 mutant yeast treated with 15-acetyldeoxynivalenol (15ADON).


title: 3ADON_rep1

description:
pdr5_3ADON_1
Gene expression data from PDR5 mutant yeast treated with 3-acetyldeoxynivalenol (3ADON).


title: DON_rep3

description:
pdr5_DON_3
Gene expression data from PDR5 mutant yeast treated with deoxynivalenol (DON).

source_name: PDR5 mutant strain, DON

value: deoxynivalenol


title: old_c307


title: DNA_muscle_control_4

description: SAMPLE 4


title: DNA_muscle_control_2

description: SAMPLE 2


title: DON_rep1

description:
pdr5_DON_1
Gene expression data from PDR5 mutant yeast treated with deoxynivalenol (DON).


title: DNA_muscle_control_5

description: SAMPLE 5


title: old_c304


title: old_c300


title: old_c295


title: DNA_muscle_high-fat_2

description: SAMPLE 24


title: DNA_muscle_control_1

description: SAMPLE 1


title: DON_rep2

description:
pdr5_DON_2
Gene expression data from PDR5 mutant yeast treated with deoxynivalenol (DON).


title: Control_DMSO_rep3

description:
pdr5_DMSO_3
Gene expression data from PDR5 mutant yeast treated with DMSO control.

source_name: PDR5 mutant strain, control

value: DMSO control


title: old_c277


title: Control_DMSO_rep2

description:
pdr5_DMSO_2
Gene expression data from PDR5 mutant yeast treated with DMSO control.


title: old_c287


title: old_c291


title: old_c268


title: old_c267


title: old_c261


title: Sw_H1N1_2009_CA04_Day7_E5_28

first: Michael

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to Agilent Porcine Gene Expression Microarray slides.

scan_protocol: Dry slides were scanned on an Agilent Technologies Scanner (Model G2505C) using the XDR setting.

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 package.

organism: Sus scrofa

source_name: lung, CA04 virus infection, day 7

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

extract_protocol: Lung tissue was homogenized in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol). RNA was isolated from lung lysates by precipitation using phenol-choloroform-isoamyl alcohol, then washed with isopropanol and resuspended in RNase-free water. The RNA concentration was measured using a Thermo Scientific Nanodrop 2000TM and the integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer.

treatment_protocol:
Four-week-old crossbred pigs (Sus Scrofa) were inoculated intratracheally with either 10^6 TCID50/pig egg-derived 2009 pandemic influenza A/California/04/2009 virus (n = 5) or mock inoculated with non-infectious cell culture supernatant (control; n = 4). Animals were euthanized on day 7 post-infection and lung samples were used for microarray.
Lung samples were stored in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol) at -80°C until processing.

tag: breed

value: crossbred

value: lung

value: CA04 virus infection

tag: time of sample collection

value: day 7 post-infection


title: Sw_H1N1_2009_Mock_Day7_E5_13

source_name: lung, mock infection, day 7

value: mock infection


title: old_c274


title: Sw_H1N1_2009_Mock_Day7_E5_44


title: Sw_H1N1_2009_CA04_Day7_E5_27


title: Control_DMSO_rep1

description:
pdr5_DMSO_1
Gene expression data from PDR5 mutant yeast treated with DMSO control.


title: Sw_H1N1_2009_CA04_Day7_E5_25


title: old_c254


title: old_c251


title: Sw_H1N1_2009_Mock_Day7_E5_12_B


title: old_c250


title: Sw_H1N1_2009_Mock_Day7_E5_11


title: old_c239


title: Sw_H1N1_2009_CA04_Day7_E5_26


title: old_c242


title: Sw_H1N1_2009_CA04_Day7_E5_24


title: old_c230


title: TEKi_rep2

city: Singapore

first: Yifeng

last: Xu

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

description: This sample is of TEKi Arabidopsis. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed  following NimbleGen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Arabidopsis thaliana

source_name: Day 7 TEKi Ler

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Wild-type Ler and T3 plants of the amiTEK were grown at MS medium plates and harvested at DAG 7

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

value: TEK knockdown

tag: phenotype

value: Late flowering time

value: seedling


title: TEKi_rep1


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs and with 4uM BIO for additional 24hrs, biological rep2

status: Public on Sep 11 2012

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

description: gene expression data from aggregated nephron progenitors exposed to constitutive activation of Wnt/b-catenin signaling

hyb_protocol: We followed the protocol suggested by Affymetrix.

