title: Sand_Control_Rep3

city: Dübendorf

first: David

middle: R

last: Johnson

address: Uberlandstrasse 133

department: Environmental Microbiology

country: Switzerland

institute: Eawag

description: Gene expression 1 hour inoculation control

hyb_protocol: Sixty ng of labeled cDNA was loaded onto each microarray, hybridized for 17 hours at 65ºC, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60ºC for 30 minutes) was omitted.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR: Hi:100% and XDR Lo:10%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 021656_D_F_20081007) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rhizorhabdus wittichii RW1

source_name: Sphingomonas wittichii, exponentially grown, sand inoculation control

label_protocol: cDNA was synthesized from total RNA and directly labeled with cyanine-3-dCTP using a modification of a protocol described elsewhere (Gaillard et al., 2010, BMC Microbiol. 10:153). Briefly, each 50-µL reaction contained 10 µg of total RNA, 1.25 µg of random hexanucleotide primers (Promega), 100 µM each of unlabeled dATP, dGTP, and dTTP (Invitrogen), 25 µM of unlabeled dCTP (Invitrogen), 25 µM of cyanine-3-labeled dCTP (Perkin-Elmer), 25 U SUPERase•In (Ambion), and 400 U Superscript II reverse transcriptase (Invitrogen). Reactions were performed by heating at 42ºC for 2 hours followed by 70ºC for 10 min. RNA was then removed by adding 100 mM NaOH, heating to 65ºC for 20 min, and neutralizing with 100 mM HCl and 300 mM sodium acetate (pH 5.2). Labeled cDNA products were purified using the MinElute PCR purification kit (Qiagen) and the quantity and incorporation frequency of cyanine-3-labeled dCTP were calculated using the MICROARRAY function on a NanoDrop Spectrophotometer.

growth_protocol: Sphingomonas wittichii strain RW1 was obtained from Rolf-Michael Wittich. All cultures were grown in 100-mL culture flasks containing 20 mL of a phosphate-buffered mineral medium (medium DSM457 from the German Resource Centre for Biological Material, Braunschweig, Germany) and 5 mM of sodium salicylate as the sole carbon source. Bacterial growth was assessed from culture turbidity at 600 nm (OD600). Cells were collected from exponential phase liquid cultures (OD600 of 0.2 to 0.3) or from cells after inoculation into dry sand. Cells were collectd by vacuum filtration and the filters were stored at -80°C until processing.

extract_protocol: RNA was extracted from frozen filters using a previously described acid-phenol method (Johnson et al., 2005, Appl. Environ. Microbiol. 71:3866-3871; Johnson et al., 2008, Appl. Environ. Microbiol. 74:3533-3540). RNA samples were purified from contaminating DNA using the DNA-free kit from Ambion. The quantity and quality of the purified RNA was assessed using the A260 and A 280 values measured with the MICROARRAY function on a NanoDrop spectrophotometer (Witec AG). The integrity of RNA was further verified by agarose gel electrophoresis and the absence of DNA was verified by PCR.

treatment_protocol: For acute stress assays, nine culture flasks containing standard DSM457 medium were inoculated with a single stationary-phase culture of strain RW1. After cultures reached the mid-exponential phase (OD600 of 0.2 to 0.3), three cultures each were diluted into 180 mL of sodium chloride-amended DSM457 medium (solute potential decreased by 0.25 MPa), into polyethylene glycol (MW of 8000)-amended DSM457 medium (matric potential decreased by 0.25 MPa), or into standard DSM457 medium (control cultures). The cultures were then incubated for 30 min, cells were collected by vacuum filtration, and the filters were frozen with liquid nitrogen and stored at -80°C until further processing.For chronic stress assays, three culture flasks containing sodium chloride-amended DSM457 medium (solute potential decreased by 0.25), three culture flasks containing polyethylene glycol (MW of 8000)-amended DSM457 medium (matric potential decreased by 0.25 MPa), and three culture flasks containing standard DSM457 medium (control cultures) were inoculated with a single stationary-phase culture of strain RW1. After inoculation, the cultures were grown for approximately 24 hours until reaching the mid-exponential phase (OD600 of 0.2 to 0.4). Cells were then collected by vacuum filtration and the filters were frozen with liquid nitrogen and stored at -80°C until further processing.For sand desiccation experiments, seven culture flasks containing standard DSM457 medium were inoculated with a single stationary-phase culture of RW1. After the cultures reached the mid-exponential phase (OD600 of 0.2 to 0.3), cells were collected by centrifugation and the cell pellets were suspended in 100 µl of the remaining medium. Four of the 100-µL cell suspensions were then each inoculated into a 15-mL plastic tube containing two grams of dry sand and homogenized by mixing. The amount of liquid added was approximately 10% of the water holding capacity of the sand, at which level more than 70% of the inoculated RW1 cells remained viable after 60 min of incubation in the sand. The remaining three 100-µL cell suspensions were each inoculated into a 15-mL plastic tube that did not contain sand to serve as controls. All seven 15-mL tubes were then incubated for 60 min on a tube roller at 50 rpm and room temperature. After incubation, cells were extracted from the four sand treatments by adding five mL of a saline solution to each tube, vortexing the mixture, and filtering the suspension through a 70 µm pore-size cell strainer. Cells were then collected from the strainer filtrate by vacuum filtration and the filters were frozen with liquid nitrogen and stored at -80°C until further processing. For the three control cultures, two grams of sand and five mL of saline solution were added simultaneously to the samples after incubation for 60 min and cells were then immediately collected as described for the sand treatment samples.

tag: phase

value: Inoculation phase


title: Segregant 1b

status: Public on Jan 19 2011

type: RNA

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0

data_processing: initial filtering:mean red signal must be greater than 3 times the mean red background signal  print-tip-loess within-array normalization, quantile between-array normalization. R 2.9.2 software and limma bioconductor package used. All gpr files are Cy3 (test) to Cy5 (pool of 30)

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Segregant 1b

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

growth_protocol: Fermentation experiments and precultures were carried out at 28°C on a 1L synthetic medium MS300 (BELY et al. 1990). Extraction time at 50% of fermentation advancement (45g of released CO2).

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

tag: strain

value: Segregant 1b

tag: genetic background

tag: rmax

tag: fd

tag: cp

tag: nass

tag: suc

tag: gly

tag: ace

tag: pyr

source_name: Pool of the 30 segregants

value: Pool of the 30 segregants


title: Muscle_FoodIncludingChlorella_Swimming

city: Kyoto

first: Toru

last: Mizoguchi

state: Kyoto

address: 369, Karasuma-dori, Gojo, Shimogyo-ku

department: Research and Development Department

country: Japan

institute: Sun Chlorella Corp.

description: Gene expression after 14days in swimming and Chlorella intake mouse muscle

hyb_protocol: We used One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) v5.5 and according to the manufacturer’s instructions.

scan_protocol: Microarray was scanned by DNA Microarray Scanner G2565BA (Agilent Technologies, Palo Alto, CA, USA).

data_processing: The intensities were measured using Agilent Feature Extraction Software 9.5 (Agilent Technologies). A global normalization was performed for the inter-chip normalization. In order to define the expression level of the gene/probe, the signal intensity of each gene on a chip was divided by the median value of the signal intensities of the entire genes on the chip.

organism: Mus musculus

source_name: Muscle, 14days, food including 0.5% Chlorella powder, swimming

label_protocol: The total RNA of each group was pooled (n = 10 for each group) and labeled with Cyanine 3 (Perkin Elmer, Boston, MA, USA) using 500 ng of total RNA, according to the manufacturer’s instructions, which generated one-color labeled cRNAs.

extract_protocol: A part of the muscle tissue was then placed in RNAlater RNA Stabilization Reagent (Qiagen, Inc., Valencia, CA, USA) and was kept overnight at 4°C and subsequently stored at  20°C. RNA was isolated using an RNeasy Mini Kit (Qiagen) and was purified according to the manufacturer’s instructions. RNA purity and concentration were evaluated with a spectrophotometer using an absorbance ratio of 260/280 nm.

tag: gender

value: male

tag: age

value: Six-week-old

tag: tissue

value: swimming and Chlorella intake muscle


title: Sand_Treatment_Rep1

description: Gene expression 1 hour inoculation treatment (inoculation into dry sand)

source_name: Sphingomonas wittichii, exponentially grown, sand inoculation treatment


title: sax[kg07525]_1_3 (1631824013-E2)

city: East Lansing

first: Ian

last: Dworkin

state: MI

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

country: USA

institute: Michigan State University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using BeadStudio version 3.0.14 ( llumina Inc)

data_processing: The data were median normalised using custom R scripts

label: biotin

organism: Drosophila melanogaster

source_name: Drosophila wing imaginal disc

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit (ambion)

growth_protocol: Larvae for each genotype were grown in bottles, and late third instar larvae were collected, sexed, and the wing imaginal discs were dissected out.

extract_protocol: RNA extraction was performed using a modified protocol for the RNAeasy kit (Qiagen), with DNase I treatment. We Used ~ 40-50 imaginal discs for each biological replicate

value: Samarkand

tag: line number

tag: allele

tag: developmental stage

value: Third instar larvae

value: Wing imaginal disc

tag: biological replicate

tag: technical (labeling) replicate

tag: sentrix_id (slide)

tag: sentrix position (array)

tag: hybridization date


title: Sand_Treatment_Rep4

tag: phase


title: Sand_Treatment_Rep2


title: skeletal muscle sample at T1, pig 1

city: Bologna

first: Giuliano

last: Galimberti

address: Via delle Belle Arti, 41

country: Italy

institute: Università di Bologna

description: Gene expression data from porcine skeletal muscle at 2 hours after death

hyb_protocol: labeled cRNA was fractionated and hybridized with the GeneChip® Porcine Genome Array according to the standard procedures provided by the manufacturer. Affymetrix Fluidics Station 450 was used to wash and stain the chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinylated cRNA

scan_protocol: Fluorescent images were captured using Affymetrix Gene Chip® Scanner 3000 7G (Affymetrix)

data_processing: Raw CEL files were background-subtracted, normalized and summarized with the Robust Multi-array Average (RMA) algorithm (Irizarry et al., 2003) contained in the affy package (Bioconductor)

organism: Sus scrofa

source_name: Porcine skeletal muscle (3-5 g portion), sampled from the left leg, at 2 hours after death

label_protocol: biotin-labeled cRNA was syntethized using the GeneChip IVT labeling kit (Afffimetrix) from 5 mg of total RNA

growth_protocol: 3-5 g portions of semimebranosus muscle from 3 commercial hybrid pigs of female sex ( of about 160 kg each) raised in the same commercial farm

extract_protocol: total RNA was extracted with RNeasy Midi kit (Qiagen, Hamburg, Germany) following the protocol for animal tissue

treatment_protocol: portions were collected at 20 minutes, 2, 6 and 24 hours after slaughtering under normal conditions at the same abattoir

value: female

value: semimembranosus muscle

tag: time

value: 2 hours after death


title: skeletal muscle sample at T2, pig 3

description: Gene expression data from porcine skeletal muscle at 6 hours after death

source_name: Porcine skeletal muscle (3-5 g portion), sampled from the left leg, at 6 hours after death

value: 6 hours after death


title: Segregant 3a

source_name: Segregant 3a

tag: strain

value: Segregant 3a

tag: genetic background

tag: rmax

tag: fd

tag: cp

tag: nass

tag: suc


title: Segregant 22d

source_name: Segregant 22d

value: Segregant 22d

tag: gly

tag: ace

tag: pyr


title: GBM1

city: Rennes

first: Amandine

last: Etcheverry

address: 2 rue Henri Le Guilloux

institute: CNRS UMR 6290 - IGDR

description: serie 1

hyb_protocol: Hybridizations were performed following the manufacturer's recommendations (protocol version 5.7)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters

organism: Homo sapiens

source_name: brain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 350 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Snap frozen tumor blocks were cryodissected in 10 um sections. To allow a paired and accurate comparison between closely related biological materials, the adjacent sections were alternatively pooled in different tubes for DNA and RNA extraction.

