title: Induced

city: Fort Collins

first: Andrey

last: Ptitsyn

state: CO

address: 1682 Canpus Delivery

department: Center for Bioinformatics

institute: Colorado State University

description:
Adipose-derived stromal/stem cells (ASC) capable of multipotential differentiation can be isolated with high yield from human subcutaneous lipoaspirates. This study reports our recent experience isolating and immunophenotypically characterizing ASCs from >60 human subjects
Total RNA was isolated from ASCs obtained from three individual donors and maintained under uninduced or adipogenic induced culture conditions for 9 days following confluence.   The RNA was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), cDNA synthesized using a Superscript cDNA Synthesis kit (Invitrogen, Carlsbad, CA) and a T7-(dT)24 primer.  Biotinylated cRNA was transcribed in vitro using a GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA), purified using a GeneChip Sample Cleanup Module, incubated in fragmentation buffer (200 mM Tris-acetate pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) at 94oC for 35 min, chilled on ice, and hybridized to a Human U133 Plus 2.0 Array of ~47,400 transcripts and variants, including 38,500 well-characterized genes.  Arrays were incubated at 45oC for 16 hrs rotating at 60 rpm, washed, stained at 25oC for 10 min with 10 μg/ml streptavidin R phycoerythrin (Vector Laboratories, Burlingame, CA), stained at 25oC for 10 min (X2) with 3 μg/ml biotinylated goat anti-streptavidin antibody (Vector Laboratories), washed, and scanned using a GeneChip Scanner 3000.  Pixel intensities were measured, expression signals were globally scaled to a target intensity value of 2500, and features extracted using GeneChip Operating Software v1.2 (Affymetrix).  Data mining and statistical analyses  were performed with Data Mining Tool v.3 (Affymetrix) algorithms.  The absolute call (present, marginal, absent) of each gene expression, the direction of change, and the fold change were identified with the above software.

data_processing:
Probe set signal intensities calculated with GeneChip Operating Software v1.2 (Affymetrix).
Data mining and statistical analyses  were performed with Data Mining Tool v.3 (Affymetrix) algorithms.

growth_protocol: ASC were isolated from human fresh human subcutaneous adipose lipoaspirate according to published methods with some minor modifications (9,15).  The lipoaspirate tissue was extensively washed with warm phosphate buffer solution to remove erythrocytes and then digested in PBS supplemented with 0.1% Collagenase of Type I (Worthington Biochemical Corporation), 1% BSA, and 2 mM CaCl2 for one hour at 37oC.   Following room temperature centrifugation at 300 X g and resuspension in Stromal Medium (DMEM/Hams F-12 Medium supplemented with 10% FBS (Hyclone, Logan UT) and 1% antibiotic/antimycotic, the stromal vascular pellet was plated at a density of 35 ml of lipoaspirate digest per T175 flasks (0.2 ml per sq cm).  After 24 hrs of incubation at 37oC, 5% CO2, the adherent cells were washed with warm PBS and maintained in Stromal Medium until 80-90% confluent.  The adherent population was harvested by digestion with trypsin (0.05%)/EDTA (1 mM) at 37oC for five minutes, washed in Stromal Medium and replated at 5 X 103 ASC per sq cm (“Passage 1” or “P1”) or used in flow cytometric analyses or cryopreserved for future use.

extract_protocol: Total RNA was isolated from ASC cultures using TriReagent (Molecular Research Center, Cincinnati, OH) according to the manufacturer’s instructions.  The total RNA (2 µg) was incubated in a 20 µl volume with Moloney Murine Leukemia Virus Reverse Transcriptase, dNTP, and olig-dT.

treatment_protocol: Trypsin harvested ASCs were washed with PBS three times and aliquots of 105 cells were incubated with phycoerythrin conjugated monoclonal antibodies directed against CD29 (eBioscience Cat # 12-0297) CD34 (Becton Dickinson Cat # 348057), CD45 (eBioscience Cat # 12-0459), CD73 (BD Pharmingen Cat # 550257), CD90 (BD Pharmingen Cat # 55596), or IgG1κ control (BD Pharmingen Cat # 555749) or FITC conjugated monoclonal antibodies directed against CD44 (BD Cat # 348057) or IgG1κ control (BD Pharmingen Cat # 554679) for 20 min on ice before being washed with PBS supplemented with 1% BSA three times and fixed in 1% formaldehyde overnight at 4oC.  For each sample, 105 events were collected on a Becton Dickinson FACScaliber flow cytometer using CELLQuest acquisition software (Becton Dickinson) and analyzed using Flow Jo software (Tree Star).  This antibody panel was selected, in part, based on the ISCT position paper on the criteria for defining MSCs (17). Confluent cultures of ASC (P1) were induced with Adipogenic Differentiation Medium (DMEM/Hams F-12, 3% FBS, 1% antibiotic/antimycotic, 0.5 mM isobutylmethylxanthine, 33 µM biotin, 17 µM pantothenate, 5 μM rosiglitazone (AK Scientific, Mountain View, CA), 1 µM dexamethasone, 1 μM insulin) for three days before being converted to Adipocyte Maintenance Medium (identical to Adipogenic Differentiation Medium without  isobutylmethylxanthine and rosiglitazone).   Cells were maintained for 9 days before fixation and Oil Red O staining.  In selected experiments, samples of uninduced and adipogenic induced ASC were harvested for total RNA isolation at days 0, 3, 6, and 9 of differentiation.  Confluent cultures of ASCs were converted to Osteogenic Medium (DMEM/Hams F-12 or DMEM, 10% FBS, 1% antibiotic/antimycotic, 10 mM β-glycerophosphate, 50 µg/ml sodium 2-phosphate ascorbate, 10-8 M dexamethasone) and maintained in culture for 9-12 days with medium changes every third day.  The cultures were rinsed three times with 150 mM NaCl, fixed in 70% ethanol, and stained with Alizarin Red.

tag: protocol

value: adipogenic induced


title: 10 min exposure to menadione, technical replicate 1 of 3, set 2

status: Public on Sep 07 2010

type: RNA

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

description: technical replicate 1 of 3

hyb_protocol: For each microarray experiment, the cDNA probes from one condition (e.g. H2O2 addition) were individually co-hybridized with cDNA probes from the relevant control sample. The fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 µl of water, to which was added 2.5 µl of salmon sperm DNA (10 mg/ml), 9 µl of 20x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7), 0.36 µl of 10% sodium dodecyl sulfate (SDS), and 9 µl of formamide. Prior to hybridization, microarray slides were prehybridized at 42°C for 45 min in prehybridization buffer (25% formamide, 5x SSC buffer, 0.1% SDS, and 1% bovine serum albumin), rinsed with water, and dried by spinning. The probe was denatured by boiling for 2 min, followed by cooling to 42°C. The probe was then applied to the microarray slide under a coverslip, placed in a humidified chamber (ArrayIt), and incubated at 42°C overnight. Following hybridization, slides were washed in 2x SSC-0.1% SDS for 5 min at 42°C, 0.1x SSC-0.1% SDS for 10 min at room temperature, and four times in 0.1x SSC for 1 min at room temperature. Slides were then rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) wavelengths using a laser-activated confocal scanner (ScanArray Gx, Perkin Elmer) at a 10µm resolution.

data_processing: The signal intensities for each spot were collected using GenePix Pro4 software (Axon Instruments, Foster City, Calif.). Spots with signal intensities below 3 times the standard deviation of the local background in both channels were excluded from further analysis. The fluorescent intensity in each wavelength (channel 1 for indodicarbocyanine (Cy5) and channel 2 for indocarbocyanine (Cy3)) was normalized using the MIDAS software (available from TIGR, http://www.tigr.org/software/) and by applying a locally weighted linear regression (Lowess). Finally, the ratio of the channels 2 to 1 was converted to log2.

molecule: total RNA

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

source_name: Total RNA of Campylobacter jejuni

label_protocol: Total RNA was converted to cDNAs in the presence of aminoallyl-dUTP with Superscript II (Invitrogen) at 42°C. The reverse transcription reaction was performed as follows: 16 µg of total RNA was combined with 10 µg of random hexamers in a 34.35-µl reaction mixture containing 8 µl of 5x Superscript II reverse transcriptase buffer and 2 µl of 0.1 M dithiothreitol. After a 5-min incubation at 65°C, the reaction mixture was brought to a final volume of 40 µl by adding (final concentrations): 0.5 mM each of dGTP, ATP, and CTP; 0.16 mM dTTP; 0.34 mM aminoallyl-dUTP; and 2 µl of Superscript II and incubated at 42°C for 120 min. At the end of the first-strand synthesis, the reaction was stopped and the RNA was hydrolyzed by adding 4 µl of 50 mM EDTA and 2 µl of 10 N NaOH and incubating at 65°C for 20 min. This reaction was neutralized by adding 4 µl of 5 M acetic acid. The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 450 µl of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 8,000 x g. This washing step was repeated three times. After the last wash, the aminoallyl-labeled probes were concentrated to less than 8 µl under vacuum in a SpeedVac and adjusted to a final volume of 10 µl by adding 1 µl of 1 M sodium carbonate (pH 9.0) and water. The resulting aminoallyl-labeled cDNA was coupled to monoreactive fluors (Amersham) by adding 10 µl of dimethyl sulfoxide containing one-sixth of one reaction vial FluoroLink indocarbocyanine or indodicarbocyanine dye and incubating for 45 min at room temperature in the dark. This reaction was quenched by adding 4.5 µl of 4 M hydroxylamine and incubating for 15 min at room temperature in the dark.

growth_protocol: C. jejuni NCTC 11168 cells were incubated overnight with stirring at 37°C under microaerophilic conditions in a 500 ml flask containing 250 ml of MEMα medium. At mid-log phase, 50 ml of the culture were dispended into flasks of 100 ml capacity and kept under microaerophilic growth conditions.

extract_protocol: Immediately after collection of samples for RNA extraction, 0.1 volumes of cold RNA degradation stop solution (10% (v/v) buffer-saturated phenol in ethanol) were added to prevent RNA turnover (14). Cells were collected by centrifugation (8, 000 x g, 10 min, 4°C) and the cell pellet was resuspended in TE buffer (50 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.5 mg mL-1 (final concentration) lysozyme. Total RNA was extracted using a hot phenol-chloroform method, precipitated with ethanol, and resuspended in RNase-free H2O. The RNA preparation was treated with DNase I to remove any contaminating genomic DNA, further purified using a QIAGEN RNeasy mini Kit (QIAGEN, Valencia, CA), and quantitated using either the RiboGreen RNA quantitation kit (Molecular Probes, Eugene, OR) or A260 values. RNA integrity was assessed by agarose gel electrophoresis, and PCR amplification was used to confirm that the preparation was free of genomic DNA. RNA samples were stored at -80°C.