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

data_processing: The data were analyzed with dChIP.

source_name: aggregated cells exposed to constitutive activation of Wnt/b-catenin signaling

label_protocol: Biotinylated aRNA were prepared by using TargetAmp 2-Round Biotin-aRNA Amplification kit 3.0 (Epicentre)

growth_protocol: The FACS isolated Six2+ cells (40,000 cells per sample) were aggregated by centrifugation at 800 x g for 5 min and cultured in 10%FBS/DMEM.

extract_protocol: RNA was isolated by using Absolutely RNA nanoprep kit (Stratagene).

treatment_protocol: 4uM BIO or the equal volume of DMSO was added in culture. After 24hrs, the media was changed as indicated.

value: mixed background


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs and with 4uM BIO for additional 24hrs, biological rep3


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs and with DMSO for additional 24hrs, biological rep1

description: gene expression data from aggregated nephron progenitors exposed to transient activation of Wnt/b-catenin signaling

source_name: aggregated cells exposed to transient activation of Wnt/b-catenin signaling


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs and with 4uM BIO for additional 24hrs, biological rep1


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs, biological rep3

description: gene expression data from aggregated nephron progenitors exposed to Wnt/b-catenin activation

source_name: aggregated cells exposed to Wnt/b-catenin activation


title: wild-type_rep2

description: This sample is of wild-type Arabidopsis. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Day 7 wild-type Ler

value: Wild-type

value: Normal flowering time


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs and with DMSO for additional 24hrs, biological rep3


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs, biological rep1


title: dispersed nephron progenitors treated with 4uM BIO for 24hrs, biological rep2

description: gene expression data from dispersed nephron progenitors exposed to Wnt/b-catenin activation

source_name: dispersed cells exposed to Wnt/b-catenin acitvation


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs, biological rep2


title: dispersed nephron progenitors treated with DMSO for 24hrs, biological rep3

description: gene expression data from dispersed nephron progenitors cultured for 24hrs

source_name: dispersed cells


title: aggregated nephron progenitors treated with DMSO for 24hrs, biological rep1

description: gene expression data from aggregated nephron progenitors cultured for 24hrs

source_name: aggregated cells


title: aggregated nephron progenitors treated with DMSO for 24hrs, biological rep2


title: dispersed nephron progenitors treated with 4uM BIO for 24hrs, biological rep1


title: freshly FACS-isolated nephron progenitors, biological rep2

description: gene expression data from freshly isolated nephron progenitors

source_name: 0hr control


title: dispersed nephron progenitors treated with DMSO for 24hrs, biological rep1


title: freshly FACS-isolated nephron progenitors, biological rep3


title: freshly FACS-isolated nephron progenitors, biological rep1


title: aggregated nephron progenitors treated with DMSO for 24hrs, biological rep3


title: dispersed nephron progenitors treated with DMSO for 24hrs, biological rep2


title: dispersed nephron progenitors treated with 4uM BIO for 24hrs, biological rep3


title: wild-type_rep1


title: pH 7.4

city: Liverpool

first: Rana

last: Rustom

address: Duncan Street

department: Metabolic and Cellular Medicine

institute: University of Liverpool

hyb_protocol: According to user manual for Nylon Atlas cDNA Expression Arrays available at www.clontech.com

scan_protocol: The arrays were exposed to Storage Phosphor Screens (Amersham Pharmacia Biotech, Little Chalfont, UK). The phosphor screens were scanned using a Biorad Personal Molecular Imager FX (Biorad, Hercules, CA, USA).

data_processing: Values were normalized using Global normalization. The software used for the analysis of the images is Clontech AtlasImageTM 2.7.

source_name: Human renal proximal tubular epithelial cells

growth_protocol: Growth medium: DMEM/Ham s F12 medium supplemented with 5.5 mM glucose, 2 mM L-glutamine, 5 ug/ml insulin, 5 ug/ml transferrin, 5 ng/ml sodium selenite, 0.4 ug/ml hydrocortisone, 5 ng/ml epidermal growth factor, 100 U/ml penicillin, 100 ug/ml streptomycin, and 10% FCS.

extract_protocol: Total RNA was isolated from HK-2 cells using Tri-reagent (Sigma, UK) as recommended by the manufacturer s protocol. The RNA content of the samples was measured using RiboGreen RNA Quantitation Reagent (Molecular Probes, Invitrogen, UK). The integrity of the total RNA was verified on a denaturing agarose-formaldehyde gel.