extract_protocol: Total RNA was isolated using NucleoSpin RNAII Kit (Macherey-Nagel)

tag: tissue

value: brain

tag: integrative analysis

value: DNA methylation data available


title: skeletal muscle sample at T0, pig 3

description: Gene expression data from porcine skeletal muscle at 20 minutes after death

source_name: Porcine skeletal muscle (3-5 g portion), sampled from the left leg, at 20 minutes after death

tag: gender

value: 20 minutes after death


title: skeletal muscle sample at T3, pig 1

description: Gene expression data from porcine skeletal muscle at 24 hours after death

source_name: Porcine skeletal muscle (3-5 g portion), sampled from the left leg, at 24 hours after death

value: 24 hours after death


title: skeletal muscle sample at T3, pig 2


title: mam[kg02641]_2_3 (1631824013-D2)

tag: line number

tag: allele

tag: developmental stage

tag: biological replicate

tag: technical (labeling) replicate

tag: sentrix_id (slide)

tag: sentrix position (array)


title: Sand_Treatment_Rep3

tag: phase

value: Inoculation phase


title: skeletal muscle sample at T3, pig 3

tag: time


title: RatLiver_5ugSe_rep3

city: Madison

first: Roger

middle: A

last: Sunde

state: WI

address: 1415 Linden Dr

department: Nutritional Sciences

institute: University of Wisconsin

description: Gene expression from liver of a rat fed 5 ug Se/g diet for 28 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat Genome 230 2.0 or Mouse Genome 430 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following the EukGE_WS2v5_450 fluidics protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GC 3000 G7 Scanner and image data was extracted using the AFX Expression Console software.

data_processing: The data were analyzed in R/Bioconductor using the GCRMA algorithm.

organism: Rattus norvegicus

source_name: liver, 5 ug Se/g diet

label_protocol: Biotinylated cRNA were prepared with ENZO IVT kits from 5 ug cDNA for mouse samples and with MessageAmp Biotin-Enhanced IVT kits from 3 ug total RNA for rat samples

growth_protocol: Weanling mice or rats were housed in hanging wire cages and fed Se-deficient diets supplemented with up to 5 ug Se/g diet for 35 or 28 days, respectively

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

treatment_protocol: Animals were anesthetized with ether and livers were perfused in situ with ice-cold 0.15 M potassium chloride.  Liver and kidney were removed and snap-frozen in liquid nitrogen for later RNA analysis.

value: liver

tag: treatment

value: 5 ug Se/g diet


title: Sand_Control_Rep1


title: dad[J1E4]_1_2 (1631824004-H1)

tag: strain

tag: hybridization date


title: ksr[J5E2]_2_2 (1631824004-H2)


title: ast[kg07563]_2_1 (1631824013-C1)


title: Sand_Control_Rep2


title: Chronic_Matric_Rep2

description: Gene expression 24 hour after exposure to matric stress

source_name: Sphingomonas wittichii, exponentially grown, matric stress for 24 hours

value: Exponential growth phase


title: Chronic_Matric_Rep3


title: Chronic_Solute_Rep3

description: Gene expression 24 hour after exposure to solute stress

source_name: Sphingomonas wittichii, exponentially grown, solute stress for 24 hours


title: cbl[kg03080]_1_1 (1631824013-C2)

value: Samarkand


title: Chronic_Matric_Rep1


title: Ptc[k02507]_1_2 (1631824013-B1)

value: Third instar larvae


title: tkv[k19713]_3_1 (1631824004-F1)

value: Wing imaginal disc


title: sbb[BG01610]_1_3 (1631824004-E2)


title: rho[kg07115]_2_1 (1631824004-F2)


title: Bs[k07909]_2_1 (1631824004-G1)


title: drk[k02401]_1_1 (1631824004-G2)


title: Acute_Matric_Rep3

description: Gene expression 30 min after exposure to matric stress

source_name: Sphingomonas wittichii, exponentially grown, matric stress for 30 min


title: dad[J1E4]_1_1 (1631824018-D1)


title: Acute_Matric_Rep2


title: skeletal muscle sample at T0, pig 2

value: female


title: mam[BG02477]_1_1 (1631824004-E1)


title: rho-6[kg05638]_2_1 (1631824004-D1)


title: RatLiver_2ugSe_rep2

description: Gene expression from liver of a rat fed 2 ug Se/g diet for 28 days

source_name: liver, 2 ug Se/g diet

value: 2 ug Se/g diet


title: RatLiver_5ugSe_rep2


title: RatLiver_2ugSe_rep1


title: mam[kg02641]_2_2 (1631824004-D2)


title: Samarkand_3_2 (1631824004-C2)


title: mad[kg00581]_2_2 (1631824004-C1)


title: Acute_Solute_Rep2

description: Gene expression 30 min after exposure to solute stress

source_name: Sphingomonas wittichii, exponentially grown, solute stress for 30 min


title: Acute_Solute_Rep1


title: Chronic_Control_Rep1

description: Gene expression 24 hour control

source_name: Sphingomonas wittichii, exponentially grown, no stress


title: skeletal muscle sample at T0, pig 1

value: semimembranosus muscle


title: skeletal muscle sample at T1, pig 2

value: 2 hours after death


title: Chronic_Control_Rep2

description: Gene expression 24 hour control


title: Chronic_Solute_Rep1


title: Chronic_Solute_Rep2


title: RatLiver_0.08ugSe_rep1

description: Gene expression from liver of a rat fed 0.08 ug Se/g diet for 28 days

source_name: liver, 0.08 ug Se/g diet

value: 0.08 ug Se/g diet


title: RatLiver_0.24ugSe_rep3

description: Gene expression from liver of a rat fed 0.24 ug Se/g diet for 28 days

source_name: liver, 0.24 ug Se/g diet

value: 0.24 ug Se/g diet


title: Muscle_NormalFood_Nonswimming

description: Gene expression after 14days in nonswimming mouse muscle

source_name: Muscle, 14days, normal food, nonswimming

value: male

tag: age

value: Six-week-old

value: nonswimming muscle


title: Acute_Solute_Rep3


title: RatLiver_0.8ugSe_rep1

description: Gene expression from liver of a rat fed 0.8 ug Se/g diet for 28 days

source_name: liver, 0.8 ug Se/g diet

value: 0.8 ug Se/g diet


title: RatLiver_0.08ugSe_rep3


title: Acute_Matric_Rep1


title: RatLiver_5ugSe_rep1


title: RatLiver_0.08ugSe_rep2


title: RatLiver_SeDef_rep3

description: Gene expression from liver of a rat fed a Se-deficient diet for 28 days

source_name: liver, Se deficient

value: Se deficient


title: RatLiver_0.8ugSe_rep3

value: liver


title: RatLiver_2ugSe_rep3


title: Gap1[mip-w+]_1_2 (1631824004-B2)

source_name: Drosophila wing imaginal disc


title: RatLiver_0.24ugSe_rep1


title: RatLiver_0.24ugSe_rep2


title: RatLiver_0.8ugSe_rep2


title: RatLiver_SeDef_rep2


title: ast[kg07563]_2_3 (1631824004-A1)


title: pnt[kg04968]_1_1 (1631824004-A2)


title: NormalMammaryTissue_NonIrradiated_2

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression of control normal tissue

hyb_protocol: Labeled RNA was hybridized to DNA microarrays (Whole Rat Genome Microarray Kit, Agilent) using the Gene Expression Hybridization Kit (Agilent) at 65°C for 17 h and washed with Gene Expression Wash Buffers 1 and 2 (Agilent).

scan_protocol: Microarrays were then scanned (DNA Microarray Scanner, Model G2565BA; Agilent) using one color scan setting for 4x44K array slides (scan area, 61x21.6 mm; scan resolution, 5 um; scanning mode, single pass; extended dynamic range, on; dye channel, Green; Green PMT for XDR-Hi, 100%; and Green PMT for XDR-Lo, 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and grid 014879_D_F_20100118) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as not positive and significant or not above background were excluded. The median normalized signal intensity from the three non-irradiated control signals were compared with each hybridized sample and log2 transformed.

source_name: Normal mammary tissue, non-irradiated

label_protocol: Cyanine 3–labeled complementary RNA was generated from total RNA samples of tumors and normal mammary tissues from age-matched rats using the Low RNA Input Linear Amplification Kit Plus (Agilent Technologies, Inc., Santa Clara, CA).

extract_protocol: Total RNA was extracted from frozen carcinomas and from frozen normal mammary tissues of 7-week-old rats using the Maxwell 16 Total RNA Purification kit (Promega Co., Madison, WI).