treatment_protocol: To investigate the transcriptional responses of C. jejuni to oxidant exposure, hydrogen peroxide (H2O2), cumene hydroperoxide (CHP), or menadione sodium bisulfite (MND) was added to the 50 ml broth at a final concentration of 1 mM. The stock solutions of H2O2 and MND were prepared in water at a concentration of 0.882 M and 1 M respectively, while the stock solution of CHP was prepared in DMSO at a concentration of 0.578 M. The same amount of water or DMSO was added to the bacterial culture that served as reference samples for the transcriptional profile study in response to H2O2, MND or CHP. Furthermore, to investigate the transcriptional response of C. jejuni to H2O2 exposure in the presence of excess iron, ferrous sulfate was added to the bacterial culture at a final concentration of 40 µM, 15 min prior to H2O2 exposure. To identify the PerR regulon, the wild-type strain C. jejuni NCTC 11168 and the perR mutant were grown in 500 ml flasks containing 250 ml of MEMα medium. At mid-log phase, 50 ml of the cultures were transferred to 100 ml flasks and ferrous sulfate and/or H2O2 were added as described above. Ten minutes following the addition of H2O2 the cells were collected and the total RNA extracted.

tag: phase

value: mid-log phase

tag: medium

value: MEM

tag: treatment

value: 10 min exposure to menadione


title: PerR regulon, after iron addition and 10 min exposure to H2O2, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3

source_name: Total RNA of Campylobacter jejuni perR mutant

tag: strain

value: perR mutant of Campylobacter jejuni NCTC 11168


title: Uninduced

status: Public on Oct 01 2010

country: USA

hyb_protocol: Arrays were incubated at 45oC for 16 hrs rotating at 60 rpm, washed, stained at 25oC for 10 min with 10 μg/ml streptavidin R phycoerythrin (Vector Laboratories, Burlingame, CA), stained at 25oC for 10 min (X2) with 3 μg/ml biotinylated goat anti-streptavidin antibody (Vector Laboratories), washed, and scanned using a GeneChip Scanner 3000.

scan_protocol: Pixel intensities were measured, expression signals were globally scaled to a target intensity value of 2500, and features extracted using GeneChip Operating Software v1.2 (Affymetrix).

label: biotin

organism: Homo sapiens

source_name: Adipose-derived stromal/stem cells (ASC)

value: uninduced (control)


title: PerR regulon, after iron addition and 10 min exposure to H2O2, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3


title: AAF-OX_3-week-old_rep1

status: Public on Sep 30 2010

city: Taipei

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Standard Affymetrix GeneChip hybridization protocol

scan_protocol: Standard Affymetrix GeneChip scanning protocol

organism: Arabidopsis thaliana

label_protocol: Standard Affymetrix GeneChip labeling protocol

extract_protocol: Pine Tree Method, for preparation of total RNA from plant tissues. Plant Molecular Biology Reporter(1993) 11: 113-116

tag: transgenic arabidopsis

value: Over-expression of AAF

tag: background

tag: developmental stage

tag: tissue

value: Rosette leaf

tag: growth condition

value: 16hr light/ 8hr dark


title: 10 min exposure to cumene hydroperoxide, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3

value: 10 min exposure to cumene hydroperoxide


title: Triple fusioned hippocampus of control mice

status: Public on Sep 28 2010

city: Seoul

first: Yoo-Hun

last: Suh

address: 28 Yongon-dong

country: South Korea

institute: Seoul National University

description: male

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on GE Healthcare/Amersham Biosciences CodeLink UniSet

scan_protocol: Processed slides were scanned using an Axon GenePix 4000B Scanner with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 µm. Images for each slide were analyzed using the CodeLinkTM Expression Analysis Software v4.1(GE Healthcare Life Science).

data_processing: The CodeLinkTM Expression Analysis Software v4.1(GE Healthcare Life Science) was used

organism: Mus musculus

source_name: Triple fusioned hippocampus of 11month-old control mice

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit         Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: gender

value: male


title: Col-0_3-week-old_rep1

tag: genotype


title: 10 min exposure to menadione, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3


title: 10 min exposure to menadione, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3


title: PerR regulon, 10 min after iron addition, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3

value: 10 min after iron addition


title: PerR regulon in MEM medium, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3


title: 10 min exposure to cumene hydroperoxide, technical replicate 1 of 3, set 2

description: technical replicate 1 of 3


title: 10 min exposure to cumene hydroperoxide, technical replicate 2 of 3, set 2

description: technical replicate 2 of 3


title: Immortalized intermediate cells, BHPrE1

status: Public on Sep 15 2010

type: genomic

city: Nashville

first: yajun

last: yi

state: TN

address: 2215 Garland Ave

institute: vanderbilt univ

description: Promega's pooled normal male DNA served as a reference (Cat#G1471).

hyb_protocol: standard hybridization performed by Belfer Center

scan_protocol: standard scanning performed by Belfer Center

data_processing: log2 ratio based on circular binary segmentation algorithm

molecule: genomic DNA

source_name: BHPrE1 DNA

label_protocol: standard labeling performed by Belfer Center

extract_protocol: QIAGEN DNeasy

tag: cell line

tag: cell line description

value: spontaneously immortalized adult human benign prostatic epithelial cells

tag: cell type

value: putative intermediate cell

source_name: pooled normal human DNA

tag: sample type

value: reference


title: PerR regulon, 10 min after iron addition, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3


title: Primary cells, BHPrE

source_name: Primary BHPrE DNA

value: BHPrE

value: primary cells from benign prostate surgical sample, parent cells of BHPrE1


title: 10 min exposure to H2O2, technical replicate 5 of 6, set 1

description: technical replicate 5 of 6

value: 10 min exposure to H2O2


title: PerR regulon in MEM medium, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3

value: mid-log phase


title: 10 min exposure to iron and H2O2, technical replicate 1 of 3, set 2

description: technical replicate 1 of 3

value: MEM

value: 15 min after iron addition

value: 15 min exposure to iron and 10 minute exposure to H2O2


title: 10 min exposure to menadione, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3

value: 10 min exposure to menadione


title: PerR regulon in MEM medium, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3

value: perR mutant of Campylobacter jejuni NCTC 11168


title: 10 min exposure to H2O2, technical replicate 3 of 6, set 2

description: technical replicate 3 of 6


title: PerR regulon, 10 min after iron addition, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3


title: 10 min exposure to H2O2, technical replicate 1 of 6, set 2

description: technical replicate 1 of 6


title: 10 min exposure to cumene hydroperoxide, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3


title: 10 min exposure to H2O2, technical replicate 3 of 6, set 1

description: technical replicate 3 of 6


title: 10 min exposure to H2O2, technical replicate 2 of 6, set 2

description: technical replicate 2 of 6


title: 10 min exposure to H2O2, technical replicate 6 of 6, set 1

description: technical replicate 6 of 6


title: 10 min exposure to iron and H2O2, technical replicate 2 of 3, set 2

description: technical replicate 2 of 3


title: Immortalized progenitor cells, NHPrE1

source_name: NHPrE1 DNA

value: putative progenitor cell


title: 10 min exposure to cumene hydroperoxide, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3


title: 10 min exposure to iron and H2O2, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3


title: 10 min exposure to cumene hydroperoxide, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3


title: 10 min exposure to H2O2, technical replicate 4 of 6, set 1

description: technical replicate 4 of 6


title: 10 min exposure to iron and H2O2, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3


title: 10 min exposure to H2O2, technical replicate 1 of 6, set 1

description: technical replicate 1 of 6


title: 10 min exposure to H2O2, technical replicate 2 of 6, set 1

description: technical replicate 2 of 6


title: 10 min exposure to iron and H2O2, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3


title: 10 min exposure to iron and H2O2, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3


title: E13.5 testes, Dmrt(-,-), biological rep2

status: Public on Jun 30 2010

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

description:
Dmrt1 (-/-) testes expression E13.5.
Krentz-1669B(--)_012908-2

hyb_protocol: Hybridized to Affymetrix 430 2.0 microarrays.

scan_protocol: Affymetrix.

data_processing: CEL files were normalized using the GC-RMA algorithm as implemented in the Genedata Expressionist Software Package.

source_name: E13.5 testes Dmrt1(-,-)

label_protocol: 100ng of total RNA was amplified and labeled using NuGen Ovation labeling kit.

growth_protocol: Gonads were dissected from E13.5 embryos and placed in RNAlater (Qiagen).

extract_protocol: RNA was prepared using Allprep Micro Kit (Qiagen).

value: testis

value: Dmrt(flox/flox) outcrossed to 129S6/SvEvTac

tag: age


title: E13.5 testes, Dmrt(-,-), biological rep3

description:
Dmrt1 (-/-) testes expression E13.5.
Krentz-1736B(--)_012908-3


title: P. gingivalis bone 3

status: Public on Jul 15 2010

city: Gainesville

first: Kesavalu

middle: Naidu

last: Lakshmyya

state: FL

address: 1600 SW Archer road, D11-24

department: Periodontology

institute: University of Florida, College of Dentistry

description: Gene expression data from P. gingivalis infected tissue.

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using dChip. Gene Ontology was categorised using BRB array tools, DAVID EASE and NetAffx.Onto-Express was used to construct functional profiles

source_name: P. gingivalis infected bone 3

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

growth_protocol: P. gingivalis strain 381was cultured in CDC blood agar plates under anaerobic conditions for 72 hours and counted using bacterial counting chamber and suspended in reduced transport fluid at 1.5X1011 cells per ml.

