title: Ptr_BELA18-4-rep1

description: wildtype

source_name: Populus trichocarpa BELA18-4 wt

value: low

tag: phenotype (glucose)

tag: phenotype (density-alpha cellulose)

value: high/high

tag: phenotype (hemicellulose-lignin)

value: low/low

tag: phenotype (density-lignin)

tag: phenotype (alpha cellulose-hemicellulose (glucose-xylose))

tag: phenotype (alpha cellulose-lignin)


title: Day10 MDI repl1 vs TBT 10 nM repl3

status: Public on Feb 25 2013

type: RNA

city: Antwerp

first: Anna

last: Pereira-Fernandes

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

hyb_protocol: 825 ng of both Cy3 and Cy5 labelled cRNA were co-hybridized on a 44K Whole Rat Genome Oligo Microarray (G4131F, Agilent) for 17h at 60°C in a continuous rotation Agilent hybridization oven. Slides were subsequently washed with Agilent wash buffers and acetonitrile and finally submersed in stabilization and drying solution (Agilent Technologies, Diegem, Belgium) to prevent ozone-induced Cy5-degradation. A separate v+2 A-optimal hybridization design was used for each time-point. Using this design each exposure condition is represented by three biological replicates, with each biological replicate analysed in technical duplicate while applying the dye swap principle to correct for dye bias.

scan_protocol: Arrays were scanned at 532 and 635 nm using a Genetix Personal 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing:
The images were analysed using the Genepix Pro software 4.1 (Axon Instruments) for spot identification and for quantification of the fluorescent signal intensities. Statistical analysis of microarray data was performed with the R package limma. Briefly, spots for which red or green FG < BG + 2SD on all arrays were deleted before analysis (FG: medium foreground intensity; BG: average local background intensity calculated over the full microarray; SD: standard deviation of local background intensities). After background correction (backgroundCorrect, method “normexp”, offset = 50) of the median intensity data, loess normalisation (normalizeWithinArrays) was applied. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. Exposure versus control contrasts were fitted to the linear models and considered significant if p<0.05 and ǀlog2FCǀ>0.75 (log2 fold change).
Since a loop design was used for this microarray design, the final contrasts between the conditions (DMSO vs MDI; DMSO vs TBT 10 nM and DMSO vs TBT 50 nM) were added in separate .txt sheets with the log2 based FC values and the adjusted p-value for each ID.  The .txt files are linked as supplementary files on the Series record.
The .txt files report loess normalized log2 based fold-change Cy5/Cy3.

molecule: total RNA

organism: Mus musculus

source_name: Day10 MDI repl1

label_protocol: Low Input Quick Amplification Labeling Kit (LIQA, Agilent, Diegem, Belgium), according to the protocol of the manufacturers. Briefly, starting from 200 ng of total RNA, poly-A RNA was reverse transcribed using a poly dT-T7 primer. The resulting cDNA was used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP or Cyanine 5-CTP. The amplified and labelled RNA samples were purified separately on an RNeasy purification column (Qiagen).

growth_protocol: 3T3-L1 murine cell line (ATCC CRL-173) were cultured in 75 cm2 Nunc cell culture flasks in standard growth medium (DMEM high glucose, Gibco BRL, 31885-023) supplemented with 10% heat inactivated Newborn Calf serum, 100 U/mL Penicillin, 100 µg/mL Streptomycin (Life Technologies) and 1 mM sodium pyruvate  and phenol red as pH indicator. Cells were grown in a 37°C incubator under a 5% CO2 atmosphere and cultures were routinely verified as mycoplasma free with the PCR-based VenorTM GeM Mycoplasma Detection kit (Sigma-Aldrich, Bornem, Belgium). At 70-90% confluence, cells were detached with 0.25% tryspin/EDTA during 3 min (37°C). The  trypsin was neutralized with growth medium and cells were split, with a maximum of 12 passages. Every 2-3 days, medium was refreshed.

extract_protocol: Total RNA extracted using the Qiagen RNeasy mini kit

treatment_protocol: Cells were seeded in 6- well plates at a density of 200,000 cells/well and grown until confluence. Standard medium of 2 days post-confluent cells was replaced by mature medium containing 10% Heat Inactivated Foetal Bovine Serum (FBS, Life Technologies) instead of Newborn Calf Serum and the test compound, Tributyltin Chloride (TBT-Cl, Acros Chemicals, Geel, Belgium), was added for 10 days, changing the medium every 2-3 days. TBT was dissolved in DMSO with a final maximal concentration of 0.1%. Therefore, a solvent control (0.1% DMSO) was included in each experiment. As positive control, 2 days post-confluent cells were stimulated for 48h in mature medium containing a MDI hormonal cocktail (0.5 mM isobutyl methylxanthine, 0.25 µM dexamethasone and 10 µg/mL insulin) and another 8 days in mature medium containing only insulin (10 µg/mL) and changed every 3 days. In the following experiments and results, 2 days post-confluent cells are indicated by the ‘day 0’ time point. After exposure, cells were harvested for RNA extraction at day1 and day10.

tag: cell line

tag: agent

value: MDI

tag: time

source_name: Day10 TBT 10 nM repl3

value: TBT

tag: agent concentration

value: 10 nM


title: Day10 TBT 10 nM repl1 vs MDI repl1

source_name: Day10 TBT 10 nM repl1


title: bic_unstimulated_1

status: Public on Feb 26 2013

city: Philadelphia

first: E

middle: John

last: Wherry

address: 421 Curie Blvd.

country: USA

institute: University of Pennsylvania

hyb_protocol: cDNA was amplifoeed with NuGen WT Ovation Pico kit and hybridized to Affymetrix GeneChip Mouse Gene 1.0 ST microarrays at the University of Pennsylvania’s Microarray facility.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Power Tools were used to process and quantile normalize fluorescent hybridization signals using Robust Multichip Averaging. Transcript values were log2 normalized.

label: biotin

source_name: bic unstimulated

label_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

growth_protocol: CD8 T cells were purified by negative selection with magnetic beads (EasySep, Stemcell Technologies) from uninfected wild-type or miR-155 deficient (bic-/-) C57BL/6 mice and stimulated in vitro with 1microgram/ml plate-bound anti-CD3 and 5microgram/ml plate-bound anti-CD28 for 48hrs. Unstimulated, purified CD8 T cells from the same mice were used as control.

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

tag: stimulation

value: unstimulated

tag: genotype

value: bic-/-

tag: genetic background

tag: cell type

value: CD8 T cell


title: HealthyDonor_1-0h

city: Munich

first: Jacek

last: Puchałka

address: Lindwurmstrasse 2a

department: University Children's Hospital

country: Germany

institute: Munich University Hospital

hyb_protocol: The hybridization was done using the Affy Hybridization, wash and stain kit according to the manufacturers protocol.

scan_protocol: The arrays were scanned using the GeneChip 3000 7G Scanner with AGCC software version 3.0

data_processing:
The were processed with various packages from Bioconductor suite. The intensities were background corrected, normalized, and the expression values computed by Robust Microchip Average methodology (package oligo). hours) were identified.
probe group file: Bioconductor package pd.hugene.1.0.st.v1 (v. 3.0.2) was used
meta-probeset file: Bioconductor package pd.hugene.1.0.st.v1 (v. 3.0.2) was used

organism: Homo sapiens

source_name: PBMC

label_protocol: The labeled target was prepared from 100ng total RNA using Ambion WT Expression kit and the Affymetrix terminal labeling kit.

growth_protocol: PBMC separated on Ficoll gradient

extract_protocol: Ethanol extraction of total RNA.

treatment_protocol: Stimulation with anti-CD3 and anti-CD28 antibodies for 6h, 12h, 18h. Unstimulated samples as a controls.

tag: patient status

value: Healthy Donor


title: HealthyDonor_2-0h


title: Be2C_DMSO_24h_Repl3

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Be2C_CT_SF11

hyb_protocol: FS450_0002 for theHuman GeneChip PrimeView arrays

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: GeneChip Command Console AGCC software  3.2.4 was used to generate the CEL files.  The computational pipeline was run on the bioinformatics platform GenomeSpace (http://www.genomespace.org/).  Data were extracted from the  CEL files and preprocessed by applying  RMA and the quantile normalization procedures implemented in  the ExpressionFileCreator module of the  GenePattern software platform (Broad Institute, http://www.broadinstitute.org/cancer/software/genepattern/).

source_name: Be2C cell line, DMSO treated

label_protocol: Biotin: GeneChip® 3' IVT Express labeling kit

growth_protocol: Kelly and Be(2)-C cells were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin with glutamine

extract_protocol: RNA was extracted using Qiagen Rneasy Mini Kit (74104)

treatment_protocol: Kelly and Be(2)-C cells were treated in triplicate with either DMSO or JQ1 1μM for 24 hours

tag: treatment

value: DMSO

tag: replicate


title: Be2C_DMSO_24h_Repl2

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Be2C_CT_SF09


title: Be2C_JQ1_24h_Repl1

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Be2C_JQ1_SF08

source_name: Be2C cell line,  JQ1 treated


title: Be2C_DMSO_24h_Repl1

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Be2C_CT_SF07


title: Spleen monocytic cells from day 14 post LCMV ARM infection - replicate 3

city: SÃO PAULO

first: Helder

middle: I.

last: Nakaya

state: SÃO PAULO

address: AVENIDA PROFESSOR LINEU PRESTES, 580, Block 17

country: Brazil

institute: Universidade de São Paulo

description:
Arm_mono3
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from day 14 lymphocytic choriomeningitis virus (LCMV) Armstrong infected mice

hyb_protocol: Biotinylated cRNA was then normalized to 150ng/ul and 10ul were used to hybridize onto Illumina MouseWG-6 v2.0 Expression BeadChips.

scan_protocol: Scanning was performed by the Illumina iScan.

data_processing: Arrays were analyzed by the Illumina GenomeStudio Gene Expression Module with default parameters to generate standard data tables with no background subtraction or normalization. Next, the expression levels were background-corrected by Maximum Likelihood Estimation (MLE) and normalized by quantile using MBCB R package (Allen et al., 2009).