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (2 Gy, 0.6 Gy/min) at 3 or 7 weeks of age. Rats were fed AIN-76A diet containing 23.5% corn oil  after 9 weeks of age. At 50 weeks of age, rats with palpable tumors were killed using ether anesthesia and tumors were collected.

value: mammary

tag: age at irradiation

value: non-irradiated

source_name: Normal mammary tissue, non-irradiated, mean value of 3 Samples


title: RatLiver_SeDef_rep1

tag: tissue


title: Acute_Control_Rep1

description: Gene expression 30 min control

value: Exponential growth phase


title: Acute_Control_Rep2

description: Gene expression 30 min control


title: Acute_Control_Rep3

description: Gene expression 30 min control


title: Liver Mouse11_Sample01 [validation]

status: Public on Jan 18 2011

city: Bar Harbor

first: Peter

middle: Thomas

last: Vedell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA was hybridized onto GeneChip® Mouse Gene 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner, quantified, and exported to .CEL file format  using the GeneChip® Operating Software.

data_processing:
Probes were mapped to 34760 probe sets using the R/mogene10stv1.r3cdf  package. The .CEL files were processed using the R/affy package using the Robust Multichip Average normalization method. The probe sets were mapped to genes using the R/mogene10sttranscriptcluster.db package. Pairwise scatter plots of intensities by array, density plots of intensities by array were produced int the R statistical software. Also, variance component analysis that incorporated all known experimental factors, was conducted in R statistical software in order to verfiy that technical artifacts were a minimal influence on results. .
The normalized data was determined by applying the robust multichip average (RMA) quantile normalization  method (Bolstad et al. 2003)  across all samples.  The normalized data is given on a log base 2 scale.

source_name: C57BL/6J male mouse

label_protocol: Labeling occurs by terminal deoxynucleotidyl transferase (TdT), where biotin is added by a Affymetrix Labeling Reagent.

growth_protocol: We obtained twelve C57BL/6J male mice from The Jackson Laboratory. Six pairs of littermates were pair-housed from weaning and put on a 5k52 diet (standard chow containing 6% fat).

extract_protocol: Livers were extracted, perfused with RNase-free DEPC-treated PBS, cut into pieces not exceeding 0.5 cm in any dimension, and placed in 15 ml conical tubes.  The pieces were divided into 2 aliquots and stored in RNAlater (Ambion, Austin TX).  Each kidney aliquot consisted of one complete kidney.  Tissues were homogenized in TRIzolTM (Invitrogen, Carlsbad, CA).  Total RNA was isolated by standard TRIzolTM  methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Santa Clara, CA).  The RNA was then treated with DNase1 (Qiagen, Valencia, Ca.) according to the manufacturer’s methods.    Total RNA was then reverse transcribed followed by second strand cDNA synthesis.

treatment_protocol: At 10 weeks, body weight was recorded and the mice were euthanized by cervical dislocation. Dissection procedures were started  at 11:00 a.m. after a 4-hour fasting period and were completed within a one-hour time window.

tag: body weight (g)

tag: age (days)


title: Samarkand_4_1 (1631824004-B1)

value: Samarkand

tag: line number

value: Third instar larvae


title: E. coli O157:H7 86-24 in LB at 37oC at OD 4.0

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

description: RNA extracted from E. coli 86-24 cells grown (OD=4.0) in LB at 37ºC

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: Channel 1

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: E. coli O157:H7 86-24 was inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 250 rpm and 37°C for an absorbance of 4.0 at 600 nm.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104).


title: Liver Mouse04_Sample02 [validation]

tag: gender


title: Chronic_Control_Rep3

description: Gene expression 24 hour control


title: E. coli O157:H7 EDL933 in LB at 37oC at OD 4.0

description: RNA extracted from E. coli EDL933 cells grown (OD=4.0) in LB at 37ºC

extract_protocol: E. coli O157:H7 EDL933 was inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 250 rpm and 37°C for an absorbance of 4.0 at 600 nm.  Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C.  RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104).


title: Liver Mouse12_Sample01 [validation]


title: Liver Mouse08_Sample01 [validation]


title: Liver Mouse09_Sample02 [validation]


title: Liver Mouse10_Sample02 [validation]


title: Liver Mouse08_Sample02 [validation]


title: Liver Mouse06_Sample02 [validation]


title: Liver Mouse05_Sample02 [validation]


title: Liver Mouse12_Sample02 [validation]


title: Liver Mouse02_Sample02 [validation]


title: Liver Mouse07_Sample02 [validation]


title: Liver Mouse01_Sample02 [validation]


title: Liver Mouse03_Sample02 [validation]


title: Liver Mouse09_Sample01 [validation]


title: Liver Mouse10_Sample01 [validation]


title: Liver Mouse11_Sample02 [validation]


title: Liver Mouse06_Sample01 [validation]


title: Liver Mouse04_Sample01 [validation]


title: A. aceti_Ethanol_#1

status: Public on Jan 17 2011

city: Bunkyo-ku

first: Hiroyuki

last: Arai

state: Tokyo

address: Yayoi 1-1-1

department: Department of Biotechnology

institute: The University of Tokyo

description: This sample is of A. aceti NBRC14818 grown on ethanol. It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed with Hybridization System 4 according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

scan_protocol: Array scanning was performed with MS200 Microarray Scanner according to the NimbleGen Arrays User´s Guide for Gene Expression Analysis (Roche NimbleGen).

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, and background correction as implemented in the NimbleScan software 2.5 (Roche NimbleGen).

organism: Acetobacter aceti NBRC 14818

source_name: A. aceti, ethanol replicate 1

label_protocol: Labeling of double stranded cDNA synthesized with the Superscript Double-Stranded cDNA Synthesis Kit (Invitrogen) was performed according to the instructions for NimbleGen Arrays User’s Guide for Gene Expression Analysis by Roche NimbleGen using One-Color DNA Labeling Kit (Roche NimbleGen).

growth_protocol: A. aceti was cultivated in ethanol medium consisting of 1% yeast extract and 1% ethanol in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.4.

extract_protocol: Total RNA was extracted by a hot-phenol method. After contaminated DNA was eliminated by RQ1 DNase (Promega) treatment, RNA was purified by RNeasy mini columns (Qiagen).

treatment_protocol: The culture was mixed with 2 volumes of RNAprotect Bacterial Reagent (Qiagen) before RNA purification.

tag: genotype

value: wild type

tag: carbon source

value: ethanol


title: A. aceti_Ethanol_#2

description: This sample is of A. aceti NBRC14818 grown on ethanol. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, ethanol replicate 2


title: A. aceti_Acetate_#1

description: This sample is of A. aceti NBRC14818 grown on acetate. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, acetate replicate 1

growth_protocol: A. aceti was cultivated in acetate medium consisting of 1% yeast extract and 1% sodium acetate in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3.

value: acetate


title: A. aceti_Acetate_#2

description: This sample is of A. aceti NBRC14818 grown on acetate. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, acetete replicate 2


title: A. aceti_Glucose_#1

description: This sample is of A. aceti NBRC14818 grown on glucose. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, glucose replicate 1

growth_protocol: A. aceti was cultivated in glucose medium consisting of 1% yeast extract and 3.6% D-glucose in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3.

value: glucose


title: Liver Mouse07_Sample01 [validation]


title: Liver Mouse03_Sample01 [validation]


title: A. aceti_Mix_#2

description: This sample is of A. aceti NBRC14818 grown on mix of ethanol and glucose. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, ethanol + glucose replicate 2

growth_protocol: A. aceti was cultivated in mix medium consisting of 1% yeast extract, 1% ethanol and 3.6% D-glucose in Erlenmeyer flask with rotary shaking. Total RNA was extracted when optical density at 600 nm was 0.3.

value: ethanol + glucose


title: A. aceti_Mix_#1

description: This sample is of A. aceti NBRC14818 grown on mix of ethanol and glucose. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, ethanol + glucose replicate 1


title: dsap18 embryos (Biological Replicate2, Dye-swap 1)

city: Barcelona

first: Sergi

last: Beltran

address: Baldiri Reixac 10

department: Serveis Cientificotècnics

country: Spain

institute: Universitat de Barcelona

description: A total of four microarrays were hybridized in biological replicate pairs, such that the total RNA from dsap18 mutant animals (dsap18^117/Df(3R)sbd^45 0-24h staged embryos) and control animals (rescued dsap18^117/Df(3R)sbd^45 0-24h embryos containing a dsap18-HA transgene) used as starting material came from different extractions. Both arrays from each pair were hybridized with the same amplified RNA from sample and common reference (obtained using the Amino-Allyl Messageamp II aRNA Amplification Kit from Ambion, Inc) but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.

hyb_protocol: Samples were diluted in 2X Hybridization Buffer #5185-5973(Agilent Technologies) and hybridization was carried out at 60ºC for 18 hours with a G2534A SureHyb Chamber in a G2545A Hybridization Oven (Agilent Technologies).

scan_protocol: GenePix Results (GPR) data files were obtained for each microarray with an Axon 4000B scanner and GenePix Pro 6 (Axon Instruments, Inc).

data_processing: GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the "normexp" method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Quality of spots was assesed by spot size, foreground versus background signals, saturation and coincidence between differently calculated ratio measures and R2 of regression ratio.

label_protocol: 1.5ug total RNA were amplified and indirectly labelled with Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc). Fragmentation was done with RNA Fragmentation Reagents #8740(Ambion, Inc).

growth_protocol: Flies were kept on standard media at 25ºC.

extract_protocol: Embryos were dechorionated and total RNA extraction was performed with RNeasy Mini Kit (QIAGEN Inc.). Quality was assessed using the Eukaryote Total RNA Nano Assay on a 2100 Bioanalyzer (Agilent Technologies).

value: Rescue (control) flies carry a dsap18-HA transgene in chrX.

tag: stage

value: embryo

value: 0-24h old

value: whole embryos

value: dsap18^117 corresponds to a null mutation generated by P-element mobilization from EP(3)3462. Df(3R)sbd45, which uncovers dsap18 , was obtained from the Bloomington Stock Center.


title: Liver Mouse05_Sample01 [validation]

value: male


title: A. aceti_Glucose_#2

description: This sample is of A. aceti NBRC14818 grown on glucose. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: A. aceti, glucose replicate 2


title: Gene expression in revR mutant biol rpt 2

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

hyb_protocol: Microarrays were pre-hybridised in a solution of 25 % formamide, 5X SSC, 0.1 % SDS and 10 mg/ml of herring sperm DNA at 42˚C for 45 mins.  Labelled cDNA was hybridised to the prehybridised microarrays according to the instructions provided with the Geneisphere 3DNA 900MPX kit

scan_protocol: The dried microarrays were scanned using a GMS418 microarray scanner (Affymetrix), scans were aquired using GMS scanner software (V.1.51.0.42) (Affymetrix) and quantified using Imagene version 5.1 (BioDiscovery).

data_processing: Quantified ImaGene files from four independant microarray experiments were analysed using the LIMMA software package for R.  Each microarray experiment was performed using an independant biological replicate, thus providing four independant biological replicates with two dye-swaps.  Spot intensities were firstly normalised per print tip group before being normalised between arrays using a Lowess algorithm.  Spot intensities were then log2 transformed and expression values calculated as the ratio of log2 intensity of revR mutant/wild-type.

organism: Clostridium perfringens str. 13

source_name: revR mutant during exponential growth

label_protocol: cDNA synthesis and labelling with Cy3 or Cy5 using 4 μg of total RNA was performed according to the Genisphere 3DNA 900MPX kit (Genisphere) according to the manufacturer's instructions.

growth_protocol: Bacterial strains were cultured for 4 hrs at 37˚C in sterile TPYG broth (5 % [w/v] tryptone, 0.5 % [w/v] proteose peptone, 0.3 % [w/v] yeast extract and 0.1 % [w/v] sodium thioglycolate, supplimented with sterile glucose to a final concentration of 0.38 % [v/v] after autoclaving) under anaerobic conditions.