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

treatment_protocol: P. gingivalis was injected at 1.5 x 109 (N = 10) into the soft tissues overlying the calvaria of the mice for 3 days. A control group (N = 9) was injected with vehicle once daily for 3 days. Mice were euthanized 8 h after the last injection.  The calvarial bones and overlying soft tissues from 5 mice in each group were excised, snap frozen in liquid nitrogen, and stored at –80°C until RNA isolation.

value: calvarial bones

tag: infection

value: P. gingivalis

value: 9 weeks


title: E13.5 testes, wt, biological rep1

description:
Dmrt1 (+/-) testes expression E13.5.
Krentz-1759C(wt)_012908-4

source_name: E13.5 testes wt

value: Dmrt(+/-) outcrossed to 129S6/SvEvTac


title: E13.5 testes, wt, biological rep2

description:
Dmrt1 (+/-) testes expression E13.5.
Krentz-1737H(wt)_012908-5


title: P. gingivalis soft tissue 5

source_name: P. gingivalis infected tissue 5

value: soft tissues overlying calvarial bones


title: P. gingivalis bone 1

source_name: P. gingivalis infected bone 1


title: P. gingivalis bone 2

source_name: P. gingivalis infected bone 2


title: P. gingivalis soft tissue 3

source_name: P. gingivalis infected tissue 3


title: E13.5 testes, Dmrt(-,-), biological rep1

description:
Dmrt1 (-/-) testes expression E13.5.
Krentz-1742B(--)_012908-1


title: P. gingivalis bone 4

source_name: P. gingivalis infected bone 4


title: P. gingivalis soft tissue 1

source_name: P. gingivalis infected tissue 1


title: P. gingivalis soft tissue 4

source_name: P. gingivalis infected tissue 4


title: P. gingivalis bone 5

source_name: P. gingivalis infected bone 5


title: P. gingivalis soft tissue 2

source_name: P. gingivalis infected tissue 2


title: 1d Alt temp (20:30°C), rep 1 & dry seeds, rep 1

status: Public on Jun 01 2010

city: Fargo

first: Michael

middle: E

last: Foley

state: ND

address: 1605 Albrecht Blvd

institute: USDA-ARS

hyb_protocol: Arrays were pre-hybridized with a soln. of BSA, SDS and Dehardts. Arrays were then rinsed in 2XSSC/2%SDS, then water, and then 100 EtOH before being spun dry. Labeled cDNAs were mixed in a volume of 26.4 ul water, 7.65 ul 2XSSC, 7.2 ul 2%SDS, and 3.75 ul tRNA (10 mg/ml). cDNA was heated to 95 C for 5 minutes, spun down and placed on the array under a cover slip. Arrays were hybridized ON at 60 C. Washing was done by consecutive 5 minute rinses in 2XSSC/2%SDS, 1XSSC/0.2%SDS, 1XSSC/0.2%SDS again, 0.1XSSC, 0.1XSSC again, and spun dry.

scan_protocol: Arrays were scanned using a Genepix 4000b under default conditions for normalizing signal intensities.

data_processing: Raw signal intensities of all DNA-containing spots were up-loaded as single color files into GeneMaths XT microarray data analysis program. Intensity data was log transformed, and normalized between arrays using default parameters.

organism: Euphorbia esula

source_name: Leafy spurge seeds: 1d Alt temp (20:30°C), rep 1

label_protocol: Total RNA was reverse transcribed and labeled with Invitrogen Alexaflour 555 or 647 dyes using the two-step method suggested by the manufacturer.

growth_protocol: Natural field conditions. Seeds harvested by hand in late June and early July 2006.

extract_protocol: Seeds were placed in liquid nitrogen and ground to a fine powder. The Pine Tree extraction procedure was used to isolate total RNA (Chang S, Puryear, J. and Cairney, J. (1993) A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-116).

treatment_protocol: Seeds were collected and stored at -20°C. See Foley & Chao 2008 Growth Regulators and Chemicals Stimulate Germination of Leafy Spurge (Euphorbia esula) seeds Weed Sci. 56_516-522 and Foley 2008 Temperature and Moisture Status Affect Afterripening of Leafy Spurge (Euphorbia esula) Seeds. Weed Sci. 56_237-243. Unless the treatment was dry seeds, the seeds were placed in Petri dishes containing sterile distilled water and lined with one Whatman #1 filter paper. Dishes were maintained in non-lighted incubators in boxes lined with wet paper towels to maintain high relative humidity for 21d at 20°C, or for 21d at 20:30°C (8:16 h), or for 21d at 20°C plus 1, 2, and 3 days and germination at 20:30°C (8:16 h). Germination was normally determined daily under normal laboratory light and was judged visually by cracking of the seed coat. After the appropriate incubation period, e.g., 1, 2, 3, and 21 days, or when germinated they were placed in liquid N2 and stored at -80°C prior to RNA extraction.

tag: specimen

value: Leafy spurge seeds harvested in 2006 in Fargo, ND.

value: seed

source_name: Leafy spurge seeds: dry seeds, rep 1


title: 21d Alt temp (20:30°C), rep 1 & 3d Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 21d Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 3d Alt temp (20:30°C), rep 1


title: 1d at 20°C, rep 1 & Germ Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 1d at 20°C, rep 1

source_name: Leafy spurge seeds: Germ Alt temp (20:30°C), rep 1


title: 2d Alt temp (20:30°C), rep 1 & 1d Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 2d Alt temp (20:30°C), rep 1


title: 21d at 20°C, rep 1 & 3d at 20°C, rep 1

source_name: Leafy spurge seeds: 21d at 20°C, rep 1

source_name: Leafy spurge seeds: 3d at 20°C, rep 1


title: 21d C (20°C) + 2d Alt temp (20:30°C), rep 1 &  21d C (20°C) + 1d Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 21d Const (20°C) + 2d Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 21d Const (20°C) + 1d Alt temp (20:30°C), rep 1


title: 21d Const (20°C) + 1d Alt temp (20:30°C), rep 1 &  21d at 20°C, rep 1


title: 21d C (20°C) + Germ Alt temp (20:30°C), rep 1 &  21d C (20°C) + 3d Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 21d Const (20°C) + Germ Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: 21d Const (20°C) + 3d Alt temp (20:30°C), rep 1


title: 3d at 20°C, rep 1 & 2d at 20°C, rep 1

source_name: Leafy spurge seeds: 2d at 20°C, rep 1


title: Germ Alt temp (20:30°C), rep 1 & 21d Alt temp (20:30°C), rep 1


title: 3d Alt temp (20:30°C), rep 1 & 2d Alt temp (20:30°C), rep 1


title: 3d Alt temp (20:30°C), rep 2 &  2d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 3d Alt temp (20:30°C), rep 2

growth_protocol: Natural field conditions. Seeds harvested by hand in late June and early July 2007.

value: Leafy spurge seeds harvested in 2007 in Fargo, ND.

source_name: Leafy spurge seeds: 2d Alt temp (20:30°C), rep 2


title: 21d Const (20°C) + 3d Alt temp (20:30°C), rep 1 & 21d Const (20°C) + 2d Alt temp (20:30°C), rep 1


title: E13.5 testes, wt, biological rep3

description:
Dmrt1 (+/-) testes expression E13.5.
Krentz-1669A(wt)_012908-6

source_name: E13.5 testes wt


title: 2d Alt temp (20:30°C), rep 2 &  1d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 1d Alt temp (20:30°C), rep 2


title: Dry seeds, rep 1 &  21d Const (20°C) + Germ Alt temp (20:30°C), rep 1

source_name: Leafy spurge seeds: Dry seeds, rep 1


title: normal lung - 2

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

description: Normal tumor-free adult mouse lung.

hyb_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix 430-2.0 arrays as recommended by the manufacturer.

scan_protocol: Gene Chip Scanner 3000.

data_processing: RMA

label: streptavidin

source_name: Normal mouse

label_protocol: As recommended by the manufacturer (Affymetrix, Santa Clara).

extract_protocol: RNA was isolated with Trizol and twice amplified with a RiboAmp RNA amplification kit.

value: wild-type

value: lung


title: 1d Alt temp (20:30°C), rep 2 &  dry seeds, rep 2

source_name: Leafy spurge seeds: dry seeds, rep 2


title: triple knockout lung cancer - 13

description: Mouse lung tumors dissected from the mice that were infected with Adenovirus expressing Cre recombinase via nasal instillation and then aged for 6 months.

source_name: RB-p53-p130 triple knockout mouse

value: Rb Δ/Δ; p53 Δ/Δ; p130 Δ/Δ

value: lung tumor


title: 21d Alt temp (20:30°C), rep 2 & 3d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 21d Alt temp (20:30°C), rep 2


title: triple knockout lung cancer - 12


title: double knockout lung cancer - 9

description: Mouse lung tumors dissected from the mice that were infected with Adenovirus expressing Cre recombinase via nasal instillation and then aged for 8-12 months.

source_name: RB-p53 double knockout mouse

value: RbΔ/Δ; p53 Δ/Δ


title: 1d Const temp (20°C), rep 2 & Germ Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 1d Const temp (20°C), rep 2

source_name: Leafy spurge seeds: Germ Alt temp (20:30°C), rep 2


title: double knockout lung cancer - 10


title: 2d Const temp (20°C), rep 2 & 1d Const temp (20°C), rep 2

source_name: Leafy spurge seeds: 2d Const temp (20°C), rep 2


title: HB_2

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

institute: Taiwan National Health Research Institute

description: Hepatoblastoma (epithelial type)

hyb_protocol: Array hybridizations were carried out with 490μl of hybridization mixtures for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37℃ in Oligo aCGH Wash Buffer 2 (Agilent).

scan_protocol: The hybridized arrays were scanned using an Agilent G2565BA DNA microarray scanner (Agilent Technologies). The ScanControl Software (Agilent Technologies) was used for image acquisition. In brief, the arrays were imaged at a resolution of 5 μm. Excitation of Cy3 and Cy5 was performed at a wavelength of 532 and 635 nm, respectively. A laser power of 100% was used. Each array was subjected to a series of scans. The signals were digitized into 16 bit/pixel, yielding a maximum detection range from 1 to 65536; i.e., almost five orders of magnitude.

data_processing: After image acquisition, data extraction, normalization and transformation were carried out by using Agilent Feature Extraction Software, version 8.1.1 (Agilent Technologies), procedures listed as follow:  (1) Place Grid, find and measure spots  -define what is the array format of the image to be processed.  (2) Flag outliers  a. Compute population outliers- flag features and local backgrounds as population outliers if the minimum number of replicates is met and the mean signals varies significantly from the distribution.  b. Compute NonUniform outliers- flag features and local backgrounds as NonUniform if the pixel distribution is outside the boundary defined by the three-parameter noise model.  (3)   Compute Background, bias and error              Background subtraction→ signal correction → choose error model   (4) Dye normalization –   a. Use rank consistent probes.  b. Normalization correction methods: Linear method  (5) Compute ratios- the log ratio values are capped to 4 with appropriate signs in positive and negative directions.  Subsequent data analysis was performed with the other custom analytical software, CGH Analytics (version 3.5.14, Agilent Technologies). The Linear smoothing algorithm is used in the Moving Average approach to smooth the data sets with window size of 5 Mb.

source_name: Hepatoblastoma patient 2

label_protocol: Genomic DNA was completely fragmented with AluI and RsaI (Promega, Madison, WI, USA ), followed by purification with QIAprep Spin Miniprep Kit (Qiagen). All of the digested DNAs were subjected to labeling reactions using Agilent’s Genomic DNA Labeling Kit PLUS per manufacturer’s instructions. For each array-CGH experiment, we used DNA isolated from NPC cell line as experimental genome (cyanine 5 UTP-labeled) and the commercial healthy Caucasian male genome (Promega) as reference (cyanine 3 UTP-labeled).

extract_protocol: Genomic DNA were isolated by using DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The TW01 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). The HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. Both cell lines were without any treatment before extraction of genomic DNA.