label: Biotin

source_name: Spleen

label_protocol: Illumina TotalPrep RNA Amplification Kit Protocol according to manufacturer's protocol. Briefly, 150-500ng of total RNA was reverse transcribed with an oligo(dT) primer bearing a T7 promoter to generate first strand cDNA. The cDNA then underwent second strand synthesis and cleanup. Next, this cDNA was used as a template for in vitro transcription with biotin-UTP to generate biotinylated cRNA.

extract_protocol: RNA extracted using Trizol (Invitrogen) protocol according to the manufacturer’s instructions.

treatment_protocol: CD11b+ Ly6Chi Gr-1int monocytic cells were FACS-sorted.

tag: strain

value: CD11b+ Ly6C-hi Gr-1-int monocytic cells

tag: infection

value: LCMV Armstrong

tag: tissue

value: spleen

value: monocytic cells


title: Spleen monocytic cells from day 14 post LCMV C13 infection - replicate 3

description:
Cl13_mono3
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from day 14 lymphocytic choriomeningitis virus (LCMV) Clone 13 infected mice

value: LCMV Clone 13


title: Spleen monocytic cells from day 14 post LCMV C13 infection - replicate 2

description:
Cl13_mono2
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from day 14 lymphocytic choriomeningitis virus (LCMV) Clone 13 infected mice


title: Be2C_JQ1_24h_Repl3

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Be2C_JQ1_SF12


title: Day10 TBT 10 nM repl2 vs MDI repl2

source_name: Day10 TBT 10 nM repl2

source_name: Day10 MDI repl2


title: Spleen monocytic cells uninfected - replicate 3

description:
Naive_mono3
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from naïve mice

value: Uninfected


title: Be2C_JQ1_24h_Repl2

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Be2C_JQ1_SF10


title: Day10 TBT 50 nM repl3 vs DMSO repl3

source_name: Day10 TBT 50 nM repl3

value: 50 nM

source_name: Day10 DMSO repl3


title: Day10 TBT 50 nM repl2 vs TBT 10 nM repl1

source_name: Day10 TBT 50 nM repl2


title: Day10 TBT 10 nM repl3 vs TBT 50 nM repl1

source_name: Day10 TBT 50 nM repl1


title: Day10 MDI repl3 vs TBT 50 nM repl3

source_name: Day10 MDI repl3


title: Day10 DMSO repl2 vs TBT 10 nM repl2

source_name: Day10 DMSO repl2


title: Day10 DMSO repl1 vs TBT 50 nM repl2

source_name: Day10 DMSO repl1


title: Day10 TBT 50 nM repl1 vs DMSO repl1


title: Kelly_JQ1_24h_Repl3

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Kelly_JQ1_SF06

source_name: Kelly cell line,  JQ1 treated

value: Kelly


title: Day10 DMSO repl1 vs DMSO repl2


title: male brain 109, selenium

city: Moscow

first: Maia

middle: J

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Affymetrix Zebrafish Genome Arrays (~14,900 transcripts) were hybridized with fragmented biotinylated cRNA for 16 h at 45 °C with constant rotation (45 rpm), and processed using the Affymetrix GeneChip Fluidic Station 450. Streptavidin-conjugated phycoerythrin (SAPE) was used for staining, followed by amplification using a biotinylated anti-streptavidin antibody.

scan_protocol: Another round of SAPE was performed prior to scanning using a GeneChip Scanner 3000 (Affymetrix). All microarray procedures were performed at the Genomics Core Facility of the Center for Reproductive Biology at Washington State University (Pullman, WA).

data_processing: CEL files containing raw data were processed and analyzed using R software and Bioconductor packages. Microarray data were examined for physical anomalies on the chip by pseudo chip and residual error visualizations. Quality Assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport. The arrays were pre-processed using the Robust Multi-array Average (RMA) procedure using the affy package. Next, unexpressed and low variability genes were removed by unbiased filtering. Probesets with less than a median log2 signal value of 5.00 were removed from further analysis. A filter on interquartile range was also applied to remove low variability genes. Genes with an interquartile range of less than 0.5 across all chips in the experiment were excluded. We performed an additional filtration step to reduce the genes down to annotated Ensembl genes.

organism: Danio rerio

source_name: Zebrafish male adult brain selenium supplemented

label_protocol: For each array, 10 μg of total RNA were converted to cDNA. Biotinylated cRNA was then produced in vitro using the GeneChip expression 3′ amplification one-cycle target labeling kit (Affymetrix, Santa Clara, CA, USA).

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

treatment_protocol: 1 year old sexually mature adult zebrafish were fed diets with either control levels of selenium (1.4ppmSe) or supplemented with sodium selenite (5.6ppmSe) for 14 days.

value: whole brain

value: Transgenic Mosaic 1

tag: age

value: 1 year old (sexually mature adult)

tag: Sex

value: male

value: selenium supplemented


title: Kelly_DMSO_24h_Repl2

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Kelly_CT_SF03

source_name: Kelly cell line, DMSO treated


title: Spleen monocytic cells from day 14 post LCMV ARM infection - replicate 1

description:
Arm_mono1
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from day 14 lymphocytic choriomeningitis virus (LCMV) Armstrong infected mice


title: Spleen monocytic cells from day 14 post LCMV ARM infection - replicate 2

description:
Arm_mono2
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from day 14 lymphocytic choriomeningitis virus (LCMV) Armstrong infected mice


title: Day10 DMSO repl3 vs DMSO repl1


title: Spleen monocytic cells uninfected - replicate 1

description:
Naive_mono1
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from naïve mice


title: Kelly_DMSO_24h_Repl3

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Kelly_CT_SF05


title: Kelly_JQ1_24h_Repl1

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Kelly_JQ1_SF02


title: Kelly_JQ1_24h_Repl2

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Kelly_JQ1_SF04


title: Day1 DMSO repl1 vs DMSO repl2

source_name: Day1 DMSO repl1

source_name: Day1 DMSO repl2


title: Day1 TBT 50 nM repl3 vs DMSO repl3

source_name: Day1 TBT 50 nM repl3

value: TBT

source_name: Day1 DMSO repl3


title: Spleen monocytic cells uninfected - replicate 2

description:
Naive_mono2
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from naïve mice

source_name: Spleen


title: Spleen monocytic cells from day 14 post LCMV C13 infection - replicate 1

description:
Cl13_mono1
Freshly isolated splenic CD11b+ Ly6C-hi Gr-1-int monocytic cells from day 14 lymphocytic choriomeningitis virus (LCMV) Clone 13 infected mice


title: Day1 DMSO repl3 vs DMSO repl1


title: Day1 DMSO repl2 vs TBT 10 nM repl2

source_name: Day1 TBT 10 nM repl2

value: 10 nM


title: Kelly_DMSO_24h_Repl1

description:
The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
Kelly_CT_SF01


title: Day1 TBT 50 nM repl1 vs DMSO repl1

source_name: Day1 TBT 50 nM repl1


title: Gestation day 4.5 uterine luminal epithelium-2

city: ATHENS

first: Shuo

last: Xiao

state: GA

address: 501 DW BROOKS DR

department: Physiology and Pharmacology

institute: University of Georgia

description: Postimplantation uterine luminal epithelium

hyb_protocol: ollowing fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 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: Microarray data was analyzed by GeneSpring 12.1 GX. The negative and missing values were threshold to 1 before being taken the log transformation. Percentile shift normalization was performed to overcome the difference among different arrays, and the lowest 20 percentile of the intensity values were removed. The fold change of 2, P<0.05 and an absolute value of mean difference greater than 200 between two groups were selected to indicate significantly upregulated and downregulated transcripts.

source_name: uterine luminal epithelium

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

growth_protocol: C57BL6/129svj mixed background wild type (WT) mice were housed in polypropylene cages with free access to regular food and water  in a reverse osmosis system in University of Georgia. The animal facility is on a 12-hour light/dark cycle (6:00 AM to 6:00 PM) at 23±1°C with 30-50% relative humidity. All methods used in this study were approved by the Animal Subjects Programs of the University of Georgia and conform to National Institutes of Health guidelines and public law.

extract_protocol: About 1/3 of a uterine horn from each euthanized female was frozen on dry ice. The remaining uterine tissue was processed for LE isolation  using 0.5% dispase enzyme and gentle scraping. The isolated LE sheets from D3.5 and D4.5 uteri were subjected to total RNA isolation using TRIzol.

treatment_protocol: Young virgin females (2-4 months old) were mated naturally with WT stud males and checked for a vaginal plug the next morning. The day a vaginal plug identified was designated as gestation day 0.5 (D0.5, mating night as D0). Uterine tissues were collected from euthanized females between 11:00 hours and 12:00 hours on D3.5 and D4.5, respectively. The pregnancy status was determined by the presence of blastocyst(s) in the D3.5 uterus or implantation site(s) in the D4.5 uterus.

value: uterine luminal epithelium

tag: developmental stage

value: Gestation day 4.5

tag: background strain


title: Gestation day 4.5 uterine luminal epithelium-3


title: Day1 DMSO repl1 vs TBT 50 nM repl2

tag: cell line

tag: agent

value: DMSO

source_name: Day1 TBT 50 nM repl2


title: Day1 MDI repl3 vs TBT 50 nM repl3

source_name: Day1 MDI repl3

value: MDI

tag: time

tag: agent concentration


title: Gestation day 4.5 uterine luminal epithelium-1


title: Day1 TBT 10 nM repl2 vs MDI repl2

source_name: Day1 MDI repl2


title: Gestation day 3.5 uterine luminal epithelium-2

description: Preimplantation uterine luminal epithelium

value: Gestation day 3.5


title: Gestation day 3.5 uterine luminal epithelium-3


title: Day1 TBT 10 nM repl3 vs TBT 50 nM repl1

source_name: Day1 TBT 10 nM repl3


title: caput of epididymides from vasectomized 48 years old man

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

description: RS_Vas-queue-45ans_(miRNA-1_0_2Xgain).CEL

hyb_protocol: One ug of each total RNA samples were labeled using the FlashTag Biotin HSR (Genisphere, Hatfield, PA), and hybridized O/N on the GeneChip miRNA Array v1.0 (Affimetrix, Santa Clara, CA), according to the manufacturer’s recommendations.Wash and stain was made with Fluidics Station 450, using fluidics script FS450_00(Affymetrix).