extract_protocol: Cells were harvested from 15 ml aliquots of bacterial culture by centrifugation at 5800 x g for 10 mins.  Cell pellets were treated with lysozyme (10 mg/ml) for 15 mins prior to RNA extraction using TriZol (Invitrogen) according to the manufacturer's instructions.  Repeated rounds to DNase I digestion and Trizol extraction were performed until  DNA contaminiation was removed.

treatment_protocol: Gene expression was compared between a revRmutant of C. perfringens strain 13 and wild-type

value: revR mutant

source_name: wild-type strain 13 during exponential growth

value: wild-type


title: Hep3B-LIP control without epression of LIP Hep-16

status: Public on Jan 16 2011

city: ROUEN

first: Jean

middle: Philippe

last: SALIER

address: Bvd Gambetta

department: Inserm Unit 519

institute: Faculty of Medicine and Pharmacy

description: cells transfected by the Tet-OFF system which provides a doxycyclin controlled  LIP over-expression

hyb_protocol: Hybridization of the [α 33P]-labelled targets onto a cDNA array was done after preincubating the membrane in a mixture (50mL) of 50% deionized formamide, 5xSSPE (20xSSPE is 3M NaCl, 0.23M NaH2PO4, 20mM EDTA, pH 7.4), 5x Denhardt's solution, 1% SDS, 5% dextran sulfate, 200μg/mL heatdenatured salmon sperm DNA at 42°C for 3h in a rolling bottle. The labelled targets in 25mL of the same mixture were next incubated with the membrane at 42°C for 18 hrs, prior to membrane washing (two washes at 68°C for one hour each) with 50mL of a 2xSSPE / 0.5% SDS mixture.

scan_protocol: Quantitative signals were obtained by membrane autoradiography for 46-48 hours onto an europium screen that was next scanned with a 100µm resolution in a Phosphorimager SI (Molecular Dynamics)

data_processing: The scanned 16-bit in a Linux workstation and the spots were automatically identified and analyzed with XdotsReader software, version 1.8 (COSE, Le Bourget, France). A global background was calulated over the entire image as the mean of a local background measured around each spot and it was automatically substracted from every spot signal. Next, the mean signal associated to negative control spots was calculated over the entire image. For all genes under study, a spot whose signal was below a given threshold (2 SD above the average signal for negative controls) was considered to be non-significant (p<0.05). Finally, the mean signal associated to negative control spots was automatically substacted from the signal for every significant spot. Data normalization was based on the mean of the signals provided by the complete set of spots per image.

source_name: Hep3BLIP control without epression of LIP

label_protocol: Within each RNA preparation prepared as above the target poly(A) mRNAs were labelled as follows : 10μg total RNAs in a 20μL solution containing dATP/dGTP/dTTP (0.5mM each) and 1μg 5'(dT23)VN3' oligonucleotide were heated at 65°C for 5min, cooled down to 4°C, added with 7μL 5x first-strand buffer (Tris-HCl buffer 250mM, pH 8.3, KCl 375mM, MgCl2 15mM), 2μL DTT 0.1M, 1μL (40u.) RNAse OUT as an RNAse inhibitor (Invitrogen) and 5μL [α 33P]dCTP (10mCi/mL, from Amersham) and incubated at 42°C for 2min prior to the addition of 200u. SuperScriptII RNAse H(-) reverse transcriptase (Invitrogen) and a further incubation at 42°C for 1h. A chase was done by adding 1μL dNTPs (10mM each) and 200u. SuperScriptII and incubating at 42°C for 1h. The RNAse inhibitor was next destroyed at 70°C for 15min and the RNA templates were digested with 2u. RNAseH (Invitrogen) at 37°C for 20min. Finally, free [α 33P]dCTP was eliminated by gel filtration onto a Nick Column G-50 (Amersham-Pharmacia Biotech) and the resulting, labelled cDNAs were immediately used for hybridization.

extract_protocol: Chomczynski, P., and Sacchi, N. 1987. Single-step method of RNA isolation by acid guanidium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162: 156-159.

tag: Hep3B tTA4-pTRE-LIP-flag  cultured with doxycycline


title: Sample051090873-Caucasian American-Case

city: Buffalo

first: hua

last: zhao

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Cancer Institute

hyb_protocol: Two hundred ng of total RNA from each sample were labeled and hybridized on Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina), according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).

scan_protocol: Standard Illumina scanning protocol

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

source_name: Plasma

extract_protocol: Total RNA, including miRNA from plasma, was isolated using the miRNeasy kit (Qiagen) with minor modifications. The quality and quantity of the RNA was evaluated by 260/280 ratio using NanoDrop spectrophotometry (NanoDrop ND-1000 Technologies Inc.) and Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: race

value: Caucasian American

tag: disease state

value: early stage breast cancer

value: plasma


title: Sample051520945-Caucasian American-Case

label_protocol: Two hundred ng of total RNA from each sample were labeled and hybridized on Human v2 MicroRNA Expression BeadChips (Cat. no. MI-102–1024; Illumina), according to the manufacturers recommendations (Illumina MicroRNA Expression Profiling Assay Guide).


title: Sample001000497-African American-Control

value: African American

value: Control


title: Sample053200849-Caucasian American-Case


title: Hep3B-LIP control without epression of LIP Hep-17


title: Sample050270915-African American-Case


title: Sample001000320-African American-Control


title: Sample001000239-Caucasian American-Control


title: Sample001000181-African American-Control


title: Sample042571018-African American-Case


title: Sample043520824-Caucasian American-Case


title: Sample043240765-African American-Case


title: Sample001000304-African American-Control


title: Sample042990890-Caucasian American-Case


title: Liver Mouse02_Sample01 [validation]

value: liver


title: dsap18 embryos (Biological Replicate2, Dye-swap 2)


title: Hep3B-LIP control without epression of LIP Hep-18


title: Hep3B-LIP control without epression of LIP Hep-20


title: Hep3B-LIP control without epression of LIP Hep-19


title: Sample001001851-African American-Control


title: Sample073611731-African American-Case


title: Sample052080808-African American-Case


title: Sample001001905-Caucasian American-Control


title: Gene expression in revR mutant biol rpt 1


title: Gene expression in revR mutant biol rpt 4


title: Sample001000197-Caucasian American-Control


title: Sample070091501-African American-Case


title: Sample043080798-Caucasian American-Case


title: Sample001000167-Caucasian American-Control


title: Sample040630464-African American-Case


title: Sample051600904-Caucasian American-Case


title: Sample060050829-Caucasian American-Case


title: Sample041910694-Caucasian American-Case


title: Hep3B-LIP expressing LIP Hep-11

source_name: Hep3BLIP expressing LIP

tag: Hep3B tTA4-pTRE-LIP-flag  cultured without doxycycline during 10 days


title: Gene expression in revR mutant biol rpt 3


title: Hep3B-LIP expressing LIP Hep-15


title: dsap18 embryos (Biological Replicate1, Dye-swap 2)


title: Hep3B-LIP expressing LIP Hep-14


title: Hep3B-LIP expressing LIP Hep-12


title: Liver Mouse01_Sample01 [validation]


title: Sample001000449-African American-Control


title: Sample050620621-African American-Case


title: dsap18 embryos (Biological Replicate1, Dye-swap 1)

value: Rescue (control) flies carry a dsap18-HA transgene in chr2.


title: Hep3B-LAP control without expression of LAP Hep-10

description: cells transfected by the Tet-OFF system which provides a doxycyclin controlled  LAP over-expression

source_name: Hep3BLAP control without expression of LAP

tag: Hep3B tTA4-pTRE-LAP-flag  cultured with doxycycline


title: Sample090151309-Caucasian American-Case


title: Sample001001826-African American-Control


title: Sample001001804-Caucasian American-Control


title: Sample001001801-Caucasian American-Control


title: Sample001001917-African American-Control


title: Sample001002063-Caucasian American-Control


title: Sample001001372-African American-Control


title: Sample071311205-African American-Case


title: Sample001001856-African American-Control


title: Sample001001903-Caucasian American-Control


title: Hep3B-LAP  expressing LAP Hep-4

source_name: Hep3BLAP  expressing LAP

tag: Hep3B tTA4-pTRE-LAP-flag  cultured without doxycycline during 10 days


title: Hep3B-LAP control without expression of LAP Hep-8


title: Hep3B-LAP  expressing LAP Hep-3


title: Hep3B-LAP  expressing LAP Hep-2


title: Hep3B-LIP expressing LIP Hep-13


title: Hep3B-LAP control without expression of LAP Hep-9


title: Hep3B-LAP control without expression of LAP Hep-6


title: Hep3B-LAP  expressing LAP Hep-5


title: Sample001002045-Caucasian American-Control


title: Sample001002048-Caucasian American-Control


title: Sample082170390-African American-Case


title: Hep3B-LAP control without expression of LAP Hep-7


title: Hep3B-LAP  expressing LAP Hep-1


title: T8C5_T16C3(3)

status: Public on Jan 15 2011

city: Houston

first: Delphine

last: Saulnier

state: TX

address: Feigin Center, Suite 830, 1102 Bates Avenue

department: Pathology

institute: Baylor College of Medicine

description: Biological replicate 3 of 3. Dye swap 2

hyb_protocol: For hybridization, yeast tRNA and salmon testes DNA were added to labeled cDNA along with a formamide hybridization buffer. Samples were applied to slides, and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

scan_protocol: Arrays were scanned on a Axon instruments GenePix 4000B scanner.  Images were processed using GenePix Pro software (version 4.1)  and hybridization was carried out at 42 degrees Celsius in Corning microarray hybridization chambers overnight.  Slides were then washed sequentially for four minutes in each of the following buffers: 1X SSC and 0.2% SDS, 0.1X SSC and 0.2% SDS, and 0.1X SSC

data_processing: Data normalization between and within array using LOWESS

organism: Limosilactobacillus reuteri

source_name: Bacteria, reference

label_protocol: 2 ug of total RNA were primed with 2.5 ug of random hexamers (Qiagen) at 70 degrees Celsius for 10 minutes. Reverse transcription was then carried out using Superscript III (Invitrogen) with 500 uM each dATP, dCTP, and dGTP, 300 uM dTTP, and 200 uM aminoallyl dUTP. After reverse transcription, RNA was removed by hydrolysis and cDNA was cleaned. cDNA was then labeled using CyDye Post-labeling reactive dye packs (Amersham).

growth_protocol: Bacterial cells were grown for 8h (T8), 12h (T12), 16h (T16) and 24h (T24) in LDMIII at 37C in anaerobic conditions

extract_protocol: At the specified times, 5 ml of bacterial were collected and mixed with an equal part of ice-cold methanol. Cell pellets were centrifuged, washed, and resuspended in 0.25 units/ul mutanolysin. After incubation at 37 degrees Celsius for 20 minutes, total RNA was collected according to the manufacturer's instructions with the Qiagen RNeasy Kit.