value: male

value: 2 months

value: Peripheral blood lymphocytes

tag: health state

value: Hepatoblastoma

source_name: Commercialized normal Caucasian genome pool

value: Healthy


title: double knockout lung cancer - 8

extract_protocol: RNA was isolated with Trizol and twice amplified with a RiboAmp RNA amplification kit


title: 21d C at 20°C, rep 2 & 3d C at 20°C, rep 2

source_name: Leafy spurge seeds: 21d Constant at 20°C, rep 2

source_name: Leafy spurge seeds: 3d Constant at 20°C, rep 2


title: 3d Const temp (20°C), rep 2 & 2d Const temp (20°C) rep 2

source_name: Leafy spurge seed: 3d Const temp (20°C), rep 2

source_name: Leafy spurge seed: 2d Const temp (20°C) rep 2


title: double knockout lung cancer - 7

description: Mouse lung tumors dissected from the mice that were infected with Adenovirus expressing Cre recombinase via nasal instillation and then aged for 8-12 months

hyb_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix 430-2.0 arrays as recommended by the manufacturer

scan_protocol: Gene Chip Scanner 3000


title: 21d at 20°C + 1d Alt temp (20:30°C), rep 2 & 21d C (20°C), rep 2

source_name: Leafy spurge seeds: 21d at 20°C + 1d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 21d C (20°C), rep 2


title: 21d at 20°C + 3d Alt temp (20:30°C), rep 2 & 21d at 20°C + 2d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 21d at 20°C + 3d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 21d at 20°C + 2d Alt temp (20:30°C), rep 2


title: Primary cells, NHPrE

source_name: Primary NHPrE DNA

value: NHPrE

value: primary cells from prostate, cannot be passed in cell culture, parent cells of NHPrE1

source_name: pooled normal human DNA

value: reference


title: 21d @ 20°C + Germ Alt temp (20:30°C), rep 2 & 21d @ 20°C + 3d Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 21d Const (20°C) + Germ Alt temp (20:30°C), rep 2

source_name: Leafy spurge seeds: 21d Const (20°C) + 3d Alt temp (20:30°C), rep 2


title: double knockout lung cancer - 6

description: mouse lung tumors dissected from the mice that were infected with Adenovirus expressing Cre recombinase via nasal instillation and then aged for 8-12 months

source_name: RB-p53 double knockout mouse


title: triple knockout lung cancer - 11

description: mouse lung tumors dissected from the mice that were infected with Adenovirus expressing Cre recombinase via nasal instillation and then aged for 6 months

source_name: RB-p53-p130 triple knockout mouse


title: double knockout lung cancer - 2


title: 2d Alt temp (20:30°C), rep 3 & 1d Alt temp (20:30°C), rep 3

source_name: Leafy spurge seeds: 2d Alt temp (20:30°C), rep 3

growth_protocol: Natural field conditions. Seeds harvested by hand in late June and early July 2008.

value: Leafy spurge seeds harvested in 2008 in Fargo, ND.

source_name: Leafy spurge seeds: 1d Alt temp (20:30°C), rep 3


title: double knockout lung cancer - 3


title: double knockout lung cancer - 4


title: Dry seeds, rep 2 & 21d Const (20°C) + Germ Alt temp (20:30°C) rep 2

source_name: Leafy spurge seeds: dry seeds, rep 2

source_name: Leafy spurge seeds: 21d Const (20°C) + Germ Alt temp (20:30°C) rep 2


title: double knockout lung cancer - 5


title: 3d Alt temp (20:30°C), rep 3 & 2d Alt temp (20:30°C) rep 3

source_name: Leafy spurge seeds: 3d Alt temp (20:30°C), rep 3

source_name: Leafy spurge seeds: 2d Alt temp (20:30°C) rep 3


title: 21d at 20°C + 2d Alt temp (20:30°C), rep 2 & 21d at 20°C + 1d Alt temp (20:30°C), rep 2

source_name: Leafy spruge seeds: 21d at 20°C + 2d Alt temp (20:30°C), rep 2

source_name: Leafy spruge seeds: 21d at 20°C + 1d Alt temp (20:30°C), rep 2


title: double knockout lung cancer - 1


title: 1d Alt temp (20:30°C), rep 3 & dry seeds, rep 3

source_name: Leafy spurge seeds: dry seeds, rep 3


title: 1d Const temp (20°C), rep 3 & Germ Alt temp (20:30°C), rep 3

source_name: Leafy spurge seeds: 1d Const temp (20°C), rep 3

source_name: Leafy spurge seeds: Germ Alt temp (20:30°C), rep 3


title: 2d Const temp (20°C), rep 1 & 1d Const temp (20°C), rep 1

source_name: Leafy spurge seeds: 2d Const temp (20°C), rep 1

value: Leafy spurge seeds harvested in 2006 in Fargo, ND.

source_name: Leafy spurge seeds: 1d Const temp (20°C), rep 1


title: 21d Alt temp (20:30°C), rep 3 & 3d Alt temp (20:30°C) rep 3

source_name: Leafy spurge seeds: 21d Alt temp (20:30°C), rep 3

value: seed

source_name: Leafy spurge seeds: 3d Alt temp (20:30°C) rep 3


title: 2d Const temp (20°C), rep 3 & 1d Const temp (20°C), rep 3

source_name: Leafy spurge seeds: 2d Const temp (20°C), rep 3


title: c-Myb chip aby upstate stimulated_I

status: Public on May 01 2010

city: Albuquerque

first: Gavin

last: Pickett

state: NM

address: 2325 Camino de Salud NE

department: Genomics

institute: UNM

description: ChIP: Chip data anayzed by MAT software for cells stimulated with estrogen for 24 hours with anti-c-Myb clone 1-4 Millopore

hyb_protocol: Samples were hybed according to Affymetrix protocol

scan_protocol: Samples were scanned according to Affymetrix protocol (GeneChip Scanner 3000)

data_processing:
Result files display c-Myb binding sites designated statistically significant ( p= 1X10^-5). Each file is normalized to control antibody (pre-immune serum) or input (fraction without antibody).
This Sample was normalized by MAT software relative to input.

source_name: estrogen stimulated Upstate ChIP DNA

label_protocol: Samples were labeled according to Affymetrix protocol for tiling arrays

growth_protocol: Cells were cultured at 1X10^6 per/ ml and grown for 16 hours in normal DMEM supplemented with 10 %FBS and subjected to ChIP with two independent c-Myb antibodies. Confluent cells were compared to cells deprived from estrogen for 48 hours in phenol red free medium supplemented with 5% charcoal stripped serum for 48 hours and subsequently stimulated with 10nM 17 beta estradiol for 24 hours.

extract_protocol: DNA was extracted according to ChIP protocol.

tag: protocol

tag: antibody

value: anti-c-Myb

source_name: input (fraction without antibody estrogen stimulated)


title: c-Myb chip aby VKN confluent_I

description: ChIP: Chip data anayzed by MAT software for cells cultured to confluence with anti-c-Myb rabbit serum

source_name: Confluent VKN ChIP DNA

value: confluent

source_name: input (fraction without antibody confluent cultures)


title: dimethylH3K4 chip confluent_I

description: ChIP: chip data analyzed by MAT software for cells cultured to confluence with anti-dimethyl H3K4 Millipore

source_name: Confluent Dimethyl H3K4 ChIP DNA

value: anti-dimethyl H3K4


title: WT+5mM Zn 1h vs WT-Zn_Exp_2

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 um, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 oC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 um. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas.bioinfo.cnio.es) was used to preprocess the data: merge replicates and remove inconsistent replicates (Maximum distance to median of replicates=0.5). The normalization method we used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes.

organism: Saccharomyces cerevisiae

source_name: Wild type strain in log phase culture treated with 5mM ZnCl2

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. ZnCl2 was added to a final concentration of 5 mM and the culture was grown for 60 more minutes before cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: 5 mM ZnCl2 for 1h

tag: strain

value: wild type

source_name: Wild type strain in log phase culture

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. The culture was grown for 60 more minutes before cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.

treatment_protocol: Untreated cells


title: c-Myb chip aby upstate stimulated

description: ChIP: Chip data anayzed by MAT software for cells stimulated with estrogen for 24 hours with anti-c-Myb clone 1-2 Millopore

data_processing:
Result files display c-Myb binding sites designated statistically significant ( p= 1X10^-5). Each file is normalized to control antibody (pre-immune serum) or input (fraction without antibody).
This Sample was normalized by MAT software relative to control antibody.

source_name: control (pre-immune rabbit serum estrogen stimulated)

value: control antibody (pre-immune serum)


title: normal lung - 1

description: Normal tumor-free adult mouse lung.

source_name: Normal mouse

value: wild-type

value: lung


title: pif1 mutant vs wild type_Exp_2

source_name: pif1 mutant strain in log phase culture

growth_protocol: Grown at 28 ºC in 50 ml of YPD rich medium until A660=0.6. Cells were harvested by centrifugation and washed with cold water. Dried cell pellet was kept at -80 ºC until RNA purification.


title: pif1+5mM Zn 1h vs pif1_Exp_2

source_name: pif1 mutant strain in log phase culture treated with 5mM ZnCl2

tag: strain by4741


title: 21d Const temp (20°C), Rep 3 & 3d Const (20°C ), Rep 3

source_name: Leafy spurge seeds: 21d Const temp (20°C), Rep 3

source_name: Leafy spurge seeds: 3d Const temp (20°C), Rep 3


title: pif1 mutant vs wild type_Exp_1


title: dimethylH3K4 chip stimulated

description: ChIP: Chip data anayzed by MAT software for cells stimulated with estrogen for 24 hours with anti-dimethyl H3k4  Millopore

source_name: estrogen stimulated dimethyl H3k4 ChIP DNA


title: 21d Const 20°C + 2d Alt temp (20:30°C), Rep 3 & 21d Const 20°C + 1d Alt temp (20:30°C), Rep 3

source_name: Leafy spurge seeds: 21d Const (20°C) + 2d Alt temp (20:30°C), Rep 3

source_name: Leafy spurge seeds: 21d Const (20°C) + 1d Alt temp (20:30°C), Rep 3


title: Germ Alt temp (20:30°C), rep 3 & 21d Const (20°C) + Germ Alt temp (20:30°C) rep 3

source_name: Leafy spurge seeds: Germ Alt temp (20:30°C), rep 3

source_name: Leafy spurge seeds: 21d Const (20°C) + Germ Alt temp (20:30°C) rep 3


title: dimethylH3K4 chip stimulated_I

source_name: input (fraction without antibody estrogen stimulated)


title: WT+5mM Zn 1h vs WT-Zn_Exp_1


title: pif1+5mM Zn 1h vs WT+5mM Zn 1h_Exp_2

treatment_protocol: 5mM ZnCl2 for 1h


title: pif1+5mM Zn 1h vs WT+5mM Zn 1h_Exp_1


title: pif1+5mM Zn 1h vs pif1_Exp_1


title: 21d Const 20°C + Germ Alt temp (20:30°C), Rep 3 & 21d Const + 3d Alt temp (20:30°C), Rep 3

hyb_protocol: Arrays were pre-hybridized with a soln. of BSA, SDS and Dehardts. Arrays were then rinsed in 2XSSC/2%SDS, then water, and then 100% EtOH before being spun dry. Labeled cDNAs were mixed in a volume of 26.4 ul water, 7.65 ul 2XSSC, 7.2 ul 2%SDS, and 3.75 ul tRNA (10 mg/ml). cDNA was heated to 95 C for 5 minutes, spun down and placed on the array under a cover slip. Arrays were hybridized over night at 60 C. Washing was done by consecutive 5 minute rinses in 2XSSC/2%SDS, 1XSSC/0.2%SDS, 1XSSC/0.2%SDS again, 0.1XSSC, 0.1XSSC again, and spun dry.