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affymetrix)

data_processing: Data were analyzed using the miRNA QC Tool software for quality control (www.affymetrix.com <http://www.affymetrix.com> ) and CEL files were imported and analyzed with the Partek Genomics Suite 6.5 software (Partek Incorporated, St Louis, MO).Signals were RMA normalized.

source_name: cauda of epididymides_vasectomized

label_protocol: Briefly, 1 mg of each total RNA samples were labeled using the FlashTag Biotin HSR (Genisphere, Hatfield, PA) according to the manufacturer’s recommendations

growth_protocol: human epididymides were obtained through our local organ transplantation program (Québec Transplant, QC, Canada) from three donors of 45, 47 and 48 years of age, with no known pathologies that could affect reproductive function.

extract_protocol: Total RNAs were extracted as previously described (Thimon et al, 2007) using Trizol reagent (Invitrogen, Burlington, ON, Canada). Total RNA was purified on RNeasy mini kit column (Qiagen, Mississauga, ON, Canada).

treatment_protocol: Artificial circulation was maintained during the surgery to preserve organ’s integrity. Epididymides were collected and processed within 3 hours after surgery.  Tissues were dissected into 3 anatomical regions (caput, corpus and cauda), immediately frozen in liquid nitrogen and stored at -80oC until use. Semen samples were obtained by masturbation from healthy volunteer control donors, as well as from vasectomized men and from vasovasostomized men consulting for postsurgical spermogram follow-up at the clinical andrology laboratory of our institution. Semen samples were obtained by masturbation from healthy volunteer control donors, as well as from vasectomized men and from vasovasostomized men consulting for postsurgical spermogram follow-up at the clinical andrology laboratory of our institution.

tag: subject(s)

value: vasectomized donor

value: 48 yrs

value: epididimus

tag: tissue region

value: cauda


title: caput of epididymides from vasectomized 45 years old man

description: RS_Vas-queue-47ans_(miRNA-1_0_2Xgain).CEL

value: 45 yrs


title: Day1 TBT 50 nM repl2 vs TBT 10 nM repl1

value: 50 nM

source_name: Day1 TBT 10 nM repl1


title: caput of epididymides from vasectomized 47 years old man

description: RS_Vas-queue-1980_(miRNA-1_0_2Xgain).CEL

value: 47 yrs


title: cauda of epididymides from vasectomized 47 years old man

description: RS_Vas-corps-1980_(miRNA-1_0_2Xgain).CEL

source_name: caput of epididymides_vasectomized

value: caput


title: Day1 MDI repl1 vs MDI repl3

source_name: Day1 MDI repl1


title: Gestation day 3.5 uterine luminal epithelium-1


title: Day1 MDI repl2 vs MDI repl1


title: corpus of epididymides from vasectomized 47 years old man

source_name: corpus of epididymides_vasectomized

value: corpus


title: MC1645_MCR6004_BM

type: genomic

city: Phoenix

first: Angela

middle: Stewart

last: Baker

state: AZ

address: 445 N. Fifth Street

department: Division of Integrated Cancer Genomics

institute: Translational Genomics Research Institute

hyb_protocol: Labeled DNA was purified using Vivaspin 500 columns (Satorius Stedim Biotech, Goettingen, Germany).   Equal amounts of labeled, purified tumor and reference DNA were hybridized to the microarray in a rotary oven at 65oC for 40 hours at a rotation speed of 20 rpm.

scan_protocol: Slides were scanned with the Agilent G2505B scanner using the default settings.

data_processing: Scanner images were extracted using Feature Extraction software version 10.1(Agilent, Santa Clara, CA).  Log2 data was imported into Agilent DNA Analytics 4.0.81 software for visualization and quality assessment.

molecule: genomic DNA

source_name: Promega female gDNA

label_protocol: Tumor DNA and DNA from a normal female reference (Promega, Madison, WI) were independently digested with Bovine DNAse I (Ambion, Austin, TX) and directly labeled with Cy5 and Cy3, respectively using the BioPrime Array CGH Genomic Labeling Module (Invitrogen, Carlsbad, CA).

extract_protocol: Tumor cells were isolated from 5-50cc bone aspirates and ACK lysis was used to lyse red blood cells.  Mononuclear cells were incubated with anti-CD138 coated magnetic beads for tumor cell purification. Cells were washed from magnetic beads and genomic DNA was isolated using Trizol reagent (Invitrogen) extraction techniques.  Further purification included treatment with Proteinase K and RNAse A and phenol-chloroform extraction.

tag: condition

value: Normal

source_name: CD138+ plasma cell genomic DNA

value: Myeloma


title: corpus of epididymides from vasectomized 45 years old man

description: RS_Vas-tete-47ans_(miRNA-1_0_2Xgain).CEL


title: cauda of epididymides from vasectomized 45 years old man

description: RS_Vas-corps-47ans-R_(miRNA-1_0_2Xgain).CEL


title: MC1648_MCR6009_BM


title: cauda of epididymides from vasectomized 48 years old man

description: RS_Vas-corps-45ans_(miRNA-1_0_2Xgain).CEL


title: MC0933_MCR6001_BM


title: corpus of epididymides from vasectomized 48 years old man

description: RS_Vas-tete-45ans_(miRNA-1_0_2Xgain).CEL


title: cold_JZ_rcf1_2

city: College Park

first: Jianhua

last: Zhu

state: MD

address: 2102 Plant Sciences Building

department: Plant Science and Landscape Architecture

institute: University of Maryland

description:
A firefly luciferase reporter gene driven by the cold stress-responsive CBF2 promoter (-1500 bp to -1 bp upstream of the transcription start site) was introduced into Arabidopsis plants in the Columbia glabrous1 (gl1) background.
rcf1-1 under cold stress

hyb_protocol: Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.

scan_protocol: Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.

data_processing: We first re-mapped the tiling array probes to the Arabidopsis genome (TAIR10) using SOAP2 and kept only probes that perfectly matched to a unique position in the genome for subsequent analyses. We then created a custom Chip Definition File (CDF) using the probe mapping result and used the aroma.affymetrix framework to quantile-normalize raw tiling array data. To identify retained introns, we first calculated the log2 signal intensity for each annotated intron (TAIR10) based on the trimmed-mean of signal intensities from all mapped probes. Introns with less than three mapped probes or low expression (log2 expression value < 5 in all samples) were not further considered. We then used the SAM algorithm to identify introns with significantly elevated expression in the rcf1-1 mutant samples relative to the wild type. A FDR (False Discovery Rate) of 0.05 was used as the significance cutoff.

organism: Arabidopsis thaliana

source_name: rcf1-1, cold stress 4°C 12 h

label_protocol: dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded cDNA Synthesis Kit.

growth_protocol: Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were routinely grown under cool, white light (~120 μmol m-2 s-1) at 21 ± 1℃ with a 16-h-light/8-h-dark photoperiod.

extract_protocol: RNA was extracted with Trizol (Invitrogen) and phenol:chloroform:isoamyl (25:24:1, PH 5.2) and precipitated with NaAc and Ethanol. RNA was then washed with 70% Ethanol and dissolved in water.

treatment_protocol: Fourteen-day-old Arabidopsis wild type and rcf1-1 seedlings grown on MS agar medium were subjected to cold stress at 4°C for 12 h.

tag: genotype/variation

value: rcf1-1 mutant

value: whole seedlings

tag: Stage

value: Fourtheen-day-old


title: cold_JZ_rcf1_3


title: Day1 TBT 10 nM repl1 vs MDI repl1

value: TBT

value: 10 nM


title: cold_JZ_WT_3

description:
A firefly luciferase reporter gene driven by the cold stress-responsive CBF2 promoter (-1500 bp to -1 bp upstream of the transcription start site) was introduced into Arabidopsis plants in the Columbia glabrous1 (gl1) background.
Wild type under cold stress

source_name: Wild type, cold stress 4°C 12 h

value: Wild type


title: Day1 MDI repl1 vs TBT10 nM repl3

value: MDI

source_name: Day1 TBT10 nM repl3


title: MC1643_MCR6000_BM


title: cold_JZ_WT_2


title: MC1640_MCR6008_BM


title: cold_JZ_rcf1_1


title: shRNA-PGC1a #66, rep-2

city: Boston

first: Pere

last: Puigserver

address: 450 Brookline Av. CLSB-11144

institute: Dana-Farber Cancer Institute

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, GCS3000, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file    annotate probes  yes The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file  annotate probes  yes.

source_name: A375P cells expressing PGC1a shRNA 66

label_protocol: The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) waas purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.

extract_protocol: Total RNA was isolated using RNeasy (Qiagen) according to the manufacturer's instructions. The Dana Farber Cancer Institute Microarray Core synthesized single-stranded cDNA from the extracted RNA. RNA ws converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out.

tag: cell type

value: Melanoma cell line

tag: cell line name

tag: expression

value: PGC1a shRNA 66


title: shRNA-PGC1a #66 rep-1


title: MC1632_MCR6017_BM


title: AA40


title: AA39


title: AA38


title: AA34


title: MC1635_MCR6006_BM


title: AA35


title: MC1637_MCR6007_BM


title: seminal vesicles from semen of vasectomized

value: vasectomized donors

tag: tissue

value: semen (pool of 3 donnors)

value: seminal microvesicles (SMVs)


title: cold_JZ_WT_1


title: shRNA-PGC1a #65 rep-2

source_name: A375P cells expressing PGC1a shRNA 65

value: PGC1a shRNA 65


title: JZ_rcf1_3

description:
A firefly luciferase reporter gene driven by the cold stress-responsive CBF2 promoter (-1500 bp to -1 bp upstream of the transcription start site) was introduced into Arabidopsis plants in the Columbia glabrous1 (gl1) background.
rcf1-1 under normal condition

source_name: rcf1-1, under normal growth condition

treatment_protocol: Fourteen-day-old Arabidopsis wild type and rcf1-1 seedlings grown on MS agar medium without cold treatment were used to extract total RNA.