tag: strain

tag: time

source_name: Bacteria, test


title: T8C3_T24C5(2)

description: Biological replicate 2 of 3. Dye swap 1


title: T8C3_T24C5(1)

description: Biological replicate 1 of 3. Dye swap 1


title: T8C5_T24C3(1)

description: Biological replicate 1 of 3. Dye swap 2


title: T8C5_T16C5(2)

description: Biological replicate 2 of 3. Dye swap 2


title: T8C3_T24C5(3)

description: Biological replicate 3 of 3. Dye swap 1


title: T8C5_T24C3(3)

description: Biological replicate 3 of 3. Dye swap 2


title: T8C5_T24C5(2)

description: Biological replicate 2 of 3. Dye swap 2


title: T8C3_T16C5(3)

description: Biological replicate 3 of 3. Dye swap 1


title: T8C5_T16C3(1)

description: Biological replicate 1 of 3. Dye swap 2


title: T8C3_T16C5(2)

description: Biological replicate 2 of 3. Dye swap 1


title: T8C5_T12C3(1)

description: Biological replicate 1 of 3. Dye swap 2


title: T8C5_T12C3(3)

description: Biological replicate 3 of 3. Dye swap 2


title: T8C5_T12C5(2)

description: Biological replicate 2 of 3. Dye swap 2


title: T8C3_T12C5(3)

description: Biological replicate 3 of 3. Dye swap 1


title: T8C3_T16C5(1)

description: Biological replicate 1 of 3. Dye swap 1


title: T8C3_T12C5(2)

description: Biological replicate 2 of 3. Dye swap 1


title: T8C3_T12C5(1)

description: Biological replicate 1 of 3. Dye swap 1


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 2

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

institute: École normale supérieure

description: Biological replicate two of three.

hyb_protocol: Microarrays were pre-hybridized during 1 hour at 42°C in 5x SSC, 0.1% SDS, 1% BSA, washed with distilled water and dried. They were hybridized overnight at 42°C in 25% formamide, 5x SSC, 0.1%SDS with Cy5- and Cy3-labelled cDNA, washed in 1x SSC, 0.2% SDS at 42°C, in 0.1x SSC, 0.2% SDS and two times in 0.1x SSC at room temperature and finally were spin-dried.

scan_protocol: The hybridized microarrays were scanned using Genepix 4000B (Molecular Devices, Sunnyvale, CA, USA) and the resulting image files analyzed by GenePix Pro 5.0 software (Axon).

data_processing: For each GenePix output file, two filters were applied, one to clear out spots and another one to discard saturating spots where the median foreground intensity was greater than 60,000 in one of the two channels. The resulting median foreground intensities were normalized, without background signal subtraction, using a global Lowess correction followed by a print-tip median normalization step (Lemoine et al., 2006).

molecule: polyA RNA

source_name: Isolated Schwann cells culture 3

label_protocol: The labelling of the RNA (5 ug) was carried out by incorporation of amino-allyl dUTP.

extract_protocol: mRNA was extracted using the micro scale RNA isolation kit (Ambion). Amplification of RNA samples for microarray experiments was achieved using the Amino Allyl MessageAmpTM aRNA kit (Ambion). Quantity and integrity of the RNA were measured with the RNA 6000 nano assay kit by the Agilent 2100 Bioanalyser (Agilent Technologies, Germany). All kits were used according to the manufacturer’s instructions.

treatment_protocol: B6D2 wild type and heterozygote Krox20GFP(DT)/+  (Vermeren al 2003) embryos were used for dorsal root ganglion (DRG) and Schwann Cells (SC) cultures respectively. DRG cultures: DRG were dissected from E17.5 embryos. After dissociation for 10 min at 37°C on a rocking table in Ca and Mg-free HBSS containing collagenase type I (130 U/ml), dispase I (2.5 mg/ml), followed by mechanical dissociation, cells were resuspended in DRG medium: DMEM supplemented with L-glutamin (2 mM), Horse serum (5%) and 2.5s NGF (50 ng/ml) (BD Biosciences), and plated onto 60 mm diameter dishes or 12 mm diameter CML coverslips that were coated with poly-L-lysine (PLL, 10 µg/ml, Sigma) and rat collagen type I (5 µg/cm2, Sigma). After 1 day, cytosine arabinoside (10 µM) was added for 2 days to the medium to get rid of non neuronal cells and cells were then maintained in DRG medium. SC cultures: Sciatic nerves were dissected from E17.5 embryos into ice-cold Ca, Mg-free HBSS and dissociated by incubating for 20 min at 37°C on a rocking table in Leibovitz medium (L15, Gibco) containing collagenase type I (130 U/ml) (Gibco), dispase I (2.5 mg/ml) (Roche), followed by mechanical dissociation. Cells were plated onto PLL and collagen coated dishes, and maintained in SC medium : 1:1 ratio of DMEM and Ham’s F12 (Gibco), 10% Fetal Calf Serum (FCS) supplemented with Na-selenite (0.5 ng/ml) (Sigma), progesterone (0.63 ng/ml) (Sigma), putrescine (1.6 µg/ml) (Sigma), transferring (0.1 mg/ml) (Sigma), insulin (0.5 µg/ml) (Sigma), forskolin (2 µM) (Sigma), heregulin (10 ng/ml) (Sigma), gentamycin (50 µg/ml), fungizone (2.5 µg/ml).  Indirect magnetic cell sorting: The mouse SC purification was performed using the technique of magnetic cell separation based on SC membrane expression of the low affinity Nerve Growth Factor receptor (p75NGFR) (Manent et al, 2003) according to manufacturer’s instructions (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Purity of SCs after magnetic cell sorting was quantified after immunolabelling as the percentage of p75NGFR- and S100- positive cells with respect to the total of cells counted. At least 100 cells per condition were counted and experiments were repeated 11 times. Results were expressed as mean ± SD, and statistical analysis was performed using Student’s t test. The purified population (enriched to 97 ± 2 % of SC, n=11) was either plated on coated dish or seeded onto DRG neurons and cocultures were then maintained for 1 to 4 days. Fluorescence activated cell sorting (FACS). Cells from SC-DRG cocultures were collected by trypsinisation and kept on ice in 0.1 M PBS containing 0,2% FCS. FITC fluorescent cells (GFP+ SCs) were sorted using a MoFlow cytometer (Becton Dickinson) and collected in lysis buffer (Ambion) to start the RNA extraction and to prevent any RNA degradation. An aliquot of cells isolated by FACS was preserved in 0.1 M PBS 0,2% FCS and cells were seeded for a couple of hours to allow them to attach to check cell sorting efficiency by immunocytochemistry using an anti-GFP antibody.

tag: cell type

value: Isolated Schwann cells

source_name: Schwann cells cocultured with neurons culture 3

value: Schwann cells cocultured with neurons


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 3 dye swap

description: Biological replicate three of three dye swap.

source_name: Isolated Schwann cells culture 4

tag: tissue

source_name: Schwann cells cocultured with neurons culture 4


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 3

description: Biological replicate three of three.


title: CCTLL-1 with array type poplar from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

description: This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Populus x canadensis

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: leaf - Plants were grown in 10-liter pots filled with peat/sand mix (50/50 v/v amended with 1g/l CaMg(CO2)3 and fertilised with Nutricote T100 (13-13-13-2, N-P-K-Mg + trace elements)). In the greenhouse, temperature oscillated with outside irradiance but kept in the range 15-26 °C, and air humidity during day oscillated in the range 50-75%. Irradiance depended on outside and varied in the range 300-850 µmol m-1 s-1 (cloudy-sunny), and was over750 µmol m-1 s-1 most of the experience. During the 3 days preceding harvest, mean day temperature was 25°C, humidity was 65% and light was 850 µmol m-1 s-1.

extract_protocol: Pool of extract, 75-CCTL-L:1ug, 87-CCTL-L:1ug, 105-CCTL-L:1ug.

treatment_protocol: no treatment

tag: hybrid

value: populus deltoides x populus nigra

tag: harvest date

tag: clone

value: Carpacio

value: leaf


title: CAMIL-2 with array type poplar from Affymetrix

growth_protocol: leaf - Plants were grown in 10-liter pots filled with peat/sand mix (50/50 v/v amended with 1g/l CaMg(CO2)3 and fertilised with Nutricote T100 (13-13-13-2, N-P-K-Mg + trace elements)). In the greenhouse, temperature oscillated with outside irradiance but kept in the range 15-26 °C, and air humidity during day oscillated in the range 50-75%. Irradiance depended on outside and varied in the range 300-850 µmol m-1 s-1 (cloudy-sunny), and was over750 µmol m-1 s-1 most of the experience. During the 3 days preceding harvest, mean day temperature was 25°C, humidity was 65% and light was 850 µmol m-1 s-1.

extract_protocol: Pool of extract, 129-CAMI-L:1ug, 85-CAMI-L:1ug, 90-CAMI-L:1ug.

treatment_protocol: Name:AMI - environmental treatment - abiotic stress,water deficit:time 12day . AMI : Acclimated response to mild water deficit : soil relative extractable water (REW) was reduced and maintained in the range 20-30 % of field capacity for 12 days.