source_name: Leafy spurge seeds: 21d Constant 20°C + Germ Alt temperature (20:30°C). Seeds harvested upon cracking of the seed coat. Rep 3

source_name: Leafy spurge seeds: 21d Const (20°C) + 3d Alt temp (20:30°C). Rep 3


title: c-Myb chip aby Upstate confluent_I

description: ChIP: Chip data analyzed by MAT software for cells cultured to confluence with anti-c-Myb clone 1-3 Millipore

source_name: Confluent Upstate ChIP DNA

source_name: input (fraction without antibody confluent cultures)


title: 3d Const temp (20°C), rep 3 & 2d Const temp (20°C), rep 3

source_name: Leafy spurge seeds: 3d Const temp (20°C), rep 3

source_name: Leafy spurge seeds: 2d Const temp (20°C), rep 3


title: 21d Const (20°C) + 3d Alt temp (20:30°C) & 21d Const (20°C) + 2d Alt temp (20:30°C)

source_name: Leafy spurge seed: 21d Const (20°C) + 3d Alt temp (20:30°C), rep 3

source_name: Leafy spurge seed: 21d Const (20°C) + 2d Alt temp (20:30°C), rep 3


title: Dry seeds, Rep 3 & 21d Constant 20°C + Germ Alt temperature (20:30°C), Rep 3

source_name: Leafy spurge seeds: Dry, Rep 3

source_name: Germinating seeds imbibed for 21d at 20 C followed by 20:30 C alternating temperatue. Leafy spurge seeds: 21d Constant 20°C + Germ Alt temperature (20:30°C). Seeds harvested upon cracking of the seed coat. Rep 3

extract_protocol: Seeds were harvested and placed in liquid nitrogen and ground to a fine powder. The Pine Tree extraction procedure (Chang S, Puryear, J. and Cairney, J. : A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter 1993, 11:113-116.) was used to isolate total RNA.


title: c-Myb chip aby VKN stimulated_I

description: ChIP: Chip data anayzed by MAT software for cells stimulated with estrogen for 24 hours with anti-c-Myb rabbit serum

source_name: estrogen stimulated VKN ChIP DNA


title: c-Myb chip aby VKN stimulated

source_name: control (pre-immune rabbit serum estrogen stimulated)


title: dimethylH3K4 chip confluent

source_name: Confluent Dimethyl H3K4 ChIP DNA

source_name: control (pre-immune rabbit serum confluent cultures)


title: BMSC-NGF treated

city: Morgantown

first: Stephanie

last: Rellick

state: WV

address: 1 Medical Center Drive P.O. Box 9300 West Virginia University Health Sciences Center

institute: West Virginia University

description: Group 2

hyb_protocol: Hybridization was completed using the Oligo GeArray following the manufacturer's protocol. (http://www.sabiosciences.com/support_manual.php)

scan_protocol: Array images were acquired by exposing the images to x-ray film and digital images were acquired by scanning the developed x-ray films.

data_processing: Images were scanned and analyzed using the GeArray Expression analysis suite software from SuperArray.  Background subtraction was performed using the minimum values and samples were normalized to GAPDH (positions 103, 104)

label: Biotin

source_name: BMSC-NGF treated

label_protocol: Labeling was completed using the Oligo GEArray TrueLabeling-AMP 2.0 kit following the manufacturer's protocol. (http://www.sabiosciences.com/support_manual.php)

growth_protocol: BMSC were maintained in Minimum Essential Medium, Alpha (α-MEM) supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, 100 mg/ml streptomycin, 100 IU/ml penicillin , and 5x10-5M 2-β mercapthanol at 37˚C in 6% CO2.

extract_protocol: Total cellular RNA was extracted from the BMSC using the RNeasy Mini RNA isolation kit (Qiagen) following the manufacturer's protocol. (http://www1.qiagen.com/Products/ RnaStabilizationPurification/RNeasySystem/RNeasyMini.aspx)

treatment_protocol: BMSC were serum deprived (1% FBS) for 24 hrs and then treated with recombinant human NGF (100ng/ml) or BDNF (100ng/ml) for 24hrs before the cells were collected and total RNA isolated

value: primary bone marrow stromal cells


title: BMSC-BDNF treated

description: Group 3

source_name: BMSC-BDNF treated


title: c-Myb chip aby VKN confluent

source_name: Confluent VKN ChIP DNA


title: BMSC-control

description: Group 1

source_name: BMSC-control


title: REH

first: Stephen

last: Akers

hyb_protocol: Hybridization was carried out on the OligoGEArray following the manufacture's protocol. (SABiosciences http://www.sabiosciences.com/support_manual.php?pfamily=microarrays)

scan_protocol: Array images were acquired by exposing the array to X-ray film.  Digital images were aquired by scanning the developed x-ray films.

data_processing: Digital images were analyzed using the GEArray Expression Analysis Suite 2.0.  Background was corrected for by subtracting the intensity values at empty spots (positions 116 and 117).  Signal intensities were then normalized to GAPDH (position 121).

source_name: REH ALL cell line (ATCC:  CRL-8286)

label_protocol: Labeling was carried out using the OligoGEArray TrueLabeling-AMP Kit following the manufacturer's protocol. (SABiosciences http://www.sabiosciences.com/support_manual.php?pfamily=microarrays)

growth_protocol: ALL cells were cultured in Iscove's DMEM supplemented with 10% fetal bovine serum, 2mM l-glutamine, 0.05uM 2-mercaptoethanol, 1U/mL penicillin, and 0.1mg/mL streptomycin.  Cells were maintained at a density of 1x10^6 cells/mL.

extract_protocol: Total cellular RNA was extracted from 10x10^6 leukemic cells using the RNeasy Mini kit (Qiagen) following the manufacturer's protocol. (http://www1.qiagen.com/Products/RnaStabilizationPurification/RNeasySystem/RNeasyMini.aspx#Tabs=t0)

treatment_protocol: ALL cells were left untreated to obtain information about baseline extracellular matrix and adhesion molecule expression.

value: REH


title: Nalm-27

source_name: Nalm-27 ALL cell line (Fujisaki Cancer Center, Japan)


title: c-Myb chip aby Upstate confluent

description: ChIP: Chip data analyzed by MAT software for cells cultured to confluence with anti-c-Myb clone 1-1 Millipore

source_name: Confluent Upstate ChIP DNA


title: JM-1

source_name: JM-1 ALL cell line (ATCC:  CRL-10423)


title: Tetraploid F2 vs tetraploid F3 Col-0 (line 1326-12) seedlings Replicate 4

city: Freising

first: Ramon

middle: Angel

last: Torres-Ruiz

address: Emil-Ramann-Str. 8

department: Genetik

country: Germany

institute: Technische Universität München, WZW

description: Biological replicate 4

hyb_protocol: cRNA (835ng) mixed with blocking agent and fragmentation buffer was incubated at RT (30 min) and fragmentation stopped with 2X hybridisation buffer. The mix was immediately loaded onto the microarray. Hybridization was performed at 65ºC for 17 hrs. The slides were subjected to three washing steps.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner G2565 (resolution: 5µm; channels: red & green; XDR: yes).

data_processing: Feature extraction and further processing was performed with the supplied Agilent feature extraction software (v.9.5.).  Probe sequences of the Agilent Chip were realigned to cDNA sequences of the TAIR7 gene annotation requiring a complete match (100% identity) of the probe sequences to the respective transcript sequence. Normalization and analysis of differential gene expression was restricted to probes uniquely matching one particular TAIR7 gene locus. These probes are indicated by flag=1 in the sheet of the processed expression values of the matrix sheet. TAIR7 transcript names for each probe are shown in the 'name' column of the matrix sheet if one probe mapped uniquely and specifically one alternative splice variant of the respective  locus, otherwise the TAIR7 locus identifier is reported for probes completely matching at least two alternative splice variants of the respective gene locus. Using the R/LIMMA package mean background intensities were subtracted from median red and green signals. M-values were normalized by the loess method for each array separately (“within array normalization”) and are shown as log2 Cy5/Cy3 ratios in the sample data tables.

source_name: Total RNA from 1326-12

label_protocol: RNA (500ng) without detectable degradation and impurities was mixed with a spike-in mix, T7-promoter primer and denatured for 10 min followed by 2 hrs at 40ºC after addition of the cDNA master mix. The reaction was stopped at 65ºC for 15 min. The resulting cDNA was mixed with transcription master mix (with Cy3- or Cy5-label respectively) and incubated at 40ºC for additional 2 hrs. cRNA quantity and Cy3/Cy5-labelling efficiency was determined using a ND-1000 NanoDrop® spectrophotometer.

growth_protocol: Seeds were stratified for two days at 4ºC (on 0.8% agar) and transferred to a test chamber (HAEREUS) with constant light (~75 µmol photons/m2 sec) and 22ºC. About 100 seedlings per microarray analysis were harvested on the fifth day when root tips had penetrated the seed coat. Plants were grown on quartz sand and peaty mould (1:2 mixture) under constant light (~70 µmol photons/m2 sec), 40% relative humidity and 18º C in a Heareus (HEMZ 20/240/S) walk-in growth chamber equipped with OSRAM L58W-lamps (865-“LUMILUX Cool Daylight”, 530-“Warm White”, 77-“FLUORA”).

extract_protocol: Total RNA was isolated using SVtotalRNA-System (Promega) as recommended by the supplier.

treatment_protocol: Seeds without recognizable emerging roots or which appeared to have germinated prematurely were discarded (less than 1%). The 6-8th leaves were harvested when the bud of the eleventh leaf was recognizable.