title: seminal vesicles from semen of vasovasostomized

value: vasovasostomized donors

value: semen (pool of 5 donnors)


title: JZ_rcf1_2


title: MC0534_MCR0994_BM

value: Normal


title: JZ_rcf1_1


title: AA28

value: Myeloma


title: seminal vesicles from semen of controls

value: normal donors


title: MC0346_MCR6002_BM


title: JZ_WT_3

description:
A firefly luciferase reporter gene driven by the cold stress-responsive CBF2 promoter (-1500 bp to -1 bp upstream of the transcription start site) was introduced into Arabidopsis plants in the Columbia glabrous1 (gl1) background.
Wild type under normal condition

source_name: Wild type, under normal growth condition

value: whole seedlings


title: AA45


title: AA31


title: AA30


title: JZ_WT_2

value: Fourtheen-day-old


title: AA27


title: shRNA-PGC1a #65, rep-1


title: JZ_WT_1


title: CPEB1 knock-down replicate 3 Dye-swap

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios.

source_name: H.D. Myz cells transfected with an inducible CPEB1 specific sh-RNA replicate 3

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: Exponentially growing HD-Myz cells grown in Roswell Park Memorial Institute medium (RPMI-1640+glutaMAXTM-I), 10% FCS (fetal calf serum) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using the RNAspin Mini Kit (GE Healthcare). An additional treatment with DNAse was performed using the TURBO DNA-free Kit  (Ambion inc).
Quality assessment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: The CPEB1 KD HD-MyZ cell line was generated and treated as described before (Novoa, Gallego et al. 2010).

value: H.D. Myz

tag: genotype

value: CPEB1 knockdown with an inducible CPEB1-specific shRNA

source_name: H.D. Myz cells untreated replicate 3

treatment_protocol: H.D. Myz cells were untreated

value: untreated cells


title: AA22


title: shRNA-control-rep-1

source_name: A375P cells expressing Control shScr

value: Control shScr


title: shGFP-rep-2

source_name: A375P cells expressing Control shGFP

value: Melanoma cell line

value: Control shGFP


title: shGFP-rep-1


title: AA21


title: shRNA-control-rep-2


title: CPEB1 knock-down replicate 2

source_name: H.D. Myz cells transfected with an inducible CPEB1 specific sh-RNA replicate 2

source_name: H.D. Myz cells untreated replicate 2


title: PT12 estrogen withdrawal, replicate 2

status: Public on Feb 24 2013

city: Aurora

first: peter

last: kabos

address: 12801 E. 17th Avenue

department: Medicine

institute: University of Colorado Denver

description: Human breast cancer was xenografted in NOD/SCID mice

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 20 hr at 48C on HuGene 1.1ST Array strip. GeneStrips were washed and stained in the Affymetrix Gene Atlas fluidics station.

scan_protocol: GeneStrips were scanned using the Gene Atlas imaging station.

data_processing: The data were analyzed with Partek using RMA as normalization method.

source_name: Tumor

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: xenograft

tag: treatment

value: estrogen withdrawal


title: CPEB1 knock-down replicate 2 Dye-Swap


title: CPEB1 knock-down replicate 3


title: CPEB1 knock-down replicate 1 Dye-Swap

source_name: H.D. Myz cells transfected with an inducible CPEB1 specific sh-RNA replicate 1

source_name: H.D. Myz cells untreated replicate 1


title: Spike In C 20110412

city: Edmonton

first: Stephen

last: Tsoi

state: Alberta

address: 4-32G Agriculture/Forestry Cen

department: AFNS

institute: University of Alberta

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: GenePix 4200 Autoloader by Molecular Devices. Software is GenePix Pro, Acuity 4.0

data_processing: Lowess normalized within array and quantile normalized across arrays using Flexarray software.

organism: Sus scrofa

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

extract_protocol:
The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
amp protocol: This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: breed

value: Large White

tag: sample

value: cumulus-oocyte complexe


title: PT12 tamoxifen treated, replicate 3

value: tamoxifen treated


title: AA06

source_name: Promega female gDNA

source_name: CD138+ plasma cell genomic DNA


title: PT12 estrogen withdrawal, replicate 3


title: Slide6 1 C 2011 09 14

city: Madison

first: chi

last: zhou

state: WI

address: 202 S. Park Street, PAB1, Meriter Hospital

department: Department of OB/Gyn

institute: University of Wisconsin-Madison

description: Array 1

hyb_protocol: Hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

data_processing: lowess global normalized with array

source_name: 2-4-8 cell embryo

label_protocol:
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices) : This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
Labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent : ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: plh experiment

extract_protocol: PicoPure RNA Isolation Kit from Molecular Devices : The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

value: 2-4-8 cell embryo


title: PT12 tamoxifen treated, replicate 2


title: PT12 estrogen withdrawal, replicate 1


title: PT12 tamoxifen treated, replicate 1


title: PT12 estrogen treated, replicate 4

value: estrogen treated


title: CPEB1 knock-down replicate 1

tag: cell line


title: Spike In D 20110412


title: AA03

value: Normal


title: AA04

value: Myeloma


title: PT12 estrogen treated, replicate 2


title: PT12 control, replicate 3

value: control


title: AA02


title: PE4 control, replicate 1


title: AA01


title: PE4 estrogen treated, replicate 3


title: PE4 estrogen treated, replicate 1


title: PT12 control, replicate 1


title: LS174, SubAB, rep3

city: Amsterdam

first: Jarom

last: Heijmans

address: Meibergdreef 69-71

department: Tytgat Institute for liver and intestinal research

country: Netherlands

institute: Academic Medical Center

description: Replicate 3 of 3.

hyb_protocol: According to Illumina instructions.

scan_protocol: According to Illumina instructions on the BeadArray 500GX scanner.

data_processing: Data was extracted in GenomeStudio. No normalization was performed.

source_name: colon cancer cell line LS174, SubAB

label_protocol: Ambion cRNA synthesis for Illumina.

growth_protocol: DMEM 10% FCS penicillin/streptomycin.

extract_protocol: Trizol, subsequently Qiagen Rneasy cleanup.

treatment_protocol: 100 ng ml-1 SubAB or control SubAA272B for 20 hours.

value: colon cancer cells

value: SubAB


title: LS174, SubAB, rep2

description: Replicate 2 of 3.


title: LS174, control, rep1

description: Replicate 1 of 3.

source_name: colon cancer cell line LS174, control


title: PT12 estrogen treated, replicate 1


title: mock_D1_A1_1

status: Public on Feb 23 2013

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: Technical replicate 1.

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 one Agilent 4X44K Mouse Whole Genome Gene Expression Microarray (ID G4122F).

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. All arrays were required to pass Agilent QC flags. Microarray raw data have been extracted using the R Bioconductor limma package and median normalized using the NeONORM normalization method for inter-assay comparisons. Technical replicates were merged together by averaging the means of the signals, weighted by their coefficient of variation. Singular Value Decomposition Multidimensional Scaling (SVD-MDS) was used to assess the quality of the dataset by identifying outliers and subtracting biological conditions from the final dataset used for microarray analysis.

source_name: Lung, mock infection (PBS; control), day 1

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

growth_protocol: Five- to six-week-old female BALB/c mice were anesthetized and inoculated with 50 μl of phosphate-buffered salineintranasally inoculated with 106 PFU of virus (n = 45) or inoculated with phosphate-buffered saline (n = 6) in a 50 ul volume. Whole lungs were collected at days 1, 3, and 5 p.i. from infected animals (n = 3/time point/group) and from control animals (n = 2/time point) for microarray analysis. were anesthetized and inoculated with 50 μl of phosphate-buffered saline (PBS; Mock) or with 106 pfu of virus in a 50 μl volume. Nine animals per condition group were used for tarray analysis, three animals per time point. There were six condition groups: 1918 pandemic influenza virus, contemporary human H1N1 virus (A/Kawasaki/173/2001; K173), 1918HA/K173, 1918PB1/K173, 1918(3P+NP)/K173 and time-matched mocks.

extract_protocol: All TRIzol homogenates were phase-separated, and RNA was isolated from the aqueous phase using Qiagen RNeasy Mini columns according to the manufacturer's recommended protocol (Qiagen, Inc., Valencia, CA). 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: Lung tissue samples were stored in RNAlater at 4 degree C overnight and homogenized in 1ml of TRIzol reagent (Invitrogen) per 50-100 mg of tissue for subsequent RNA extraction.

tag: strain

value: BALB/c

tag: gender

value: female

value: lung

value: mock infection (PBS)

tag: time point

value: day 1 post-inoculation


title: mock_D5_A2_1

description: Technical replicate 1.

source_name: Lung, mock infection (PBS; control), day 5

value: day 5 post-inoculation


title: mock_D3_A1

source_name: Lung, mock infection (PBS; control), day 3

value: day 3 post-inoculation


title: LS174, control, rep3

description: Replicate 3 of 3.


title: PE4 estrogen treated, replicate 2


title: K173_D5_A1

source_name: Lung, K173 virus infection, day 5

value: K173 virus infection


title: LS174, control, rep2

description: Replicate 2 of 3.


title: LS174, SubAB, rep1

description: Replicate 1 of 3.


title: PE4 control, replicate 2


title: PE4 control, replicate 3


title: mock_D1_A2


title: mock_D3_A2


title: mock_D1_A1_2

description: Technical replicate 2.


title: mock_D5_A2_2

description: Technical replicate 2.


title: K173_D5_A2


title: K173_D5_A3


title: mock_D5_A1


title: K173_D3_A3

source_name: Lung, K173 virus infection, day 3


title: PT12 control, replicate 2


title: PT12 estrogen treated, replicate 3


title: K173_D3_A1_3

description: Technical replicate 3.


title: K173_D1_A3

source_name: Lung, K173 virus infection, day 1


title: 1918PB1/K173_D5_A1

source_name: Lung, 1918PB1/K173 virus infection, day 5

value: 1918PB1/K173 virus infection


title: K173_D3_A1_1

description: Technical replicate 1.


title: 1918PB1/K173_D5_A3


title: K173_D3_A2


title: K173_D1_A1


title: K173_D3_A1_2

description: Technical replicate 2.


title: K173_D1_A2


title: 1918PB1/K173_D5_A2


title: 1918PB1/K173_D1_A2_2

description: Technical replicate 2.