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 1 dye swap

description: Biological replicate one of three dye swap.

source_name: Isolated Schwann cells culture 2

value: embryo

source_name: Schwann cells cocultured with neurons culture 2


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 2 dye swap

description: Biological replicate two of three dye swap.


title: SCTLL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 118-SCTL-L:1ug, 111-SCTL-L:1ug, 128-SCTL-L:1ug.

value: Soligo


title: SAMOL-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 77-SAMO-L:1ug, 92-SAMO-L:1ug.

treatment_protocol: Name:AMO - environmental treatment - abiotic stress,water deficit:time 12day . AMO : Acclimated response to moderate water deficit : soil relative extractable water (REW) was reduced and maintained in the range 10-20 % of field capacity for 12 days


title: SAMOL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 126-SAMO-L:1ug, 95-SAMO-L:1ug, 132-SAMO-L:1ug.


title: SAMIL-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 101-SAMI-L:1ug, 94-SAMI-L:1ug.


title: CAMIL-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 84-CAMI-L:1ug, 76-CAMI-L:1ug.


title: SAMIL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 136-SAMI-L:1ug, 122-SAMI-L:1ug, 99-SAMI-L:1ug.


title: CAMOL-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 73-CAMO-L:1ug, 74-CAMO-L:1ug, 125-CAMO-L:1ug.


title: Low-density seeding cells in bipotent media 1

city: Stanford

first: Michael

last: Longaker

state: CA

address: 257 Campus Drive

department: Department of Surgery

institute: Stanford University

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58476.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Universal Reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Universal Reference

extract_protocol: Trizol; Total RNA was extracted with Trizol (Invitrogen)

value: adipose-derived stromal cells

tag: growth


title: SEARL-1 with array type poplar from Affymetrix

institute: INRA

extract_protocol: Pool of extract, 100-SEAR-L:1ug, 83-SEAR-L:1ug, 98-SEAR-L:1ug.

treatment_protocol: Name:EAR - environmental treatment - abiotic stress,water deficit:time 36hour . EAR : Early response to water deficit : watering was stopped 30h before harvest and soil relative extractable water (REW) was reduced to 20-35% of field capacity.


title: Low-density seeding cells in bipotent media 2

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58477.gif


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 1

description: Biological replicate one of three.

treatment_protocol: B6D2 wild type and heterozygote Krox20GFP(DT)/+  (Vermeren al 2003) embryos were used for dorsal root ganglion (DRG) and Schwann Cells (SC) cultures respectively. DRG cultures: DRG were dissected from E17.5 embryos. After dissociation for 10 min at 37°C on a rocking table in Ca and Mg-free HBSS containing collagenase type I (130 U/ml), dispase I (2.5 mg/ml), followed by mechanical dissociation, cells were resuspended in DRG medium: DMEM supplemented with L-glutamin (2 mM), Horse serum (5%) and 2.5s NGF (50 ng/ml) (BD Biosciences), and plated onto 60 mm diameter dishes or 12 mm diameter CML coverslips that were coated with poly-L-lysine (PLL, 10 µg/ml, Sigma) and rat collagen type I (5 µg/cm2, Sigma). After 1 day, cytosine arabinoside (10 µM) was added for 2 days to the medium to get rid of non neuronal cells and cells were then maintained in DRG medium. SC cultures: Sciatic nerves were dissected from E17.5 embryos into ice-cold Ca, Mg-free HBSS and dissociated by incubating for 20 min at 37°C on a rocking table in Leibovitz medium (L15, Gibco) containing collagenase type I (130 U/ml) (Gibco), dispase I (2.5 mg/ml) (Roche), followed by mechanical dissociation. Cells were plated onto PLL and collagen coated dishes, and maintained in SC medium : 1:1 ratio of DMEM and Ham’s F12 (Gibco), 10% Fetal Calf Serum (FCS) supplemented with Na-selenite (0.5 ng/ml) (Sigma), progesterone (0.63 ng/ml) (Sigma), putrescine (1.6 µg/ml) (Sigma), transferring (0.1 mg/ml) (Sigma), insulin (0.5 µg/ml) (Sigma), forskolin (2 µM) (Sigma), heregulin (10 ng/ml) (Sigma), gentamycin (50 µg/ml), fungizone (2.5 µg/ml).  Indirect magnetic cell sorting: The mouse SC purification was performed using the technique of magnetic cell separation based on SC membrane expression of the low affinity Nerve Growth Factor receptor (p75NGFR) (Manent et al, 2003) according to manufacturer’s instructions (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Purity of SCs after magnetic cell sorting was quantified after immunolabelling as the percentage of p75NGFR- and S100- positive cells with respect to the total of cells counted. At least 100 cells per condition were counted and experiments were repeated 11 times. Results were expressed as mean ± SD, and statistical analysis was performed using Student’s t test. The purified population (enriched to 97 ± 2 % of SC, n=11) was either plated on coated dish or seeded onto DRG neurons and cocultures were then maintained for 1 to 4 days.  Fluorescence activated cell sorting (FACS). Cells from SC-DRG cocultures were collected by trypsinisation and kept on ice in 0.1 M PBS containing 0,2% FCS. FITC fluorescent cells (GFP+ SCs) were sorted using a MoFlow cytometer (Becton Dickinson) and collected in lysis buffer (Ambion) to start the RNA extraction and to prevent any RNA degradation. An aliquot of cells isolated by FACS was preserved in 0.1 M PBS 0,2% FCS and cells were seeded for a couple of hours to allow them to attach to check cell sorting efficiency by immunocytochemistry using an anti-GFP antibody.


title: High-density seeding cells in bipotent media 1

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58472.gif


title: High-density seeding cells in bipotent media 3

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58475.gif


title: High-density seeding cells 2

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58479.gif

source_name: High-density seeding cells

value: High-density seeding cells


title: CEARL-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 81-CEAR-L:1ug, 96-CEAR-L:1ug, 97-CEAR-L:1ug.


title: Low-density seeding cells 1

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58506.gif

source_name: Low-density seeding cells

value: Low-density seeding cells


title: CEARL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 130-CEAR-L:1ug, 131-CEAR-L:1ug, 133-CEAR-L:1ug.


title: SCTLL-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 103-SCTL-L:1ug, 104-SCTL-L:1ug, 107-SCTL-L:1ug.


title: Low-density seeding cells 3

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58508.gif


title: Low-density seeding cells in bipotent media 3

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58474.gif


title: High-density seeding cells in bipotent media 2

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58473.gif


title: High-density seeding cells 3

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58526.gif


title: Low-density seeding cells 2

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58507.gif


title: High-density seeding cells 1

description:
Simple annotation: Development, fat
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58480.gif


title: CCTL08L-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 3-CCTL08-L:750ng, 22-CCTL08-L:750ng, 56-CCTL08-L:750ng.

treatment_protocol: Name:Water Deficit - environmental treatment - abiotic stress,water deficit:.


title: CAMOL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 119-CAMO-L:1ug, 108-CAMO-L:1ug, 141-CAMO-L:1ug.


title: SPEGHR-2 with array type poplar from Affymetrix

description: This project aims to identify genes of interest for control of root growth in response to water deficit in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices of cuttings grown in hydroponics and osmotically stressed with PEG. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit.

growth_protocol: root - Plant were grown in 8L pot in Hoagland ½ nutrient solution except for xxx (mmol l-1). In the growth chamber temperature was 21°C and air humidity was 70% constantly. Irradiance (16h) was 200 µmol m-1 s-

treatment_protocol: Name:PEG - environmental treatment - abiotic stress,water deficit:.

value: root


title: SCTL08L-2 with array type poplar from Affymetrix


title: SWD08L-1 with array type poplar from Affymetrix


title: CAMIR-1 with array type poplar from Affymetrix

description: This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to better discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.

growth_protocol: root - Plants were grown in 10-liter pots filled with peat/sand mix (50/50 v/v amended with 1g/l CaMg(CO2)3 and fertilised with Nutricote T100 (13-13-13-2, N-P-K-Mg + trace elements)). In the greenhouse, temperature oscillated with outside irradiance but kept in the range 15-26 °C, and air humidity during day oscillated in the range 50-75%. Irradiance depended on outside and varied in the range 300-850 µmol m-1 s-1 (cloudy-sunny), and was over750 µmol m-1 s-1 most of the experience. During the 3 days preceding harvest, mean day temperature was 25°C, humidity was 65% and light was 850 µmol m-1 s-1.

extract_protocol: Pool of extract, 84-CAMI-R:1ug, 76-CAMI-R:1ug.

treatment_protocol: Name:AMI - environmental treatment - abiotic stress,water deficit:time 12day . AMI : Acclimated response to mild water deficit : soil relative extractable water (REW) was reduced and maintained in the range 20-30 % of field capacity for 12 days

value: Carpaccio


title: SCTL08L-1 with array type poplar from Affymetrix

description: This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint

extract_protocol: Pool of extract, 86-SCTL08-L:750ng, 41-SCTL08-L:750ng, 53-SCTL08-L:750ng.


title: CWD08L-1 with array type poplar from Affymetrix


title: SCTLHR-1 with array type poplar from Affymetrix


title: SPEGHR-1 with array type poplar from Affymetrix


title: CAMIR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 129-CAMI-R:1ug, 85-CAMI-R:1ug, 90-CAMI-R:1ug.


title: SEARR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 121-SEAR-R:0.5ug, 142-SEAR-R:0.5ug, 143-SEAR-R:0.5ug.

treatment_protocol: Name:EAR - abiotic stress - abiotic stress,water deficit:time 30hour . EAR : Early response to water deficit : watering was stopped 30h before harvest and soil relative extractable water (REW) was reduced to 20-35% of field capacity.


title: SAMOR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 77-SAMO-R:1ug, 92-SAMO-R:1ug.


title: SWD08L-2 with array type poplar from Affymetrix


title: CCTLL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 134-CCTL-L:1ug, 117-CCTL-L:1ug, 139-CCTL-L:1ug.


title: SAMIR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 136-SAMI-R:1ug, 99-SAMI-R:1ug, 122-SAMI-R:1ug.


title: SCTLR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 128-SCTL-R:1ug, 118-SCTL-R:1ug, 111-SCTL-R:1ug.


title: CAMOR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 73-CAMO-R:1ug, 74-CAMO-R:1ug, 125-CAMO-R:1ug.


title: SCTLHR-2 with array type poplar from Affymetrix


title: CEARR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 81-CEAR-R:0.5ug, 96-CEAR-R:0.5ug, 97-CEAR-R:0.5ug.


title: CCTL08L-2 with array type poplar from Affymetrix


title: SEARL-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 121-SEAR-L:1ug, 142-SEAR-L:1ug, 143-SEAR-L:1ug.


title: CWD08L-2 with array type poplar from Affymetrix


title: SAMOR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 126-SAMO-R:1ug, 95-SAMO-R:1ug, 132-SAMO-R:1ug.


title: SCTLR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 103-SCTL-R:1ug, 104-SCTL-R:1ug, 107-SCTL-R:1ug.


title: CCTLR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 75-CCTL-R:0.5ug, 87-CCTL-R:0.5ug, 105-CCTL-R:0.5ug.


title: CEARR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 130-CEAR-R:0.5ug, 131-CEAR-R:0.5ug, 133-CEAR-R:0.5ug.


title: CAMOR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 119-CAMO-R:1ug, 108-CAMO-R:1ug, 141-CAMO-R:1ug.


title: CRLUNG_5072_VS_CRLUNG_5108

first: juan

middle: p

last: steibel

address: 1205 I Anthony Hall

description: CRLUNG EXPRESSION PRRSV infection title indicates Treatment and days post infection

hyb_protocol: Pigoligoarray hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc.) for 18 h at a humid 54 ℃. A low stringency experiment  was also conducted at MSU with hybridizations at 42 ℃. Following hybridization, slides were washed in 2×SSC/0.5% SDS and 0.1× SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1×SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by an Axon GenePix® 4000B scanner (Molecular Devices), and fluorescence intensity data were collected using GENEPIX® PRO 6 software (Molecular Devices) after spot alignment.

data_processing: Median intensities were extracted and normalized using a within print-tip lowess location normalization and an overall scale normalization. The resulting normalized data were expressed in the log2 scale.