tag: generation

tag: cell ploidy

value: tetrapolid

value: seedlings

value: tetraploid


title: Tetraploid F2 vs tetraploid F3 Ler-0 (line 1026-41) seedlings Replicate 1

description: Biological replicate 1

source_name: Total RNA from line 1026-41

tag: tissue


title: Tetraploid Col-0 (line 1326-12) vs tetraploid Ler-0 (line 3116-6) seedlings Replicate 4

description: Biological replicate 4

source_name: Total RNA from line 3116-6


title: Tetraploid Col-0 (line 1326-19) vs tetraploid Ler-0 (line 1026-10) seedlings Replicate 3

description: Biological replicate 3

source_name: Total RNA from 1326-19

source_name: Total RNA from line 1026-10


title: Tetraploid F2 vs tetraploid F3 Col-0 (line 1326-26) seedlings Replicate 2

description: Biological replicate 2

source_name: Total RNA from 1326-26


title: Diploid Ler-0 vs diploid Col-0 seedlings Replicate 3

description: Technical replicate 1b

source_name: Total RNA from diploid Ler-0

value: established line

value: diploid

source_name: Total RNA from diploid Col-0


title: Tetraploid F2 vs tetraploid F3 Col-0 (line 1326-28) seedlings Replicate 1

description: Biological replicate 1

source_name: Total RNA from 1326-28


title: Tetraploid F2 vs tetraploid F3 Ler-0 (line 1026-10) seedlings Replicate 3

description: Biological replicate 3


title: Tetraploid F2 vs tetraploid F3 Ler-0 (line 1026-40) seedlings Replicate 2

description: Biological replicate 2

source_name: Total RNA from line 1026-40


title: Tetraploid Col-0 (line 1326-28) vs tetraploid Ler-0 (line 1026-41) seedlings Replicate 1

description: Biological replicate 1


title: Diploid Ler-0 vs diploid Col-0 seedlings Replicate 4

description: Technical replicate 2b


title: Tetraploid Col-0 (line 1326-26) vs tetraploid Ler-0 (line 1026-40) seedlings Replicate 2

description: Biological replicate 2


title: Tetraploid F2 vs tetraploid F3 Ler-0 (line 3116-6) seedlings Replicate 4

description: Biological replicate 4


title: Tetraploid F2 vs tetraploid F3 Col-0 (line 1326-19) seedlings Replicate 3

description: Biological replicate 3


title: SUP-B15

source_name: SUP-B15 ALL cell line (ATCC:  CRL-1929)


title: Diploid Col-0 vs diploid Ler-0 seedlings Replicate 2

description: Biological replicate 2a


title: Diploid vs tetraploid Ler-0 (line 3116-6) seedlings Replicate 8

description: Biological replicate 8


title: Diploid vs tetraploid Ler-0 (line 1026-41) seedlings Replicate 5

description: Biological replicate 5


title: Diploid vs tetraploid Ler-0 (line 1026-10) seedlings Replicate 7

description: Biological replicate 7


title: Diploid vs tetraploid Ler-0 (line 3116-6) seedlings Replicate 4_2

description: Biological replicate 4


title: Diploid vs tetraploid Ler-0 (line 1026-10) seedlings Replicate 3_2

description: Biological replicate 3


title: Diploid vs tetraploid Ler-0 (line 1026-40) seedlings Replicate 6

description: Biological replicate 6


title: Diploid vs tetraploid Ler-0 (line 1026-40) seedlings Replicate 2_2

description: Biological replicate 2


title: Diploid vs tetraploid Col-0 (line 1326-28) leaves sibling3 Replicate 3

description: Biological replicate 11

value: leaves

source_name: Total RNA from 1326-28 sibling3


title: Diploid vs tetraploid Ler-0 (line 1026-41) seedlings Replicate 1_2

description: Biological replicate 1


title: Diploid vs tetraploid Col-0 (line 1326-28) leaves sibling1 Replicate 1

description: Biological replicate 9

source_name: Total RNA from 1326-28 sibling1


title: Diploid vs tetraploid Col-0 (line 1326-26) leaves sibling2 Replicate 2

description: Biological replicate 6

source_name: Total RNA from 1326-26 sibling2


title: 21d Const (20°C) + 1d Alt temp (20:30°C) & 21d Const temp (20°C)

source_name: Leafy spurge seeds: 21d Const (20°C) + 1d Alt temp (20:30°C), Rep 3

value: Leafy spurge seeds harvested in 2008 in Fargo, ND.

source_name: Leafy spurge seeds: 21d Const temp (20°C), Rep 3


title: Late puberty 1

city: leiden

first: joyce

middle: AM

last: emons

country: Netherlands

institute: lumc

description: Gene expression data from epiphyseal growth plate sample in late pubertal stage.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 3.1, from SAS. Gene expression profiling was performed using arrays of human genome 133 Plus 2.0 -type from Affymetrix. A Custom CDF Version 11 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: epiphyseal growth plate sample in late stage puberty

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

extract_protocol: Total RNA isolation was performed with an optimized method for RNA extraction from cartilage as described by Heinrichs et al. (1994) except that the protocol was started by homogenizing the sections in 1 ml guanidine thiocyanate solution. RNA extraction was followed by purification with a RNeasy kit according to the manufacturers protocol (Qiagen)

value: sample obtained from tibia (female)

tag: gender

value: female

value: epiphyseal growth plate

tag: developmental stage

value: late puberty


title: Diploid vs tetraploid Col-0 (line 1326-26) leaves sibling1 Replicate 1

description: Biological replicate 5

tag: cell line

source_name: Total RNA from 1326-26 sibling1


title: Late puberty 2


title: Diploid vs tetraploid Ler-0 (line 1026-40) seedlings Replicate 2

description: Biological replicate 2


title: Diploid vs tetraploid Col-0 (line 1326-28) leaves Replicate 1

description: Biological replicate 1


title: Diploid vs tetraploid Col-0 (line 1326-28) leaves sibling2 Replicate 2

description: Biological replicate 10

source_name: Total RNA from 1326-28 sibling2


title: Pre-puberty 2

description: Gene expression data from epiphyseal growth plate sample in pre-pubertal stage.

source_name: epiphyseal growth plate sample in prepubertal stage.

value: pre-puberty


title: Pre-puberty 1


title: Diploid vs tetraploid Ler-0 (line 1026-41) seedlings Replicate 1

description: Biological replicate 1

source_name: Total RNA from line 1026-41


title: Diploid vs tetraploid Col-0 (line 1326-12) leaves Replicate 4

description: Biological replicate 4

source_name: Total RNA from 1326-12


title: Diploid vs tetraploid Col-0 (line 1326-26) leaves sibling4 Replicate 4

description: Biological replicate 8

source_name: Total RNA from 1326-26 sibling4


title: Diploid vs tetraploid Ler-0 (line 1026-10) seedlings Replicate 3

description: Biological replicate 3

source_name: Total RNA from diploid Ler-0

source_name: Total RNA from line 1026-10


title: Diploid vs tetraploid Col-0 (line 1326-26) leaves Replicate 2

description: Biological replicate 2

source_name: Total RNA from diploid Col-0

source_name: Total RNA from 1326-26


title: Early puberty 2

description: Gene expression data from epiphyseal growth plate sample in early pubertal stage.

value: early puberty


title: Diploid vs tetraploid Col-0 (line 1326-12) seedlings Replicate 8

description: Biological replicate 8


title: Diploid vs tetraploid Ler-0 (line 3116-6) seedlings Replicate 4

description: Biological replicate 4

source_name: Total RNA from line 3116-6


title: Diploid vs tetraploid Col-0 (line 1326-19) seedlings Replicate 7

description: Biological replicate 7

source_name: Total RNA from 1326-19


title: Diploid vs tetraploid Col-0 (line 1326-26) seedlings Replicate 6

description: Biological replicate 6


title: Diploid vs tetraploid Col-0 (line 1326-19) leaves Replicate 3

description: Biological replicate 3


title: Diploid vs tetraploid Col-0 (line 1326-26) leaves sibling3 Replicate 3

description: Biological replicate 7

source_name: Total RNA from 1326-26 sibling3


title: Diploid vs tetraploid Col-0 (line 1326-28) seedlings Replicate 5

description: Biological replicate 5

source_name: Total RNA from 1326-28


title: Tetraploid (line 1326-19) vs diploid Col-0 seedlings Replicate 3

description: Biological replicate 3


title: Tetraploid (line 1326-12) vs diploid Col-0 seedlings Replicate 4

description: Biological replicate 4


title: Early puberty 1

source_name: epiphyseal growth plate sample in early pubertal stage.


title: Tetraploid (line 1326-28) vs diploid Col-0 seedlings Replicate 1

description: Biological replicate 1


title: Tetraploid (line 1326-26) vs diploid Col-0 seedlings Replicate 2

description: Biological replicate 2


title: dmucR_late logarithmic growth phase_rep2

status: Public on Apr 23 2010

type: mixed

city: College Station

first: Jenni

last: Weeks

state: TX

address: 4467 TAMU

institute: Texas A&M University

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis 16M∆mucR culture grown cells to late logarithmic growth phase (OD600=0.9), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

hyb_protocol: Printed slides were submerged in 0.2 % SDS (Ambion, Austin, TX) for 2 minutes and washed three times in containers with ample ddH2O.  The microarray slides were placed in a prehybridization solution (5X SSC (Ambion, Austin, TX), 0.1 % SDS (Ambion, Austin, TX), and 1 % (w/v) BSA (Sigma, St. Louis, MO)) pre-warmed to 45°C for a minimum of 45 minutes.  Following prehybridization, the slides were washed five times in containers containing ample ddH2O, submerged once in isopropanol, and then immediately dried by centrifugation at 207 x g for 2 minutes at room temperature in a Jouan CR422 table top centrifuge.  The resuspended labeled RNA was combined with 1 µg of labeled genomic DNA from B. melitensis 16M to a total volume of 35 µl.  The sample was heated at 95°C for 5 minutes and held at 45°C until hybridization to the microarray slide.  The labeled cDNA was combined with 1X hybridization buffer (25 % (v/v) formamide (Sigma, St. Louis, Mo), 1X SSC (Ambion, Austin, TX) and 0.1 % (v/v) SDS (Ambion, Austin, TX)) and applied to the microarray with a 22 x 60 mm LifterSlip (Erie Scientific Company, Portsmouth, NH).  The microarray was incubated in a water bath for approximately 21 hours at 42°C in a sealed hybridization chamber (Corning, Corning, NY).    After hybridization, microarray slides were washed three times with agitation at room temperature.  The first wash buffer (2X SSC (Ambion, Austin, TX) and 0.2 % (v/v) SDS (Ambion, Austin, TX)) was pre-heated to 42°C and the microarray was washed for 10 minutes, followed by a 5 minute wash in 2X SSC (Ambion, Austin, TX).  The microarray was subsequently washed a third time in 0.2X SSC (Ambion, Austin, TX) for 5 minutes.  Immediately after the last wash, the arrays were dried by centrifugation for 2 minutes at 207 x g at room temperature in a Jouan CR422 tabletop centrifuge.

scan_protocol: Slides were scanned using a commercial laser scanner GenePix 4100A (Molecular Devices, Sunnyvale, CA) and Genepix 6.1 Pro software.  The auto-PMT (photomultiplier tube) function was used to determine the optimal gain for each laser channel with each slide.