source_name: Lung, 1918PB1/K173 virus infection, day 1


title: 1918HA/K173_D5_A1

source_name: Lung, 1918HA/K173 virus infection, day 5

value: 1918HA/K173 virus infection


title: 1918PB1/K173_D3_A3_1

description: Technical replicate 1.

source_name: Lung, 1918PB1/K173 virus infection, day 3


title: 1918PB1/K173_D1_A3


title: 1918PB1/K173_D3_A3_2

description: Technical replicate 2.


title: 1918PB1/K173_D1_A1


title: 1918HA/K173_D3_A2

source_name: Lung, 1918HA/K173 virus infection, day 3


title: 1918HA/K173_D3_A3


title: 1918PB1/K173_D1_A2_1

description: Technical replicate 1.


title: 1918_10^6_D5_A1_2

description: Technical replicate 2.

source_name: Lung, 1918 virus infection, day 5

value: 1918 virus infection


title: 1918HA/K173_D1_A1

source_name: Lung, 1918HA/K173 virus infection, day 1


title: 1918_10^6_D5_A1_1

description: Technical replicate 1.


title: 1918PB1/K173_D3_A1


title: 1918HA/K173_D3_A1_2

description: Technical replicate 2.


title: 1918HA/K173_D1_A2


title: 1918HA/K173_D3_A1_1

description: Technical replicate 1.


title: 1918_10^6_D3_A3

source_name: Lung, 1918 virus infection, day 3


title: 1918HA/K173_D1_A3


title: 1918_10^6_D1_A2

source_name: Lung, 1918 virus infection, day 1


title: Embryonic stem cells sample 3 (ESC_3)

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: Embryonic stem cells (ESCs)

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol: Embryonic stem cells (ESCs, line R1) were grown under standard conditions on MEF feeder plus murine leukemia inhibitory factor (LIF).

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

tag: esc line

value: embryonic stem cells


title: 1918_10^6_D3_A1


title: 1918_10^6_D3_A2


title: Embryonic stem cells sample 2 (ESC_2)


title: 1918_10^6_D1_A1


title: Embryonic stem cells sample 1 (ESC_1)


title: 1918(3P+NP)/K173_D5_A2

source_name: Lung, 1918(3P+NP)/K173 virus infection, day 5

value: 1918(3P+NP)/K173 virus infection


title: Embryoid body (EB) assays of parthenogenetic stem cells sample 1 (EB_PSC_1)

growth_protocol: Parthenogenetic stem cells (PSCs) were subjected to differentiation in embryoid body (EB) assays and cultured for 15 days.

value: embryoid body parthenogenetic stem cells


title: Siliques - stage 17 - biological replicate 1

city: Minneapolis

first: Kevin

middle: A

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

description: Gene Expression data from Arabidopsis siliques collected at stage 17 of fruit development

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to the AtMtDEFL custom Array. GeneChips were washed and stained using the MAUI 12-bay hybridization system.

scan_protocol: GeneChips were scanned using the MAUI 12-bay hybridization system.

data_processing:
Microarray normalizations and initial analyses were performed in R using custom scripts that made use of Bioconductor routines. To implement the Stable-genes Based Quantile (SBQ) normalization (Sato et al., 2007), we first combined expression data from all 11 probes within a probe set into a single expression measure using the Bioconductor expression command, using RMA-style background correction and median polish probe summarization.  These summarized values were output from R and used as input to the SBQ perl script (Sato et al., 2007).For statistical analysis, SBQ normalized signal intensity values were Log2 transformed and statistical analysis was based on a t-test or ANOVA (P<0.05) with Benjamini and Hochberg false discovery rate multiple testing correction (Benjamini and Hochberg, 1995), and the corrected p values were designated as q values.
Note: The data for siliques was normalized separately due to the 2-step extraction procedure and are not likely to be quantitatively comparable with the rest of the data.

source_name: Arabidopsis siliques collected at tage 17 of fruit development

label_protocol: Biotinylated cRNA was prepared using the two-cycle target Affymetrix labeling protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001. And the array was hybridized with 10 ug of biotin-labelled cRNA.

value: wildtype

tag: plant age

value: 50 days old

tag: treatment-time

value: Siliques


title: Siliques - stage 17 - biological replicate 2

tag: genotype/variation


title: Siliques - stage 17 - biological replicate 3


title: Seedlings-7 days - biological replicate 3

description: Gene Expression data from Arabidopsis seedlings collected at 7days after planting on MS plates supplemented with 1% sucrose in 1% agar.

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

value: 7 days old

value: Seedlings


title: Embryoid body (EB) assays of parthenogenetic stem cells sample 2 (EB_PSC_2)

tag: cell type


title: 1918(3P+NP)/K173_D3_A3

source_name: Lung, 1918(3P+NP)/K173 virus infection, day 3

value: BALB/c

value: female

value: lung


title: 1918(3P+NP)/K173_D5_A3

value: day 5 post-inoculation


title: 1918(3P+NP)/K173_D5_A1_2

description: Technical replicate 2.


title: Parthenogenetic stem cells sample 2 (PSC_2)

source_name: Parthenogenetic stem cells (PSCs)

growth_protocol: Parthenogenetic stem cells (PSCs) were obtained from superovulated mice. Oocytes were stimulated with strontium-chloride and allowed to develop into blastocysts for isolating PSC at day 6.

value: parthenogenetic stem cells


title: 1918_10^6_D1_A3

value: day 1 post-inoculation


title: Seedlings-14 days - biological replicate 3

description: Gene Expression data from Arabidopsis seedlings collected at 14 days after planting on MS plates supplemented with 1% sucrose in 1% agar.

value: 14 days old


title: 1918(3P+NP)/K173_D5_A1_1

description: Technical replicate 1.


title: Parthenogenetic stem cells sample 1 (PSC_1)


title: 1918(3P+NP)/K173_D3_A1_2

description: Technical replicate 2.

value: day 3 post-inoculation


title: 1918(3P+NP)/K173_D3_A1_1

description: Technical replicate 1.


title: 1918(3P+NP)/K173_D1_A2

source_name: Lung, 1918(3P+NP)/K173 virus infection, day 1


title: Seedlings-14 days - biological replicate 2

source_name: Arabidopsis seedlings collected at 14 days after planting on MS plates supplemented with 1% sucrose in 1% agar.


title: Seedlings-14 days - biological replicate 1


title: Seedlings-7 days - biological replicate 2

source_name: Arabidopsis seedlings collected at 7days after planting on MS plates supplemented with 1% sucrose in 1% agar.


title: Roots-21 days biological replicate 2

description: Gene Expression data from Arabidopsis roots collected at 21 days after planting.

value: 21 days old

value: Roots


title: Roots-21 days biological replicate 3

source_name: Arabidopsis roots collected at 21 days after planting.


title: Seedlings-7 days - biological replicate 1


title: Roots-21 days biological replicate 1


title: Hrcc-9 Leaves- biological replicate 3

description: Gene Expression data from four week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 lacking hrcC and leaf samples were collected 9 hours post inoculation.

source_name: Four week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 lacking hrcC and leaf samples were collected 9 hours post inoculation.

value: 28 days old

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3000 lacking hrcC

value: 9 hours

value: Leaves


title: Hrcc-9 Leaves- biological replicate 2

value: wildtype


title: Hrcc-9 Leaves- biological replicate 1


title: Hrcc-3 Leaves- biological replicate 3

description: Gene Expression data from four week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 lacking hrcC and leaf samples were collected 3 hours post inoculation.

source_name: Four week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 lacking hrcC and leaf samples were collected 3 hours post inoculation.

value: 3 hours


title: Hrcc-3 Leaves- biological replicate 2


title: Hrcc-3 Leaves- biological replicate 1


title: 1918(3P+NP)/K173_D3_A2

value: 1918(3P+NP)/K173 virus infection


title: Parthenogenetic stem cells sample 3 (PSC_3)


title: DC3000-9 Leaves- biological replicate 3

description: Gene Expression data from four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 and leaf samples were collected 9 hours post inoculation.

source_name: Four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 and leaf samples were collected 9 hours post inoculation.

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3005


title: DC3000-9 Leaves- biological replicate 2

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3004


title: Colletotrichum infected leaves-24hpi-biological rep3

description: Gene expression data from leaves of plants innoculated with Colletotrichum trifolii

data_processing: Microarray normalizations and initial analyses were performed in R using custom scripts that made use of Bioconductor routines. To implement the Stable-genes Based Quantile (SBQ) normalization (Sato et al., 2007), we first combined expression data from all 11 probes within a probe set into a single expression measure using the Bioconductor expression command, using RMA-style background correction and median polish probe summarization.  These summarized values were output from R and used as input to the SBQ perl script (Sato et al., 2007).For statistical analysis, SBQ normalized signal intensity values were Log2 transformed and statistical analysis was based on a t-test or ANOVA (P<0.05) with Benjamini and Hochberg false discovery rate multiple testing correction (Benjamini and Hochberg, 1995), and the corrected p values were designated as q values.

organism: Medicago truncatula

source_name: Medicago truncatula leaves infected with Colletotrichum trifolii were harvested from plants at 24 hours.

value: 20 days

value: inoculated with Colletotrichum trifoli

value: 24 hours

value: leaves


title: A498 control (exp 2)

city: Lund

first: Nataliya

last: Lutay

address: Sölvegatan 23

country: Sweden

institute: Lund University

description: The second experiment with A498 cells

hyb_protocol: aRNA fragmentation and hybridisation was conducted using GeneChip® 3' IVT Express Kit and Affymetrix Human Genome U219 arrays (Affymetrix).

scan_protocol: The arrays were scanned using a GeneAtlas Personal Microarray Systems.

data_processing: The data was normalized using Robust Multi Average (RMA) implemented in the Partek® Genomics Suite™.

source_name: A498 human kidney carcinoma cell line

label_protocol: Total RNA was converted to aRNA (double stranded cDNA). aRNA labelling with biotin was performed using GeneChip® 3' IVT Express Kit (Affymetrix).