treatment_protocol: HK-2 cells were were seeded onto 6 well plates at a density of 4x104 cells/well and cultured in growth medium for 72 h. The medium was then replaced by growth media buffered to pH 7.4, 7.0 or 6.7 with 12.5 mM bis-Tris and cells were cultured for further 48 h. Media were changed to serum free media (SFM) buffered by 12.5 mM bis-Tris to pH 7.4, 7.0 or 6.7 and cells were harvested and RNA isolated after 24 h.

tag: cell type

value: Immortalised human renal proximal tubular epithelial cells


title: pH 7.0

label_protocol: According to user manual for Nylon Atlas cDNA Expression Arrays available at www.clontech.com


title: pH 6.7


title: Fibroblast_TGFBeta1_48hrs_rep2

first: Joshua

middle: David

last: Campbell

address: 72 East Concord St.

institute: Boston University

description: High molecular weight RNA was isolated, converted to cDNA, biotin-labeled, and hybridized to Human Gene 1.0 ST GeneChips. Transcript-level gene expression estimates were generated via the robust multichip average (RMA) algorithm using the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu) in R v2.9.2.

hyb_protocol: cDNA was fragmented end-labeled with a biotinylated dideoxynucleotide using terminal transferase and added to a hybridization cocktail, loaded on a Human Gene1.0 ST GeneChip and hybridized for 16 hours at 45 ºC under rotation (60 rpm). Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing:
Transcript-level gene expression estimates were generated via the robust multichip average (RMA) algorithm using the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu) in R v2.9.2.
Quantile sketch normalized transcript level expression using the RMA algorithm with the Entrez Gene CDF v11 (http://brainarray.mbni.med.umich.edu)

source_name: Whole lung tissue

label_protocol: The total RNA was converted to cDNA and subsequently amplified and biotin-labeled.

extract_protocol: High molecular weight RNA was isolated from tissue cores using the RNeasy Mini Kit (Qiagen). The RNA integrity was assessed using an Agilent 2100 Bioanalyzer and RNA purity was assessed using a NanoDrop spectrophotometer. 200ng of RNA was processed and used as starting material for the microarray studies.

tag: time

tag: ghk

value: 10 ng/ul


title: Fibroblast_GHK_48hrs_0.1nM_rep1


title: Fibroblast_GHK_48hrs_0.1nM_rep2


title: Fibroblast_TGFBeta1_48hrs_rep1


title: Fibroblast_DMSO_48_hours_rep1


title: Fibroblast_DMSO_48_hours_rep2


title: Fibroblast_GHK_48hrs_10nM_rep2


title: cancer preop 84

city: Buffalo

first: Santosh

middle: Kumar

last: Patnaik

state: NY

address: Elm and Carlton Streets

department: Thoracic Surgery

institute: Roswell Park Comprehensive Cancer Center

description: files with prefix 1_ are for Hy3 (Cy3) signals and 2_ for Hy5

hyb_protocol: Hybridization of the mix of Hy3-labeled sample and Hy5-labeled reference RNAs to the arrays at 56 C for 16 hours followed by washing was performed by Exiqon (Vedbaek, Denmark) on an HS Pro instrument (Tecan, Männedorf, Switzerland). The seventh generation miRCURY LNA microRNA arrays (Exiqon, Vedbaek, Denmark) that were used have approx. 1892 locked nucleic acid oligonucleotide probes on quadruplicate 100 µM-sized probe-spots (185 µM inter-spot distance) to detect 20 human non-microRNA small RNAs (20 array probes), 25 Exion-proprietary human miRPlus microRNAs (25 probes) and 1916 human miRBase microRNA database microRNAs (1892 probes). Thirty of the 1892+25=1917 probes recognize a total of 72 multiple microRNAs (2-6 per probe). Some of the microRNAs recognized by the 30 are also recognized by other, one-microRNA-specific probes. The array also has probes for viral, mouse and rat microRNAs.

scan_protocol: Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent, Santa Clara, CA, USA) by Exiqon (Vedbaek, Denmark).

data_processing: Array data processing was done in R (version 2.14.1) using the limma (version 3.10.2) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored, and then, between-array 'quantile' normalization. For probe-set summarization, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was >1.5; else, the mean was used.