data_processing: Spots that were flagged as bad or absent were removed from the analysis and background values were subtracted.  Raw Alexa 555 signals were normalized against the mean of the baseline Cy-5 gDNA reference.  GeneSifter (VizX Labs, Seattle, WA) was used to perform global mean normalization on the signal values already normalized to the reference channel.  Genes were retained if their signals were altered by at least a 1.5-fold change between conditions and a p value of 0.05 or less was obtained applying a Student’s t-test.  To further filter data based on biological relevance, individual pairwise comparisons were also performed on signal values after global mean normalization using Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).  Any fold-change observed between test conditions were expected to be at least 50 % greater in magnitude (e.g., 1.5-fold greater) than the fold-change observed between any two biological replicate samples.  Genes that did not meet the criteria were removed from the analysis.  For the samples extracted during the exponential growth phase, the analysis was modified to account for variation revealed by scatter plots fitted with a trend line using the normalized signal values in the wild type samples.  In addition to the analysis described above, a separate comparison was performed that included only the two similar wild type samples.  The resulting fold-change values were expected to be greater than 50 % of the value obtained for wild type 1 versus wild type 2.  A Student’s t-test was performed, retaining genes that had a p value of less than 0.05.  Genes that passed the conditions in either analysis method were considered statistically significant.

label: Alexa 555

organism: Brucella melitensis bv. 1 str. 16M

source_name: Brucella melitensis 16M∆mucR, late logarithmic phase of growth.

label_protocol: Total RNA extracted from B. melitensis 16M was transcribed into cDNA incorporating 5-(3-aminoallyl)-dUTP (aha-dUTP) for indirect labeling with Alexa Fluor 555 (Invitrogen, Carlsbad, CA), a Cy3-like fluorescein.  The cDNA synthesis combined 10 µg of total RNA, 6 µg random primers (Invitrogen, Carlsbad, CA), 1X first strand buffer (Invitrogen, Carlsbad, CA), 10 mM DTT, 0.5 mM each dATP, dTTP and dGTP, 0.3 mM dTTP (PCR grade, Invitrogen, Carlsbad, CA), 0.2 mM aha-dUTP (Invitrogen, Carlsbad, CA), 400 units SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) and 20 units protector RNAse inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 23°C for one minute and then at 46°C overnight.  The reaction was then treated with 0.4 M NaOH and incubated at 65°C for 15 minutes to stop the reaction and remove residual RNA. The pH was brought back to neutral with the addition of 0.2M HCl, then the cDNA was purified to remove unincorporated aha-dUTP and free amines using PCR Purification columns (Qiagen, Valencia, CA) with the modified wash (5 mM KPO4 (pH 8.0) and 80 % (v/v) ethanol) and elution buffers (4 mM KPO4 (pH 8.5)).  The manufacturer’s instructions were modified to include 2 washes with the substituted phosphate wash buffer, and the elution was carried out in 2 steps: 50 µl each elution (yielding 100 µl total) with a one minute incubation of the elution buffer in the column at room temperature before centrifugation. Alexa-Fluor 555 (Invitrogen, Carlsbad, CA) was coupled to the aha-dUTP incorporated into the cDNA following the coupling procedure outlined in the BioPrime® Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Carlsbad, CA) and purified using PCR purification columns (Qiagen, Valencia, CA) following manufacturer’s instructions.  Concentration and labeling efficiency of the labeled cDNA was examined using the Nanodrop® ND-1000 (Nanodrop, Wilmington, DE).  Labeled RNA samples were dried completely (Eppendorf Vacufuge, Westbury, NY) and resuspended in ddH2O immediately before hybridization to the microarrays.

growth_protocol: Brucella melitensis 16M Bv. 1 was obtained from ATCC and re-isolated from an aborted goat fetus by this lab. B. melitensis 16M Bv. 1 and its genetically modified derivatives were maintained as frozen glycerol stocks.  Strains were plated for isolation on TSA and incubated at 37°C with 5% CO2 for 3 days.  Individual 50 ml conical tubes with 5 ml of Brucella Broth (Difco Laboratories, Becton, Dickinson and Company, Franklin Lakes, NJ) were inoculated from an isolated single colony and incubated at 37ºC with agitation for 48 hours.  Cultures were then innoculated 1:1000 in Brucella Broth and grown at 37°C with agitation.  Growth curves of cultures were determined by the optical density (OD) of the culture at 600nm with bacterial colony forming units (CFU). For late logarithmic phase of growth, OD600=0.9.

extract_protocol: At harvest time, 14 % (v/v) of a cold ethanol solution containing 5 % (v/v) acidic water saturated phenol (Ultrapure, Invitrogen, Carlsbad, CA) was added to the bacterial culture and immediately centrifuged at 10900 x g for 3 minutes.  The supernatant was removed and the bacterial pellet was frozen in liquid nitrogen and stored at -80°C.  RNA was collected by re-suspending the bacterial pellets in 0.5 mg ml-1 lysozyme (Amresco, Solon, OH) dissolved in TE, followed by the addition of 0.97 % (v/v) SDS.  The cells were then incubated at 64°C for 2 minutes.  Next, 0.5 M sodium acetate (pH 5.2) was added, mixed gently by inversion and an equal volume of acidic water saturated phenol (Ultrapure, Invitrogen, Carlsbad, CA) was added and mixed well by inversion.  The bacteria-phenol mix was incubated at 64°C for 6 minutes and mixed by inversion several times every 40 seconds.  The bacteria-phenol mix was chilled on ice for 30 minutes and the layers were separated by centrifugation at 28900 x g for 13 minutes.  The aqueous layer was removed and placed in a clean tube.  An equal volume of chloroform (Sigma, St. Louis, MO) was added to the aqueous layer and mixed well by inversion.  The layers were separated by centrifugation at 20700 x g for 7 minutes.  This aqueous layer was placed into a clean tube and total RNA was precipitated by adding an equal volume of cold isopropanol and 0.1 volumes of 3M sodium acetate (pH 5.4).  RNA was precipitated for one hour at -80°C and then pelleted by centrifugation at 19000 x g for 30 minutes, washed with 80 % (v/v) ethanol, centrifuged for 5 minutes at 19000 x g, and the resulting pellets were air-dried for 20 minutes.  The dried pellets were resuspended in RNAse-free water, and subjected to DNAseI treatment. The DNA was degraded and removed by incubation with 5X DNAseI buffer (50 mM MgCl2, 50 mM Tris-Cl pH 7.5, 5 mM EDTA, 5 mM dithiothreitol (DTT)), 10 units of DNAseI (Qiagen, Valencia, CA) and 10 units of RNAse Inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 37°C for one hour.  Following the DNAseI digestion, the total RNA was further purified using the HighPure RNA isolation kit (Roche, Indianapolis, IN), following manufacturer’s instructions and included the optional (second) DNAseI incubation.  The RNA was eluted with the provided elution buffer, precipitated with 3 volumes of cold 95 % (v/v) ethanol and 0.1 volumes 3 M sodium acetate (pH 5.2) and washed with 80 % (v/v) ethanol.  The pellet was air dried for 15 minutes and then resuspended in The RNA Storage Solution (Ambion, Austin, TX).

tag: 16M bv.1 ∆mucR strain.

tag: B. melitensis 16M∆mucR (BMEI1364).


title: dluxR + exogenous C12-HSL_stationary growth_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to stationary growth phase (OD600=1.5) with 50 ng ml-1 exogenous C12-HSL (Sigma) added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M∆vjbR, stationary phase of growth with exogenous C12-HSL added.

label_protocol: Total RNA extracted from B. melitensis 16M was transcribed into cDNA incorporating 5-(3-aminoallyl)-dUTP (aha-dUTP) for indirect labeling with Alexa Fluor 555 (Invitrogen, Carlsbad, CA), a Cy3-like fluorescein.  The cDNA synthesis combined 10 µg of total RNA, 6 µg random primers (Invitrogen, Carlsbad, CA), 1X first strand buffer (Invitrogen, Carlsbad, CA), 10 mM DTT, 0.5 mM each dATP, dTTP and dGTP, 0.3 mM dTTP (PCR grade, Invitrogen, Carlsbad, CA), 0.2 mM aha-dUTP (Invitrogen, Carlsbad, CA), 400 units SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) and 20 units protector RNAse inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 23°C for one minute and then at 46°C overnight.  The reaction was then treated with 0.4 M NaOH and incubated at 65°C for 15 minutes to stop the reaction and remove residual RNA. The pH was brought back to neutral with the addition of 0.2M HCl, then the cDNA was purified to remove unincorporated aha-dUTP and free amines using PCR Purification columns (Qiagen, Valencia, CA) with the modified wash (5 mM KPO4 (pH 8.0) and 80 % (v/v) ethanol) and elution buffers (4 mM KPO4 (pH 8.5)).  The manufacturer’s instructions were modified to include 2 washes with the substituted phosphate wash buffer, and the elution was carried out in 2 steps: 50 µl each elution (yielding 100 µl total) with a one minute incubation of the elution buffer in the column at room temperature before centrifugation. Alexa Fluor 555 (Invitrogen, Carlsbad, CA) was coupled to the aha-dUTP incorporated into the cDNA following the coupling procedure outlined in the BioPrime® Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Carlsbad, CA) and purified using PCR purification columns (Qiagen, Valencia, CA) following manufacturer’s instructions.  Concentration and labeling efficiency of the labeled cDNA was examined using the Nanodrop® ND-1000 (Nanodrop, Wilmington, DE).  Labeled RNA samples were dried completely (Eppendorf Vacufuge, Westbury, NY) and resuspended in ddH2O immediately before hybridization to the microarrays.

growth_protocol: Brucella melitensis 16M Bv. 1 was obtained from ATCC and re-isolated from an aborted goat fetus by this lab.  B. melitensis 16M Bv. 1 and its genetically modified derivatives were maintained as frozen glycerol stocks.  Strains were plated for isolation on TSA and incubated at 37°C with 5% CO2 for 3 days.  Individual 50 ml conical tubes with 5 ml of Brucella Broth (Difco Laboratories, Becton, Dickinson and Company, Franklin Lakes, NJ) were inoculated from an isolated single colony and incubated at 37ºC with agitation for 48 hours.  Cultures were then inoculated 1:1000 in Brucella Broth and grown at 37°C with agitation.  50 ng/ml exogenous C12-HSL (Sigma) was added to some cultures at inoculation. Growth curves of cultures were determined by the optical density (OD) of the culture at 600nm with bacterial colony forming units (CFU).  For cells at logarithmic phase of growth, OD600=0.4; for cells at stationary phase of growth, OD600=1.5.

tag: 16M bv.1 ∆luxR strain.

tag: B. melitensis 16M∆vjbR (BMEII1116).


title: dmucR_late logarithmic growth phase_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis 16M∆mucR culture grown cells to late logarithmic growth phase (OD600=0.9), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dmucR_late logarithmic growth phase_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis 16M∆mucR culture grown cells to late logarithmic growth phase (OD600=0.9), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR_stationary growth_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to stationary growth phase (OD600=1.5), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M∆vjbR, stationary phase of growth.


title: Wild type_late logarithmic growth phase_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis culture grown cells to late logarithmic growth phase (OD600=0.9), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M, late logarithmic phase of growth.

tag: 16M bv.1 strain.


title: dluxR + exogenous C12-HSL_stationary growth_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to stationary growth phase (OD600=1.5) with 50 ng ml-1 exogenous C12-HSL (Sigma) added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR + exogenous C12-HSL_stationary growth_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to stationary growth phase (OD600=1.5) with 50 ng ml-1 exogenous C12-HSL (Sigma) added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR + exogenous C12-HSL_logarithmic growth_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to logarithmic growth phase (OD600=0.4) with 50 ng ml-1 exogenous C12-HSL (Sigma) added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M∆vjbR, logarithmic phase of growth with exogenous C12-HSL added.


title: dluxR + exogenous C12-HSL_logarithmic growth_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to logarithmic growth phase (OD600=0.4) with 50 ng ml-1 exogenous C12-HSL (Sigma) added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR_stationary growth_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to stationary growth phase (OD600=1.5), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR_logarithmic growth_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to logarithmic growth phase (OD600=0.4), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M∆vjbR, logarithmic phase of growth.


title: dluxR + exogenous C12-HSL_logarithmic growth_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to logarithmic growth phase (OD600=0.4) with 50 ng ml-1 exogenous C12-HSL (Sigma) added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: HESC HS235

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

country: France

institute: University Hospital of Montpellier

description:
The hesc lines hs235 was derived by the team of Pr. Outi Hovatta at the Karolinska Institute (Stockholm, Sweden) and cultured on human foreskin fibroblast feeder cells (crl-2429; american type culture collection, manassas, va, http: //www. atcc.org) (Hovatta et al. 2003).
The transcriptome of this hESC was compared to the transcriptome of fully reprogrammed human induced pluripotent stem cells, the parental fibroblast cells and partially reprogrammed cells.