growth_protocol: E. coli 83972 was grown on tryptic soy agar (16 h, 37˚C). The human epithelial cell line A498 (ATCC HTB44, human kidney carcinoma, Manassas, VA, USA) was cultured in RPMI-1640 supplemented with 1 mM sodium pyruvate, 1 mM non-essential amino acids, gentamicin (50μg/ml) and 5% fetal calf serum (Invitrogen). Bacteria activation of the cells was studied on confluent cell layers in 6-well tissue culture plates (Nunc, Roskilde, Denmark).

extract_protocol: Total RNA was extracted 4 hrs after treatment by RNeasy mini kit (Qiagen).

treatment_protocol: Cell culture medium was aspirated and replaced with fresh serum-free RPMI with gentamicin. E. coli 83972 was added at a concentration of 109 cfu/ml, DRB was used at a concentration of 60 μM. The control sample was treated with 0.08 % of DMSO.

tag: protocol

value: incubated with RPMI medium containing 0.08 % DMSO for 4 h


title: DC3000-9 Leaves- biological replicate 1

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

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3003


title: Colletotrichum infected leaves-24hpi-biological rep1


title: Colletotrichum infected leaves-24hpi-biological rep2


title: Patient_3_24h_inoculation

hyb_protocol: RNA hybridisation and microarray analysis was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using Affymetrix Human Genome U219 arrays (Affymetrix).

data_processing: Affymetrix data was normalized using Robust Multi Average (RMA) implemented in the free software packages R and Bioconductor.

source_name: Peripheral blood lymphocytes from patient 3 after inoculation with E. coli 83972

label_protocol: RNA labelling was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using GeneChip® 3' IVT Express Kit (Affymetrix).

growth_protocol: E. coli 83972 was cultured on tryptic soy agar (16 h, 37˚C), harvested in phosphate-buffered saline (PBS, pH 7.2, 1010 CFU/ml) and diluted as appropriate.

extract_protocol: Patient RNA was extracted from peripheral blood lymphocytes, using QIAamp RNA Blood Mini Kit (Qiagen).

treatment_protocol: Before inoculation, patients were treated with appropriate antibiotics to sterilize the urine and after an antibiotic free interval, the patients were catheterized. After emptying the bladder, 30 ml of E. coli 83972 (105 cfu/ml) in phosphate-buffered saline was instilled.

value: female

tag: bacterial numbers in urine


title: Mock leaves-24hpi-biological rep3

description: Gene expression data from leaves of plants mock innoculated with sterile water + drop of tween20 and used as control for Colletotrichum trifolii infected leaves

source_name: Medicago truncatula leaves treated with sterile water were harvested from mock inoculated plants at 24 hours.

value: mock inoculated

tag: tissue


title: Mock leaves-24hpi-biological rep2


title: Patient_2_24h_inoculation

scan_protocol: RNA hybridisation and microarray analysis was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using Affymetrix Human Genome U219 arrays (Affymetrix).

source_name: Peripheral blood lymphocytes from patient 2 after inoculation with E. coli 83972

value: male

value: 2x108 CFU/ml


title: DC3000-3 Leaves- biological replicate 3

description: Gene Expression data from four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 and leaf samples were collected 3 hours post inoculation.

source_name: Four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 and leaf samples were collected 3 hours post inoculation.

value: 28 days old

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3002


title: 1918(3P+NP)/K173_D1_A3

value: BALB/c

value: lung

value: day 1 post-inoculation


title: DC3000-3 Leaves- biological replicate 2

value: wildtype

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3001

value: 3 hours

value: Leaves


title: A498 83972 (exp 2)

description: The second experiment with A498 cells

value: incubated with 108 cfu/ml of E. coli 83972 for 4 h


title: DC3000-3 Leaves- biological replicate 1

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3000


title: Mock leaves-24hpi-biological rep1

value: 20 days

value: 24 hours

value: leaves


title: Phytophthora infected roots-4dpi-biological rep3

description: Gene expression data from hypocotyl and root segments of plants innoculated with Phytophthora medicaginis M2019

source_name: Medicago truncatula hypocotyl and root segments infected with Phytophthora medicaginis M2019 were harvested from 4dpi plants.

value: 9 days

value: inoculated with Phytophthora medicaginis M2019

value: 4 days

value: roots


title: Phytophthora infected roots-4dpi-biological rep2


title: AvrRpt2-9 Leaves- biological replicate 3

description: Gene Expression data from four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 carrying AvrRpt and leaf samples were collected 9 hours post inoculation.

source_name: Four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 carrying AvrRpt and leaf samples were collected 9 hours post inoculation.

value: 28 days old

value: Inoculated with Pseudomonas syringae pv. tomato strain DC3000 carrying AvrRpt

value: 9 hours


title: Patient_3_sterile

source_name: Peripheral blood lymphocytes from patient 3 before inoculation

value: female

value: 0 CFU/ml


title: AvrRpt2-9 Leaves- biological replicate 2

value: wildtype


title: Phytophthora infected roots-4dpi-biological rep1


title: Mock roots-4dpi-biological rep3

description: Gene expression data from hypocotyl and root segments of plants mock innoculated with sterile water and used as control for Phytophthora medicaginis M2019 infected roots

source_name: Medicago truncatula hypocotyl and root segments treated with sterile water were harvested from mock inoculated plants at 4dpi.

value: mock inoculated


title: AvrRpt2-9 Leaves- biological replicate 1

value: Leaves


title: Patient_1_24h_inoculation

source_name: Peripheral blood lymphocytes from patient 1 after inoculation with E. coli 83972

value: male


title: Patient_2_sterile

source_name: Peripheral blood lymphocytes from patient 2 before inoculation


title: AvrRpt2-3 Leaves- biological replicate 3

description: Gene Expression data from four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 carrying AvrRpt and leaf samples were collected 3 hours post inoculation.

source_name: Four-week-old Arabidopsis plants were inoculated with Pseudomonas syringae pv. tomato strain DC3000 carrying AvrRpt and leaf samples were collected 3 hours post inoculation.

value: 3 hours


title: AvrRpt2-3 Leaves- biological replicate 2


title: AvrRpt2-3 Leaves- biological replicate 1


title: Mock roots-4dpi-biological rep2


title: Mock roots-4dpi-biological rep1


title: Nodulated roots-14dpi-biological rep3

description: Gene expression data from nodulated roots excluding the roots tip of plants  innoculated with Sinorhizobium meliloti Sm1021

source_name: Medicago truncatula 5-cm root with 14 dpi nodules were collected from Sinorhizobium meliloti Sm1021 inoculated plants

value: 19 days

value: inoculated with Sinorhizobium meliloti Sm1021

value: 14 days


title: Mock Leaves- 9 hours post inoculation  - biological replicate 3

description: Gene Expression data from four-week-old Arabidopsis plants were mock-inoculated with with 5 mM MgSO4 and leaf samples were collected 9 hours post inoculation.

source_name: Four-week-old Arabidopsis plants were mock-inoculated with with 5 mM MgSO4 and leaf samples were collected 9 hours post inoculation.

value: Mock inoculated  with  5 mM MgSO7


title: Mock Leaves- 9 hours post inoculation  - biological replicate 2


title: Patient_1_sterile

source_name: Peripheral blood lymphocytes from patient 1 before inoculation


title: Nodulated roots-14dpi-biological rep1


title: Nodulated roots-14dpi-biological rep2


title: Mock Leaves- 9 hours post inoculation  - biological replicate 1


title: Mock Leaves- 3 hours post inoculation  - biological replicate 3

description: Gene Expression data from four-week-old Arabidopsis plants were mock-inoculated with with 5 mM MgSO4 and leaf samples were collected 3 hours post inoculation.

source_name: Four-week-old Arabidopsis plants were mock-inoculated with with 5 mM MgSO4 and leaf samples were collected 3 hours post inoculation.


title: Mock Leaves- 3 hours post inoculation  - biological replicate 2


title: Mock roots-14dpi-biological rep3

description: Gene expression data from root segments excluding the roots tip of plants mock innoculated with sterile water and used as control for Sinorhizobium meliloti Sm1021 innoculated roots.

source_name: Medicago truncatula 5-cm root segments treated with sterile water corresponding to the regions harvested for 14 dpi nodules were collected from mock-inoculated plants


title: Mock roots-14dpi-biological rep2


title: Mock roots-14dpi-biological rep1


title: Mycorrhizal GI roots -28dpi-biological rep3

description: Gene expression data from mycorrhizal roots excluding the roots tip of plants  innoculated with Glomus intraradices.

source_name: Medicago truncatula mycorrhizal roots of Glomus intraradices inoculated plants were harvested at 28dpi

value: 49 days

value: inoculated with Glomus intraradices

value: 28 days


title: A498 DRB (exp 2)

description: The second experiment with A498 cells

source_name: A498 human kidney carcinoma cell line

value: incubated with 60 μM DRB for 4 h


title: Mock Leaves- 24 hours post inoculation  - biological replicate 3

description: Gene Expression Data from twenty old day old Arabidopsis plants were mock-inoculated with with sterile water containing 0.02% Tween-20  and leaf samples were collected 24 hours post inoculation.

source_name: Twenty old day old Arabidopsis plants were mock-inoculated with with sterile water containing 0.02% Tween-20 and leaf samples were collected 24 hours post inoculation.

value: 28 days old

value: Mock inoculated  with  with sterile water containing 0.02% Tween-20

value: 24 hours


title: Mock Leaves- 24 hours post inoculation  - biological replicate 2


title: 1918(3P+NP)/K173_D1_A1

source_name: Lung, 1918(3P+NP)/K173 virus infection, day 1

value: BALB/c

value: female

value: lung

value: 1918(3P+NP)/K173 virus infection

value: day 1 post-inoculation


title: Mycorrhizal GI roots -28dpi-biological rep2

value: roots


title: Mycorrhizal GI roots -28dpi-biological rep1


title: Infloresences - biological replicate 3

description: Gene Expression data fron Arabidopsis inflorescences  at stages -2 to 0 days post anthesis

value: wildtype

value: 40 days old

value: Infloresences


title: Mock Leaves- 24 hours post inoculation  - biological replicate 1

value: Leaves


title: Mock GI roots-28dpi-biological rep1

description: Gene expression data from roots excluding the roots tip of plants  innoculated with sterile water and used as control for Glomus intraradices infected roots.