label: Alexa 555

label_protocol: For each sample, 1 μg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion Inc.) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After aRNA purification,some aRNAs were used for the RNA/aRNA comparison; 10 μg of aRNAs were labelled with Alexa Fluor® 555 and Alexa Fluor®  647 dyes (Invitrogen)  as appropriate for the experimental design. The labeled aRNAs (2.5 μg) were purified and combined with 65μl of Slide Hyb #1 solution (Ambion Inc.) and denatured at 70 ℃  for 5 min.

growth_protocol: 4-week old pigs (medicated and early-weaned ) were used for the study.

extract_protocol: Pigs were sacrificed at 3-7 days post infection (dpi). The 3 vaccinated pigs were sacrificed at 4dpi. Naïve pigs were sacrificed the following week. Tissues of tonsil, tracheobronchial lymph nodes (TBLN), Cranial lung (CR Lung), and distal lung (D Lung) were collected and placed at -80°C (NC Powell infected lung tissues were not available). RNA isolation and purification was performed using TRIzol® reagent and PureLinkTM kit (Invitrogen). RNA concentration and quality was determined with an RNA 6000 Pico LabChip kit using an Agilent 2100 Bioanalyzer (Agilent Technologies,Inc.)

treatment_protocol: Pigs were either infected intranasally and intramuscularly with heterologous Acute-type Minnesota strain (MNW2B) PRRSV (n=7) or NC Powell (n=4), or vaccinated with contemporary Modified Live Virus (MLV) PRRS ATP vaccine (Ingelvac®) (n=3) at a dose of 104.5 TCID50. The control group consisted of naïve pigs (n=3).

tag: sample type

tag: infection

value: 5 dpi

value: cranial lung

label: Alexa 647

value: CONTROL

value: 0 dpi


title: CRLUNG_5107_VS_CRLUNG_5071


title: CRLUNG_5068_VS_CRLUNG_5072

value: MLV

value: 4 dpi


title: CRLUNG_5073_VS_CRLUNG_5109


title: CRLUNG_5109_VS_CRLUNG_5074


title: CRLUNG_5070_VS_CRLUNG_5076

value: 3 dpi

value: 6 dpi


title: SAMIR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 101-SAMI-R:1ug, 94-SAMI-R:1ug.

value: populus deltoides x populus nigra


title: CCTLR-2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 117-CCTL-R:1ug, 139-CCTL-R:1ug, 134-CCTL-R:1ug.


title: CRLUNG_5076_VS_CRLUNG_5072


title: SEARR-1 with array type poplar from Affymetrix

extract_protocol: Pool of extract, 83-SEAR-R:1ug, 98-SEAR-R:1ug, 100-SEAR-R:1ug.


title: CRLUNG_5108_VS_CRLUNG_5068


title: MEF under 5% O2

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

description: Embryonic fibroblasts were grown under 5% O2 for 10days.

scan_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).

data_processing:
Data were analyzed with GeneSpring GX 11. The parameters for normalization are as follows:
Data transformation: Set measurement less than 0.01 to 0.01
Per chip: Normalize to 75th percentile

source_name: mouse embryonic fibroblasts, under 5% O2, day10

extract_protocol: Total RNA was isolated with Trizol.

value: embryonic fibroblasts


title: MEF under 21% O2

description: Embryonic fibroblasts were grown under 21% O2 for 10days.

source_name: mouse embryonic fibroblasts, under 21% O2, day10

label_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008).


title: CRLUNG_5072_VS_CRLUNG_5070

city: East Lansing

institute: Michigan State University


title: BLN_8025_VS_BLN_5090

description: BLN EXPRESSION PRRSV infection title indicates Treatment and days post infection

value: NCPOWEL

value: 7 dpi

value: tracheobronchial lymph nodes


title: MEF 4F under 5% O2

description: Four factor-transduced embryonic fibroblasts were grown under 5% O2 for 72 hours.

hyb_protocol: Performed as described in One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol (Agilent, Version 5.7, March 2008)

source_name: mouse embryonic fibroblasts, four factor transduced, under 5% O2, day4

tag: transduction of gene

value: Oct3/4, Sox2, Klf4, c-Myc


title: BLN_5094_VS_BLN_5093


title: CRLUNG_5074_VS_CRLUNG_5073


title: CRLUNG_5071_VS_CRLUNG_5075


title: MEF 4F under 21% O2

description: Four factor-transduced embryonic fibroblasts were grown under 21% O2 for 72 hours.

source_name: mouse embryonic fibroblasts, four factor transduced, under 21% O2, day4


title: CRLUNG_5071_VS_CRLUNG_5067


title: BLN_8022_VS_BLN_8025


title: CRLUNG_5075_VS_CRLUNG_5069


title: BLN_5118_VS_BLN_5094


title: BLN_5091_VS_BLN_5087


title: BLN_8023_VS_BLN_5089


title: CRLUNG_5067_VS_CRLUNG_5107


title: BLN_8024_VS_BLN_8023


title: DLUNG_5084_VS_DLUNG_5079

description: TONSIL EXPRESSION PRRSV infection title indicates Treatment and days post infection

value: distal lung


title: BLN_5117_VS_BLN_5088


title: BLN_5093_VS_BLN_5118


title: BLN_5096_VS_BLN_8022


title: BLN_5095_VS_BLN_8024


title: DLUNG_5086_VS_DLUNG_5082


title: DLUNG_5083_VS_DLUNG_5112


title: CRLUNG_5069_VS_CRLUNG_5071


title: DLUNG_5077_VS_DLUNG_5110


title: DLUNG_5078_VS_DLUNG_5082


title: BLN_5089_VS_BLN_5091


title: BLN_5092_VS_BLN_5117


title: DLUNG_5084_VS_DLUNG_5083


title: DLUNG_5082_VS_DLUNG_5080 (1)


title: DLUNG_5110_VS_DLUNG_5081


title: DLUNG_5082_VS_DLUNG_5080 (2)


title: DLUNG_5082_VS_DLUNG_5111


title: TONSIL_5103_VS_TONSIL_5104

value: tonsil


title: DLUNG_5079_VS_DLUNG_5081


title: DLUNG_5112_VS_DLUNG_5084


title: BLN_5091_VS_BLN_5095


title: TONSIL_5103_VS_TONSIL_5124


title: DLUNG_5081_VS_DLUNG_5085


title: BLN_5088_VS_BLN_5092


title: BLN_5095_VS_BLN_5089


title: DLUNG_5111_VS_DLUNG_5078


title: BLN_5092_VS_BLN_5090


title: TONSIL_5102_VS_TONSIL_5123


title: DLUNG_5080_VS_DLUNG_5086


title: TONSIL_5098_VS_TONSIL_5123


title: T8C5_T24C5(2)

description: Biological replicate 2 of 3. Dye swap 2

extract_protocol: At the specified times, 5 ml of bacterial were collected and mixed with an equal part of ice-cold methanol. Cell pellets were centrifuged, washed, and resuspended in 0.25 units/ul mutanolysin. After incubation at 37 degrees Celsius for 20 minutes, total RNA was collected according to the manufacturer's instructions with the Qiagen RNeasy Kit.

value: ATCC PTA 6475


title: T8C3_T24C5(3)

description: Biological replicate 3 of 3. Dye swap 1


title: T8C5_T24C3(1)

description: Biological replicate 1 of 3. Dye swap 2


title: T8C5_T24C3(3)

description: Biological replicate 3 of 3. Dye swap 2


title: BLN_5090_VS_BLN_5096


title: TONSIL_8020_VS_TONSIL_8021


title: T8C5_T16C5(2)

description: Biological replicate 2 of 3. Dye swap 2


title: TONSIL_5100_VS_TONSIL_8021


title: T8C5_T16C3(3)

description: Biological replicate 3 of 3. Dye swap 2


title: BLN_5087_VS_BLN_5114


title: TONSIL_5106_VS_TONSIL_8020


title: T8C3_T24C5(2)

description: Biological replicate 2 of 3. Dye swap 1


title: T8C3_T24C5(1)

description: Biological replicate 1 of 3. Dye swap 1


title: BLN_5096_VS_BLN_5092

value: 5 dpi


title: BLN_5114_VS_BLN_5091


title: TONSIL_5097_VS_TONSIL_5101


title: TONSIL_5104_VS_TONSIL_5124


title: TONSIL_5101_VS_TONSIL_5120


title: TONSIL_5099_VS_TONSIL_8019


title: TONSIL_5100_VS_TONSIL_5102


title: TONSIL_5097_VS_TONSIL_5120


title: TONSIL_5102_VS_TONSIL_5106


title: TONSIL_5098_VS_TONSIL_5102


title: 4T1 cells

city: Seattle

first: Bin

last: Zhang

state: WA

address: 1100 Fairview Ave North

department: Network Biology

institute: Sage Bionetworks

hyb_protocol: RNA was labeled and hybridized to Illumina Mouse Ref-8 v1.1 Expression BeadChIP microarrays according to the manufacturer’s instructions

scan_protocol: Illumina Mouse Ref-8 v2 Expression BeadChIP microarrays were scanned according to the manufacturer’s instructions.

data_processing:
Raw data were background subtracted and quantile normalized using Illumina Bead Studio software version 3
Unnormalized data are signal intensity with background subtracted; normalized data are signal intensity with background subtracted and quantile normalized using Illumina Bead Studio software

source_name: mouse breast cancer cell line

growth_protocol: cells were cultured according to standard procotols.

extract_protocol: Total RNA was isolated using Trizol and RNA purification kit.

tag: cell line

value: mouse breast cancer cell line


title: Expression profiling of 67NR cells

description: replicate 2

label_protocol: RNA was labeled and hybridized to Illumina Mouse Ref-8 v1.1 Expression BeadChIP microarrays according to the manufacturer’s instructions


title: tissue-normal-G003-rep1

city: Shanghai

first: Hong

middle: Xia

last: Wang

state: Shanghai

address: 1630# Dongfang Road

country: China

institute: Shanghai Renji Hospital

description: microRNA expression

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit(Agilent) according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.0 (Agilent) using default parameters.

source_name: normal tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using miRNA Complete Labeling and Hyb Kit(Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the mirVana RNA Isolation kit(Ambion) following the manufacturer's recommendations.

treatment_protocol: Freshly tumor tissues and adjacent normal tissues from gastric cancer patients were obtained promptly after surgery, then washed twice by ice-cold normal saline,and perserved at -80 ºC.