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: Human embryonic stem cell line HS235

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

growth_protocol: The culture medium used for hESCs culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).

extract_protocol: Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

value: HS235 obtained from the Karolinska Instute of Stockholm, Sweden

tag: cell type

value: human embryonic stem cells


title: dluxR_stationary growth phase_rep2

data_processing: Spots that were flagged as bad or absent were removed from the analysis and background values were subtracted.  Raw Alexa 555 signals were normalized against the mean of the baseline Cy5 gDNA reference.  GeneSifter (VizX Labs, Seattle, WA) was used to perform global mean normalization on the signal values already normalized to the reference channel.  Genes were retained if their signals were altered by at least a 1.5-fold change between conditions and a p value of 0.05 or less was obtained applying a Student’s t-test.  To further filter data based on biological relevance, individual pairwise comparisons were also performed on signal values after global mean normalization using Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).  Any fold-change observed between test conditions were expected to be at least 50 % greater in magnitude (e.g., 1.5-fold greater) than the fold-change observed between any two biological replicate samples.  Genes that did not meet the criteria were removed from the analysis.  For the samples extracted during the exponential growth phase, the analysis was modified to account for variation revealed by scatter plots fitted with a trend line using the normalized signal values in the wild type samples.  In addition to the analysis described above, a separate comparison was performed that included only the two similar wild type samples.  The resulting fold-change values were expected to be greater than 50% of the value obtained for wild type 1 versus wild type 2.  A Student’s t-test was performed, retaining genes that had a p value of less than 0.05.  Genes that passed the conditions in either analysis method were considered statistically significant.

label_protocol: Total RNA extracted from B. melitensis 16M was transcribed into cDNA incorporating 5-(3-aminoallyl)-dUTP (aha-dUTP) for indirect labeling with Alexa Fluor 555 (Invitrogen, Carlsbad, CA), a Cy3-like fluorescein.  The cDNA synthesis combined 10 µg of total RNA, 6 µg random primers (Invitrogen, Carlsbad, CA), 1X first strand buffer (Invitrogen, Carlsbad, CA), 10 mM DTT, 0.5 mM each dATP, dTTP and dGTP, 0.3 mM dTTP (PCR grade, Invitrogen, Carlsbad, CA), 0.2 mM aha-dUTP (Invitrogen, Carlsbad, CA), 400 units SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) and 20 units protector RNAse inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 23°C for one minute and then at 46°C overnight.  The reaction was then treated with 0.4 M NaOH and incubated at 65°C for 15 minutes to stop the reaction and remove residual RNA.    The pH was brought back to neutral with the addition of 0.2M HCl, then the cDNA was purified to remove unincorporated aha-dUTP and free amines using PCR Purification columns (Qiagen, Valencia, CA) with the modified wash (5 mM KPO4 (pH 8.0) and 80 % (v/v) ethanol) and elution buffers (4 mM KPO4 (pH 8.5)).  The manufacturer’s instructions were modified to include 2 washes with the substituted phosphate wash buffer, and the elution was carried out in 2 steps: 50 µl each elution (yielding 100 µl total) with a one minute incubation of the elution buffer in the column at room temperature before centrifugation.  Alexa-Fluor 555 (Invitrogen, Carlsbad, CA) was coupled to the aha-dUTP incorporated into the cDNA following the coupling procedure outlined in the BioPrime® Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Carlsbad, CA) and purified using PCR purification columns (Qiagen, Valencia, CA) following manufacturer’s instructions.  Concentration and labeling efficiency of the labeled cDNA was examined using the Nanodrop® ND-1000 (Nanodrop, Wilmington, DE).  Labeled RNA samples were dried completely (Eppendorf Vacufuge, Westbury, NY) and resuspended in ddH2O immediately before hybridization to the microarrays.

extract_protocol: At harvest time, 14 % (v/v) of a cold ethanol solution containing 5 % (v/v) acidic water saturated phenol (Ultrapure, Invitrogen, Carlsbad, CA) was added to the bacterial culture and immediately centrifuged at 10900 x g for 3 minutes.  The supernatant was removed and the bacterial pellet was frozen in liquid nitrogen and stored at -80°C.  RNA was collected by re-suspending the bacterial pellets in 0.5 mg/ml lysozyme (Amresco, Solon, OH) dissolved in TE, followed by the addition of 0.97 % (v/v) SDS.  The cells were then incubated at 64°C for 2 minutes.  Next, 0.5 M sodium acetate (pH 5.2) was added, mixed gently by inversion and an equal volume of acidic water saturated phenol (Ultrapure, Invitrogen, Carlsbad, CA) was added and mixed well by inversion.  The bacteria-phenol mix was incubated at 64°C for 6 minutes and mixed by inversion several times every 40 seconds.  The bacteria-phenol mix was chilled on ice for 30 minutes and the layers were separated by centrifugation at 28900 x g for 13 minutes.  The aqueous layer was removed and placed in a clean tube.  An equal volume of chloroform (Sigma, St. Louis, MO) was added to the aqueous layer and mixed well by inversion.  The layers were separated by centrifugation at 20700 x g for 7 minutes.  This aqueous layer was placed into a clean tube and total RNA was precipitated by adding an equal volume of cold isopropanol and 0.1 volumes of 3M sodium acetate (pH 5.4).  RNA was precipitated for one hour at -80°C and then pelleted by centrifugation at 19000 x g for 30 minutes, washed with 80 % (v/v) ethanol, centrifuged for 5 minutes at 19000 x g, and the resulting pellets were air-dried for 20 minutes.  The dried pellets were resuspended in RNAse-free water, and subjected to DNAseI treatment.  The DNA was degraded and removed by incubation with 5X DNAseI buffer (50 mM MgCl2, 50 mM Tris-Cl pH 7.5, 5 mM EDTA, 5 mM dithiothreitol (DTT)), 10 units of DNAseI (Qiagen, Valencia, CA) and 10 units of RNAse Inhibitor (Roche, Indianapolis, IN).  The reaction was incubated at 37°C for one hour.  Following the DNAseI digestion, the total RNA was further purified using the HighPure RNA isolation kit (Roche, Indianapolis, IN), following manufacturer’s instructions and included the optional (second) DNAseI incubation.  The RNA was eluted with the provided elution buffer, precipitated with 3 volumes of cold 95 % (v/v) ethanol and 0.1 volumes 3 M sodium acetate (pH 5.2) and washed with 80 % (v/v) ethanol.  The pellet was air dried for 15 minutes and then resuspended in The RNA Storage Solution (Ambion, Austin, TX).


title: dluxR_stationary growth_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to stationary growth phase (OD600=1.5), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR_logarithmic growth_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to logarithmic growth phase (OD600=0.4), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR_stationary growth phase_rep1


title: dluxR_logarithmic growth_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis 16M∆vjbR culture grown cells to logarithmic growth phase (OD600=0.4), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: dluxR_stationary growth phase_rep3


title: Wild type + exogenous C12-HSL_stationary growth phase_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis culture grown cells to stationary growth phase (OD600=1.5) with 50 ng ml-1 exogenous C12-HSL added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M, stationary phase of growth with exogenous C12-HSL added.


title: Wild type + exogenous C12-HSL_stationary growth phase_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis culture grown cells to stationary growth phase (OD600=1.5) with 50 ng ml-1 exogenous C12-HSL added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type_late logarithmic growth phase_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis culture grown cells to late logarithmic growth phase (OD600=0.9), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type + exogenous C12-HSL_stationary growth phase_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis culture grown cells to stationary growth phase (OD600=1.5) with 50 ng ml-1 exogenous C12-HSL added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type_late logarithmic growth phase_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis culture grown cells to late logarithmic growth phase (OD600=0.9), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type_stationary growth phase_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis culture grown cells to stationary growth phase (OD600=1.5), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M, stationary phase of growth.


title: dluxR_logarithmic growth phase_rep2


title: dluxR_logarithmic growth phase_rep1


title: Wild type + exogenous C12-HSL_logarithmic growth phase_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis culture grown cells to logarithmic growth phase (OD600=0.4) with 50 ng/ml exogenous C12-HSL added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M, logarithmic phase of growth with exogenous C12-HSL added.


title: Wild type + exogenous C12-HSL_logarithmic growth phase_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis culture grown cells to logarithmic growth phase (OD600=0.4) with 50 ng/ml exogenous C12-HSL added at inoculation, labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type_logarithmic growth phase_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis culture grown cells to logarithmic growth phase (OD600=0.4), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.

source_name: Brucella melitensis 16M, logarithmic phase of growth.


title: dluxR_logarithmic growth phase_rep3


title: Wild type_stationary growth phase_rep1

description:
Biological replicate 1 of 3.
Total RNA from Brucella melitensis culture grown cells to stationary growth phase (OD600=1.5), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type_logarithmic growth phase_rep3

description:
Biological replicate 3 of 3.
Total RNA from Brucella melitensis culture grown cells to logarithmic growth phase (OD600=0.4), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.


title: Wild type_logarithmic growth phase_rep2

description:
Biological replicate 2 of 3.
Total RNA from Brucella melitensis culture grown cells to logarithmic growth phase (OD600=0.4), labeled with Alexa 555 and hybridized to the microarray with Brucella melitensis genomic DNA labeled with Cy5.  The same genomic DNA sample was hybridized to all microarrays.