source_name: Medicago truncatula roots treated with sterile water were harvested from mock inoculated plants at 28dpi

value: 49 days

value: mock inoculated


title: Infloresences - biological replicate 1

source_name: Arabidopsis inflorescences at stages -2 to 0 days post anthesis


title: Mock Leaves- 3 hours post inoculation  - biological replicate 1

value: Mock inoculated  with  5 mM MgSO7

value: 3 hours


title: Mock GI roots-28dpi-biological rep3

value: 28 days


title: Mock GI roots-28dpi-biological rep2


title: Seeds-10to21dap-biological rep3

description: Gene expression data from a pool of 10 to 21 dap seeds

source_name: Medicago truncatula seeds were collected 10-21 days after pollination (dap) from 98-day-old plants

extract_protocol: Total RNA from Medicago seeds was extracted using the Spectrum Plant Total RNA Kit (Sigma) following the manufacturer’s instructions.

value: 98 days

value: seed


title: Seeds-10to21dap-biological rep1


title: Seeds-10to21dap-biological rep2


title: Flowers-biological rep1

description: Gene expression data from a pool of closed and open flowers

source_name: Medicago truncatula closed flowers (with petals bigger than the sepals) and open flowers were harvested from 80-day-old plants

value: 80 days

value: flower


title: Alternaria challenged dde2 mutant Leaves-24 hpi-biological rep 2

description: Gene Expression data from twenty one day old Arabidopsis dde2 mutant plants inoculated with spores of Alternaria brassicicola strain ATCC96866 and challenged leaves that were collected  24 hours after inoculation.

source_name: Twenty one day old Arabidopsis dde2 mutant plants were inoculated with spores of Alternaria brassicicola strain ATCC96866 and challenged leaves were collected 24 hours after inoculation.

value: dde2 mutant

value: 21 days old

value: Inoculated with spores of Alternaria brassicicola strain ATCC96866

value: 24 hours


title: Flowers-biological rep2


title: Flowers-biological rep3


title: Alternaria challenged dde2 mutant Leaves-24 hpi-biological rep 1


title: Alternaria challenged dde2 mutant Leaves-24 hpi-biological rep 3


title: Flower buds-biological rep3

description: Gene expression data from flower buds that were 6 - 8 mm in size (measured from the base of the bud excluding the petiole to the tip of the sepals), tightly closed and whose petals had not emerged beyond the sepals were collected

source_name: Medicago truncatula flower buds that were 6 - 8 mm in size were collected from 80-day-old plants

value: buds


title: Flower buds-biological rep1


title: Infloresences - biological replicate 2

value: wildtype

value: 40 days old


title: Alternaria challenged Leaves-24 hpi-biological rep 3

description: Gene Expression data from twenty one day old Arabidopsis plants inoculated with spores of Alternaria brassicicola strain ATCC96866 and challenged leaves that were collected  24 hours after inoculation.

source_name: Twenty one day old Arabidopsis plants were inoculated with spores of Alternaria brassicicola strain ATCC96866 and challenged leaves were collected 24 hours after inoculation.

value: Leaves


title: Alternaria challenged Leaves-24 hpi-biological rep 2


title: Stems-8week-biological rep2

description: Gene expression data from stems

source_name: Medicago truncatula stem segments consisting of the 5th and 6th internodes from the shoot apex were collected from 8-week-old plants

value: 8 weeks

value: stem


title: Stems-8week-biological rep1

description: Gene expression data from stems


title: Stems-8week-biological rep3

description: Gene expression data from stems


title: Flower buds-biological rep2


title: A498 83972 #3

description: Gene expression data from A498 cells infected with E. coli 83972

hyb_protocol: Labelled cRNAs were hybridized onto an Illumina HumanHT-12 Expression Beadchip for 16 hours at 58°C.

scan_protocol: The arrays were scanned using a BeadArray Scanner 500GX.

data_processing: Preprocessed data was normalized using the cross-correlation method.

label_protocol: RNA was reverse-transcribed to double-stranded cDNA and converted to biotin-labelled cRNA using a TargetAmp Nano-g Biotin-aRNA Labelling kit (Epicentre Biotechnologies, Madison, USA).

growth_protocol: Bacteria were cultured on tryptic soy agar (16 h, 37˚C). The human epithelial cell line A498 (ATCC HTB44, human kidney carcinoma, Manassas, VA, USA) was cultured in RPMI-1640 supplemented with 1 mM sodium pyruvate, 1 mM non-essential amino acids, gentamicin (50μg/ml) and 5% fetal calf serum (Invitrogen). Bacteria activation of the cells was studied on confluent cell layers in 6-well tissue culture plates (Nunc, Roskilde, Denmark).

extract_protocol: Total RNA was extracted 4 hrs after infection by acid guanidinium thiocyanate-phenol-chloroform extraction (Trizol, Invitrogen, USA) followed by a Qiagen RNeasy clean-up procedure.

treatment_protocol: Cell culture medium was aspirated and replaced with fresh serum-free RPMI containing  E. coli 83972 or  E. coli CFT073 (108 cfu/ml).

value: incubated with 108 cfu/ml of E. coli 83972 for 4 h

tag: serotype


title: A498 83972 #2


title: A498 control #3

description: Gene expression data from control A498 cells

value: incubated with RPMI medium for 4 h

value: Not present


title: A498 CFT073 #1

description: Gene expression data from A498 cells infected with E. coli CFT073

value: incubated with 108 cfu/ml of E. coli CFT073 for 4 h


title: A498 CFT073 #2


title: A498 control #2


title: Alternaria challenged Leaves-24 hpi-biological rep 1


title: badR-MT Array2Rep1

status: Public on Feb 22 2013

city: San Antonio

first: Janakiram

last: Seshu

state: Texas

address: One UTSA Circle

institute: The University of Texas at San Antonio

description: This sample is of  Borrelia burgdorferi B31-A3 deficient of the gene ID BB0693, gene we are calling BadR. It is the third of four mutant biological replicates used in this experiment, each from separate cultures.

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their 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: Borreliella burgdorferi B31

source_name: B. burgdorferi B31-badR-deficient strain

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

growth_protocol: WT B31-A3 and badR-deficient strains were cultured in Barbour-Stoenner-Kelly (BSK)-II medium with 6% rabbit serum (Pel-Freez) at 32°C in a CO2 (1%) incubator until mid-log phase (5x107 cells/ml).

extract_protocol: RNA preparation was accomplished using phenol chloroform extraction (Tel-Test, Inc.) followed by  DNAse I digestion twice at 37°C for 45 min with DNase I.  RNA was cleaned using RNeasy MiniElute (Qiagen Inc., Valencia, CA, USA) and the total RNA was quantified spectrophotometrically.

value: deficient of Gene ID BB0693, replaced gene with streptomycin resistant cassette


title: badR-MT Array2Rep2

description: This sample is of  Borrelia burgdorferi B31-A3 deficient of the gene ID BB0693, gene we are calling BadR. It is the fourth of four mutant biological replicates used in this experiment, each from separate cultures.


title: A3-WT Array2Rep2

description: This sample is of wild-type Borrelia burgdorferi B31-A3. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures.

source_name: B. burgdorferi B31-A3 wildtype


title: A498 83972 #1


title: Germinating_seed-24h-biological rep2

description: Gene expression data from germinating seeds

source_name: Medicago truncatula germinating seeds with radicles 8 – 12 mm long, were collected at 24 h post-germination

extract_protocol: Total RNA from Medicago germinating seeds was extracted using the Spectrum Plant Total RNA Kit (Sigma) following the manufacturer’s instructions.

value: germinating seeds


title: A3-WT Array1Rep2

description: This sample is of wild-type Borrelia burgdorferi B31-A3. It is the secondof four wild-type biological replicates used in this experiment, each from separate cultures.


title: badR-MT Array1Rep1

description: This sample is of  Borrelia burgdorferi B31-A3 deficient of the gene ID BB0693, gene we are calling BadR. It is the first of four mutant biological replicates used in this experiment, each from separate cultures.


title: badR-MT Array1Rep2

description: This sample is of  Borrelia burgdorferi B31-A3 deficient of the gene ID BB0693, gene we are calling BadR. It is the second of four mutant biological replicates used in this experiment, each from separate cultures.


title: A3-WT Array2Rep1

description: This sample is of wild-type Borrelia burgdorferi B31-A3. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures.


title: Germinating_seed-24h-biological rep3

value: Germinating seeds


title: Germinating_seed-24h-biological rep1


title: L control

city: Deajeon

first: Heui Man

last: Kim

state: Deajeon

address: 99 Daehak ro

department: College of Veterinary Medicine

country: South Korea

institute: Chungnam national university

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto an assembled Agilent's Canine Oligo Microarray (44K). The arrays were hybridized at 65oC for 17 hours using an Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as per the manufacturer's washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent's DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization. All data normalization and selection of fold-changed genes were performed using GeneSpring GX 7.3 (Agilent Technology, USA). The averages of the normalized ratios were calculated by dividing the average of the normalized signal channel intensity by the average of the normalized control channel intensity. Functional annotation of genes was performed according to the Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpring GX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

organism: Canis lupus familiaris

source_name: Uninfected dog

label_protocol: Amplified and labeled cRNA was purified using the cRNA Cleanup Module (Agilent Technology) according to the manufacturer's protocol. Labeled cRNA target was quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: In vivo (dog's lung).

extract_protocol: RNA extraction was performed using Trizol.

treatment_protocol: Influenza virus uninfected.

value: lung


title: ROE2 cells-day 9

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description:
The ROE2 cell line is derived from the tongue of an 18-day-old fetus.
ROE2 cells cultured for 9 days at 37°C.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h. The arrays were washed, and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned with a probe array scanner (Affymetrix).

data_processing: GeneChip Analysis Suite. The data were processed using RMA.