source_name: blood, lung cancer, individual 84

label_protocol: RNA was labeled by Exiqon, Vedbaek, Denmark using the miRCURY LNA microRNA Power labeling kit. Five hundred ng of RNA, as quantified using Bioanalyzer (Agilent, Santa Clara, CA, USA), was used per labeling reaction with the Cy3-like Hy3 dye. A human universal reference RNA, made by pooling contents of FirstChoice total RNA panel (Ambion, Austin, TX, USA; catalog no. AM6000), was similarly labeled with the Cy5-like Hy5 dye. Sixty-two synthetic small RNAs were spiked-in to the RNA samples before labeling as per the kit protocol.

extract_protocol: Total RNA was isolated from blood collected and stored in PAXgene Blood RNA tubes using a PAXgene Blood miRNA kit at the Roswell Park Cancer Institute, Buffalo, NY, USA as per the protocol suggested by the manufacturer (Qiagen, Valencia, CA, USA). The human universal reference RNA was made by pooling contents of FirstChoice total RNA panel that is made of RNA from different tissues of multiple individuals (Ambion, Austin, TX, USA; catalog no. AM6000).

value: blood

value: preop

tag: gender

value: female

tag: disease state

value: large cell carcinoma of lung

tag: lung disease

value: Lung cancer (before surgical resection of lung cancer)

tag: individual

source_name: Human universal reference RNA from Ambion

value: Multiple

value: Mixed


title: cancer preop 85

source_name: blood, lung cancer, individual 85

value: male

value: adenocarcinoma of lung

tag: sample type

value: Human universal reference RNA from Ambion


title: control nodule 18

source_name: blood, non-cancerous lung nodule, individual 103

value: subpleural fibrosis of lung

value: Non-cancerous lung nodule


title: Fibroblast_GHK_48hrs_10nM_rep1


title: control highrisk 29 replicate 2

source_name: blood, no lung cancer or nodule, individual 132

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)


title: cancer preop 81

source_name: blood, lung cancer, individual 81


title: cancer preop 74 replicate 2

source_name: blood, lung cancer, individual 74

value: squamous cell carcinoma of lung


title: cancer preop 82

source_name: blood, lung cancer, individual 82


title: aggregated nephron progenitors treated with 4uM BIO for 24hrs and with DMSO for additional 24hrs, biological rep2

source_name: aggregated cells exposed to transient activation of Wnt/b-catenin signaling

tag: strain

value: mixed background


title: cancer preop 83

source_name: blood, lung cancer, individual 83


title: cancer preop 75

source_name: blood, lung cancer, individual 75

value: sarcomatoid carcinoma of lung


title: cancer preop 76

source_name: blood, lung cancer, individual 76

value: blood


title: cancer preop 74 replicate 1

value: preop


title: cancer preop 73

source_name: blood, lung cancer, individual 73

value: female


title: cancer preop 77

source_name: blood, lung cancer, individual 77


title: cancer preop 80

source_name: blood, lung cancer, individual 80

value: large cell carcinoma of lung


title: cancer preop 78

source_name: blood, lung cancer, individual 78

value: Lung cancer (before surgical resection of lung cancer)


title: control nodule 17

source_name: blood, non-cancerous lung nodule, individual 102

value: granuloma of lung

value: Multiple


title: cancer postop 13

source_name: blood, lung cancer post-op., individual 83

value: postop

value: male

value: lung after resection of lung cancer

value: None (after surgical resection of lung cancer)