tag: tissue type

value: adjacent normal


title: tissue-tumor-G003-rep1

description: microRNA expression

source_name: tumor tissue

value: gastric cancer


title: T8C5_T16C3(1)

description: Biological replicate 1 of 3. Dye swap 2

source_name: Bacteria, reference

source_name: Bacteria, test


title: tissue-normal-G005-rep1

description: microRNA expression


title: tissue-tumor-G006-rep1

description: microRNA expression


title: tissue-tumor-G007-rep1

description: microRNA expression


title: tissue-tumor-G005-rep1

description: microRNA expression


title: tissue-normal-G007-rep1

description: microRNA expression


title: tissue-normal-G006-rep1

description: microRNA expression


title: TONSIL_5099_VS_TONSIL_5101


title: T8C5_T12C3(1)

description: Biological replicate 1 of 3. Dye swap 2


title: T8C5_T12C3(3)

description: Biological replicate 3 of 3. Dye swap 2


title: T8C3_T16C5(2)

description: Biological replicate 2 of 3. Dye swap 1


title: T8C3_T16C5(3)

description: Biological replicate 3 of 3. Dye swap 1


title: T8C5_T12C5(2)

description: Biological replicate 2 of 3. Dye swap 2


title: T8C3_T16C5(1)

description: Biological replicate 1 of 3. Dye swap 1


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 2 (NeuroDev2)

description: Biological replicate two of two.

extract_protocol: mRNA was extracted using the micro scale RNA isolation kit (Ambion). Amplification of RNA samples for microarray experiments was achieved using the Amino Allyl MessageAmpTM aRNA kit (Ambion). Quantity and integrity of the RNA were measured with the RNA 6000 nano assay kit by the Agilent 2100 Bioanalyser (Agilent Technologies, Germany). All kits were used according to the manufacturer’s instructions.

value: Isolated Schwann cells

value: embryo

value: Schwann cells cocultured with neurons


title: 4.9 Replicate 3

city: Wuerzburg

first: Jaroslaw

last: Zdziarski

address: Josef-Schneider Str. 2/Bau D15

department: Institut fuer Molekulare Infektionsbiologie

country: Germany

institute: Universitaet Wuerzburg

description: Biological replicate 3 of 3. Culture of re-isolate 4.9 in pooled human urine harvested at 0.15 OD

hyb_protocol: Labeled and purified probes (160 pmol each) were applied on pre-hybridized arrays and incubated for 14-16 hours. After hybridisation was completed, arrays were washed in buffers supplied by manufacture.

scan_protocol: Hybridized and washed slides were scanned using a GenePix 4000B Microarray Scanner (GE Healthcare) with a resolution of 10 μm pixel size.

data_processing: The background subtracted data was further analyzed with Acuity 4.0 (Molecular Devices) including normalization by a linear ratio-based method. For statistical significance, one sample t-test was applied with Bonferroni correction. For data analysis, a cut-off value of 1.0 (ln2) was used with p<0.09.

source_name: strain 83972

label_protocol: 10 µg of total RNA primed with Primer Hexamers (Invitrogen) were reversed transcribed at 50°C for 1 h in the presence of 400 U SuperScript III RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 30 µM dCTP, 70 µM Cy3-label or 70 µM Cy5-label

growth_protocol: For RNA isolation bacteria were grown at 37 °C in 125 ml of pooled human urine until the optical density OD600 reached 0.15.

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

treatment_protocol: Samples were treated with RNAprotect (Qiagen)

tag: protocol

value: Wild type strain grown until OD 0.15 in pooled human urine

value: re-isolate of strain ABU83972 from in vitro culture in pooled human urine after 68 days


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 1 (NeuroDev2)

description: Biological replicate one of two.

source_name: Isolated Schwann cells culture 3

source_name: Schwann cells cocultured with neurons culture 3


title: PII-4 Replicate 2

description: Biological replicate 2 of 3. Culture of re-isolate PII-4 in pooled human urine harvested at 0.15 OD

source_name: strain 83972 PII-4

value: re-isolate of strain ABU83972 from paient PII after 155 days


title: Isolated Schwann cells vs Schwann cells cocultured with neurons biological replicate 1 dye swap (NeuroDev2)

description: Biological replicate one of two dye swap.

treatment_protocol: B6D2 wild type and heterozygote Krox20GFP(DT)/+  (Vermeren al 2003) embryos were used for dorsal root ganglion (DRG) and Schwann Cells (SC) cultures respectively. DRG cultures: DRG were dissected from E17.5 embryos. After dissociation for 10 min at 37°C on a rocking table in Ca and Mg-free HBSS containing collagenase type I (130 U/ml), dispase I (2.5 mg/ml), followed by mechanical dissociation, cells were resuspended in DRG medium: DMEM supplemented with L-glutamin (2 mM), Horse serum (5%) and 2.5s NGF (50 ng/ml) (BD Biosciences), and plated onto 60 mm diameter dishes or 12 mm diameter CML coverslips that were coated with poly-L-lysine (PLL, 10 µg/ml, Sigma) and rat collagen type I (5 µg/cm2, Sigma). After 1 day, cytosine arabinoside (10 µM) was added for 2 days to the medium to get rid of non neuronal cells and cells were then maintained in DRG medium. SC cultures: Sciatic nerves were dissected from E17.5 embryos into ice-cold Ca, Mg-free HBSS and dissociated by incubating for 20 min at 37°C on a rocking table in Leibovitz medium (L15, Gibco) containing collagenase type I (130 U/ml) (Gibco), dispase I (2.5 mg/ml) (Roche), followed by mechanical dissociation. Cells were plated onto PLL and collagen coated dishes, and maintained in SC medium : 1:1 ratio of DMEM and Ham’s F12 (Gibco), 10% Fetal Calf Serum (FCS) supplemented with Na-selenite (0.5 ng/ml) (Sigma), progesterone (0.63 ng/ml) (Sigma), putrescine (1.6 µg/ml) (Sigma), transferring (0.1 mg/ml) (Sigma), insulin (0.5 µg/ml) (Sigma), forskolin (2 µM) (Sigma), heregulin (10 ng/ml) (Sigma), gentamycin (50 µg/ml), fungizone (2.5 µg/ml).  Indirect magnetic cell sorting: The mouse SC purification was performed using the technique of magnetic cell separation based on SC membrane expression of the low affinity Nerve Growth Factor receptor (p75NGFR) (Manent et al, 2003) according to manufacturer’s instructions (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Purity of SCs after magnetic cell sorting was quantified after immunolabelling as the percentage of p75NGFR- and S100- positive cells with respect to the total of cells counted. At least 100 cells per condition were counted and experiments were repeated 11 times. Results were expressed as mean ± SD, and statistical analysis was performed using Student’s t test. The purified population (enriched to 97 ± 2 % of SC, n=11) was either plated on coated dish or seeded onto DRG neurons and cocultures were then maintained for 1 to 4 days. Fluorescence activated cell sorting (FACS) Cells from SC-DRG cocultures were collected by trypsinisation and kept on ice in 0.1 M PBS containing 0,2% FCS. FITC fluorescent cells (GFP+ SCs) were sorted using a MoFlow cytometer (Becton Dickinson) and collected in lysis buffer (Ambion) to start the RNA extraction and to prevent any RNA degradation. An aliquot of cells isolated by FACS was preserved in 0.1 M PBS 0,2% FCS and cells were seeded for a couple of hours to allow them to attach to check cell sorting efficiency by immunocytochemistry using an anti-GFP antibody.


title: TONSIL_8018_VS_TONSIL_8019

value: NCPOWEL

value: 6 dpi


title: 6475C5_cfa(2)

description: Biological replicate 2 of 3. Dye swap 2

source_name: Bacteria, wild-type

growth_protocol: Bacterial cells were grown for 24h in MRS at 37C in anaerobic conditions

tag: genotype/variation

value: wild type

source_name: Bacteria, cfa mutant

value: cfa insertant


title: 6475C5_cfa(3)

description: Biological replicate 3 of 3. Dye swap 2


title: TONSIL_5105_VS_TONSIL_8018


title: PII-4 Replicate 3

description: Biological replicate 3 of 3. Culture of re-isolate PII-4 in pooled human urine harvested at 0.15 OD


title: Ankle-hTNFa overexpression and Sphk1 norm-3

city: Charleston

first: DeAnna

last: Baker

state: SC

address: 114 Doughty Street STB #416

department: Medicine

institute: Medical University of South Carolina

description: Gene expression data from ankle joint of mouse with hTNFa transgene and normal sphingosine kinase 1 activity; replicate 3

hyb_protocol: Samples were hybridized overnight to GeneChips in accordance with Affymetrix protocols.

scan_protocol: Post hybridization washing, staining and fluorescence scanning were performed using Affymetrix instrumentation in accordance with manufacturer recommendations.

data_processing: Scanned GeneChips (CEL files) were processed with Affymetrix Expression Console to obtain separate CHP files having RMA normalized expression values and MAS5 detection calls. RMA data and detection calls were merged manually and the composite data set was imported into dChip for comparison analysis.

source_name: ankle joint from a mouse at 5 months age

label_protocol: Total RNA (5 micrograms) was converted into biotin-labeled cRNA using  the SuperScript II cDNA synthesis kit (Invitrogen) and the Enzo HighYield in vitro transcription amplification kit (Enzo Life Sciences).

growth_protocol: Mice were reared and maintained using standard protocols

extract_protocol: RNA was isolated by phase separation with TRIzol reagent (Invitrogen) and further purified using RNAeasy kit (Qiagen).

treatment_protocol: Mice were anesthetized, euthanized, and ankle joints were removed by dissection.

tag: age

value: 5-month adult

tag: tnfa activity

value: over-expression

tag: sphingosine kinase 1 activity

value: normal


title: PIII-4 Replicate 1

description: Biological replicate 1 of 3. Culture of re-isolate PIII-4 in pooled human urine harvested at 0.15 OD

tag: strain

source_name: strain 83972 PIII-4

value: re-isolate of strain ABU83972 from paient PIII after 54 days


title: PIII-4 Replicate 2

description: Biological replicate 2 of 3. Culture of re-isolate PIII-4 in pooled human urine harvested at 0.15 OD


title: PIII-4 Replicate 3

description: Biological replicate 3 of 3. Culture of re-isolate PIII-4 in pooled human urine harvested at 0.15 OD


title: 4.9 Replicate 1

description: Biological replicate 1 of 3. Culture of re-isolate 4.9 in pooled human urine harvested at 0.15 OD


title: 168 FARN cells

description: replicate 2

value: 168 FARN

tag: cell type

value: mouse breast cancer cell line


title: 6475C5_cfa(1)

description: Biological replicate 1 of 3. Dye swap 2

value: ATCC PTA 6475


title: T8C3_T12C5(1)

description: Biological replicate 1 of 3. Dye swap 1

tag: time


title: T8C3_T12C5(3)

description: Biological replicate 3 of 3. Dye swap 1


title: T8C3_T12C5(2)

description: Biological replicate 2 of 3. Dye swap 1


title: TONSIL_5101_VS_TONSIL_5105

value: 5 dpi

tag: tissue

value: tonsil


title: PII-4 Replicate 1

description: Biological replicate 1 of 3. Culture of re-isolate PII-4 in pooled human urine harvested at 0.15 OD


title: 6475C3_cfa(3)

description: Biological replicate 3 of 3. Dye swap 1