organism: Rattus norvegicus

source_name: Rat oral epithelial cell line ROE2, day 9

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: ROE2 cells were cultured in DMEM/F12 medium supplemented with 2% fetal bovine serum (FBS), 1% ITES (2.0 mg/l insulin, 2.0 mg/l transferrin, 0.122 mg/l ethanolamine and 9.14 μg/l sodium selenite), and 10 ng/ml epidermal growth factor (EGF) in a collagen type I-precoated culture dish at 33˚C.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: ROE2 cells were cultured in DMEM/F12 medium supplemented with 2% FBS, 1% ITES, and 10 ng/ml EGF in a collagen type I-precoated culture dish at 33˚C. After 24 h, the culture temperature was shiftted to 37˚C, and then the cells were cultured for 0, 3, 6 and 9 days.

value: oral epithelial cell line

value: culture at 37˚C

value: day 9

tag: strain/background

value: Transgenic rat (Wistar strain) which has a tsSV40 large T-antigen gene [pSVtsA58ori(-)-2]

tag: morphology

value: epithelial-like

tag: life span

value: infinite


title: blood_pat025_T0

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

institute: University of Granada

description: CRT: Chemoradiation; Cap: Capecitabine; Capox: Capecitabine and Oxaliplaine; cTN: clinical Stage, LAR: Low anterior resection, APR: Abdmino-perineal resection; HART: Hartmann, TRG: Tumor Regression Grade; Downst: Downstaging; Downs: downsizing,  Resp: response, ypRC: complete response after chemoradiation.

hyb_protocol: Hybridization of whole genome human genes included in CodeLink bioarrays (Applied Microarrays, Tempe, AZ, USA) was performed overnight at 37°C in a shaker incubator (Innova 4080, New Brunswick®, NJ, U.S.A.). The hybridization reactions were done in duplicate.

scan_protocol: Microrrays were read with a GenePix 4000B laser scanner (Axon Instruments, CA, USA)

data_processing: Microrrays were read quantified and normalized using CodeLink Software 5.0 (Applied Microarrays, Tempe, AZ, USA).

source_name: Peripheral blood from rectal cancer patient

label_protocol: reverse transcription cRNAs were labeled with Cy5 Streptavidine (Amersham Biosciences, Sweden)

extract_protocol: Total RNAs were extracted from 12 mL of peripheral blood mononuclear cells (BCs) samples before treatment from each study participant using PAXgene Blood RNA System (PreAnalytix, Becton Dickinson, San Diego, CA, USA) according to manufacturer's instructions. Quantity and integrity of RNAs were checked by spectrophotometry in a NanoDropTM (ND-1000, DE, USA) and in an ExperionTM automated electrophoresis system (Bio-Rad, Richmond, VA, USA), respectively.

treatment_protocol: The group of study consisted of 27 locally advanced rectal cancer (LARC) patients from the Division of Colon & Rectal Surgery, HUVN, Granada, Spain. To qualify for this study, rectal carcinomas had to be on the stage II or stage III according the criteria of the International Union Against Cancer’s (UICC), without systemic metastases in the positron emission tomography scan and no known second neoplasm. The diagnosis of rectal cancer was confirmed by the histopathological analysis of endoscopic biopsies. The study was approved by the local ethics committee. Informed consent was obtained from all patients before the study. After the initial staging, all patients qualifying for this study received neoadjuvant radiotherapy (28 fractions of 1.8 Gy, 5 fractions/week) with concomitant chemotherapy (capecitabine, 825 mg/m2, twice daily alone or in combination with oxaliplatine 50 mg/m2 once weekly). Standardised surgery, including total mesorectal excision, was performed 8 weeks after the standardised CRT protocol described above.  Standard pathologic tumor staging of the resected specimen was performed according to UICC guidelines and the tumour regression grade (TRG). Mandard classifications were assigned by at least one specialized gastrointestinal pathologist. For this study, patients with TRG 1 and 2 and downstaging were considered as responders whereas patients classified with regression grades 3 to 5 and no downstaging were treated as non-responders. Downstaging was defined as reduction of pathologic staging (ypStage) in relation to pretreatment stage (cStage) (i.e., cII to ypI, cIII to ypII or ypI).

tag: crt

value: Capox

tag: ctn

tag: cir

value: APR

tag: ypt

tag: ypn

tag: trg

tag: downst

value: No

tag: downs

tag: resp

tag: yprc

tag: leucocytes (x103xml)

tag: lymphocytes (%)

tag: granulocytes (%)

tag: monocytes (x103xμl)


title: K9

source_name: Infected dog

treatment_protocol: Dogs were intranasally infected with 10^6 log10 infectious dose 50/ml of A/Korea/S1/Canine/2012 (H3N2).

tag: tissue

tag: treatment

value: influenza virus H3N2


title: blood_pat018_T0

value: LAR


title: blood_pat017_T0

value: HART


title: blood_pat013_T0

value: Cap

value: Yes


title: blood_pat014_T0


title: blood_pat011_T0


title: blood_pat023_T0


title: blood_pat026_T0


title: ROE2 cells-day 3

description:
The ROE2 cell line is derived from the tongue of an 18-day-old fetus.
ROE2 cells cultured for 3 days at 37°C.

source_name: Rat oral epithelial cell line ROE2, day 3

tag: cell line

tag: cell type

tag: time point

value: day 3

tag: strain/background

tag: morphology

tag: life span


title: blood_pat024_T0

tag: crt

tag: ctn

tag: cir

tag: ypt

tag: ypn

tag: trg


title: ROE2 cells-day 6

description:
The ROE2 cell line is derived from the tongue of an 18-day-old fetus.
ROE2 cells cultured for 6 days at 37°C.

source_name: Rat oral epithelial cell line ROE2, day 6

value: day 6


title: blood_pat010_T0

tag: downst

tag: downs

tag: resp

tag: yprc

tag: leucocytes (x103xml)

tag: lymphocytes (%)


title: blood_pat022_T0

tag: granulocytes (%)

tag: monocytes (x103xμl)


title: blood_pat021_T0


title: blood_pat020_T0


title: blood_pat009_T0


title: blood_pat027_T0


title: ROE2 cells-day 0 (control)

description:
The ROE2 cell line is derived from the tongue of an 18-day-old fetus.
ROE2 cells cultured for 0 days (control) at 37°C.

source_name: Rat oral epithelial cell line ROE2, day 0

tag: cell line

tag: cell type

tag: treatment

tag: time point

value: day 0

tag: strain/background


title: blood_pat007_T0

tag: crt

tag: ctn

tag: cir


title: blood_pat015_T0

tag: ypt

tag: ypn

tag: trg


title: blood_pat016_T0

tag: downst

tag: downs

tag: resp


title: blood_pat012_T0

tag: yprc

tag: leucocytes (x103xml)

tag: lymphocytes (%)


title: blood_pat019_T0

tag: granulocytes (%)

tag: monocytes (x103xμl)


title: A498 control #1

source_name: A498 human kidney carcinoma cell line

tag: cell line

tag: protocol

value: incubated with RPMI medium for 4 h

tag: serotype

value: Not present


title: Mock challenged_day2_30

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Head kidney dissected from individual 2 days after experimental mock infection

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Microarray data were extracted using Feature Extraction Software v9.6.1, gMedianSignal and gBGMedianSignal were used for further analyses. The spots were filtered by criterion (I/B)>8, where I is the median signal and B the background intensity. The arrays were equalized by the mean intensities. To calculate the expression ratios (ER), the samples were arranged in two groups by the time-points and for each gene the individual values were divided to the mean value of all samples from the group. These log2-ER were normalized with the locally weighted non-linear regression (Lowess).

label: Cyanine 3

organism: Sparus aurata

source_name: mock infected individual, collected 2 days post-challenge

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: tissue

value: head kidney

tag: condition


title: blood_pat008_T0

tag: crt

tag: ctn

tag: cir


title: Mock challenged_day1_19

description: Head kidney dissected from individual 1 day after experimental mock infection

source_name: mock infected individual, collected 1 day post-challenge


title: Mock challenged_day2_29

value: mock infected individual, collected 2 days post-challenge


title: Mock challenged_day1_20

value: mock infected individual, collected 1 day post-challenge


title: Mock challenged_day2_24


title: Challenged_day2_82

description: Head kidney dissected from individual 2 days after experimental infection with Ph. d. piscicida

source_name: infected individual, collected 2 days post-challenge


title: blood_pat004_T0

tag: ypt

tag: ypn

tag: trg


title: Mock challenged_day1_18


title: Mock challenged_day2_25


title: blood_pat005_T0

tag: downst

tag: downs

tag: resp


title: Challenged_day2_84

value: infected individual, collected 2 days post-challenge


title: BrCLRefMix1b 2/4/10 vs. JIMT-1 BrCL

city: Santa Monica

first: Judy

last: Dering

state: CA

address: 2825 Santa Monica Blvd. Suite 200

institute: UCLA School of Medicine

hyb_protocol: 825 ng each of labeled reference mix (Cy3 label) and individual sample (Cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent G2505C scanner. 49 experiments were scanned with extended dynamic range; MDA-MB-175, MDA-MB-330 and MDA-MB-231 were scanned without using the extended dynamic range option. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1) for 51 of the experiments. UACC-732 was extracted with version 10.7.3.1.

data_processing:
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization:: (1) no background subtraction, (2) special detrend Off, (3) adjust background globally Off, (4) red autoestimate Off, and (5) green autoestimate Off. 48 experiments were extracted with v 9.5.1.
Rosetta Resolver (v.7.2.2.0) was used for subsequent analysis of the array data.

source_name: BrCLRefMix1b 2/4/10

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following the manufacturer's instructions.

growth_protocol:
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.
All cell lines were characterized using mtDNA sequence prior to use.
All cultures were supplemented with 1% penicillin-streptomycin and 1% l-glutamine.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Kit following the manufacturer's protocol. The reference mix (BrCLRefMix1b 2/4/10) contained equal amounts of the following ten cell lines: CAMA-1, 184B5, MDA-MB-175, MDA-MB-361, MDA-MB-157, DU4475, MCF-7, MDA-MB-231, MDA-MB-468, SK-BR-3.

tag: cell type

value: mix of 10 breast cell lines

tag: sample type

value: reference

value: breast cell line


title: Challenged_day2_80


title: BrCLRefMix1b 2/4/10 vs. MCF12A BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1599 BrCL


title: Challenged_day2_83


title: BrCLRefMix1b 2/4/10 vs. HCC2157 BrCL


title: Mock challenged_day1_17