value: Mixed


title: cancer postop 12

source_name: blood, lung cancer post-op., individual 77

source_name: Human universal reference RNA from Ambion


title: cancer postop 9

source_name: blood, lung cancer post-op., individual 74

value: Human universal reference RNA from Ambion


title: cancer postop 10

source_name: blood, lung cancer post-op., individual 76


title: cancer postop 8

source_name: blood, lung cancer post-op., individual 70


title: cancer preop 72

source_name: blood, lung cancer, individual 72

value: adenocarcinoma of lung


title: cancer preop 71

source_name: blood, lung cancer, individual 71

value: squamous cell carcinoma of lung


title: cancer postop 11

source_name: blood, lung cancer post-op., individual 162


title: cancer postop 6

source_name: blood, lung cancer post-op., individual 68


title: cancer postop 5

source_name: blood, lung cancer post-op., individual 66


title: cancer postop 7

source_name: blood, lung cancer post-op., individual 65


title: cancer postop 2 later timepoint

source_name: blood, lung cancer post-op., later timepoint,  individual 72


title: cancer postop 4

source_name: blood, lung cancer post-op., individual 71


title: cancer postop 3

source_name: blood, lung cancer post-op., individual 67


title: cancer preop 70

source_name: blood, lung cancer, individual 70


title: cancer preop 69

source_name: blood, lung cancer, individual 69


title: control nodule 12

source_name: blood, non-cancerous lung nodule, individual 97

value: amyloid of lung

value: Non-cancerous lung nodule


title: cancer postop 1

source_name: blood, lung cancer post-op., individual 69

value: blood


title: control nodule 13

source_name: blood, non-cancerous lung nodule, individual 98

source_name: Human universal reference RNA from Ambion


title: cancer postop 2

source_name: blood, lung cancer post-op., individual 72


title: cancer preop 67

source_name: blood, lung cancer, individual 67

value: preop


title: control nodule 16

source_name: blood, non-cancerous lung nodule, individual 101


title: cancer preop 68

source_name: blood, lung cancer, individual 68

value: female


title: cancer preop 66

source_name: blood, lung cancer, individual 66


title: control nodule 14

source_name: blood, non-cancerous lung nodule, individual 99

value: pneumonia of lung


title: cancer preop 65

source_name: blood, lung cancer, individual 65

value: Lung cancer (before surgical resection of lung cancer)


title: control nodule 9

source_name: blood, non-cancerous lung nodule, individual 94

value: granuloma of lung


title: control nodule 10

source_name: blood, non-cancerous lung nodule, individual 95

value: Multiple


title: control nodule 8

source_name: blood, non-cancerous lung nodule, individual 93


title: control nodule 15

source_name: blood, non-cancerous lung nodule, individual 100


title: control nodule 6

source_name: blood, non-cancerous lung nodule, individual 91


title: control nodule 11

source_name: blood, non-cancerous lung nodule, individual 96

value: hamartoma of lung


title: cancer preop 61

source_name: blood, lung cancer, individual 61


title: control nodule 2

source_name: blood, non-cancerous lung nodule, individual 87


title: cancer preop 60

source_name: blood, lung cancer, individual 60

value: male


title: cancer preop 62

source_name: blood, lung cancer, individual 62

source_name: Human universal reference RNA from Ambion


title: control nodule 7

source_name: blood, non-cancerous lung nodule, individual 92


title: cancer preop 79

source_name: blood, lung cancer, individual 79


title: cancer preop 59

source_name: blood, lung cancer, individual 59


title: control nodule 5

source_name: blood, non-cancerous lung nodule, individual 90


title: cancer preop 58

source_name: blood, lung cancer, individual 58


title: control highrisk 58

source_name: blood, no lung cancer or nodule, individual 161

value: lung without lung cancer or non-cancerous nodule

value: None (no current or past lung cancer or non-cancerous nodule)


title: control highrisk 53

source_name: blood, no lung cancer or nodule, individual 156

value: Mixed


title: cancer preop 53

source_name: blood, lung cancer, individual 53

value: Human universal reference RNA from Ambion


title: control highrisk 54

source_name: blood, no lung cancer or nodule, individual 157


title: cancer preop 56

source_name: blood, lung cancer, individual 56

value: adenocarcinoma of lung


title: control highrisk 56

source_name: blood, no lung cancer or nodule, individual 159


title: control highrisk 55

source_name: blood, no lung cancer or nodule, individual 158


title: control highrisk 57

source_name: blood, no lung cancer or nodule, individual 160


title: cancer preop 55

source_name: blood, lung cancer, individual 55

value: squamous cell carcinoma of lung


title: cancer preop 54

source_name: blood, lung cancer, individual 54


title: control nodule 1

source_name: blood, non-cancerous lung nodule, individual 86


title: cancer preop 63

source_name: blood, lung cancer, individual 63

source_name: Human universal reference RNA from Ambion


title: cancer preop 64

source_name: blood, lung cancer, individual 64


title: cancer preop 57

source_name: blood, lung cancer, individual 57


title: control highrisk 52

source_name: blood, no lung cancer or nodule, individual 155


title: control nodule 3

source_name: blood, non-cancerous lung nodule, individual 88


title: control nodule 4

source_name: blood, non-cancerous lung nodule, individual 89


title: control highrisk 51

source_name: blood, no lung cancer or nodule, individual 154


title: cancer preop 52

source_name: blood, lung cancer, individual 52


title: cancer preop 51

source_name: blood, lung cancer, individual 51