title: N806_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

value: Atypical

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: large café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: plexiform neurofibromas:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: tissue


title: 24h Methanol vs unpollinated ovules (replica 1)

status: Public on May 26 2010

type: RNA

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

description:
24h Methanol (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

molecule: total RNA

organism: Solanum chacoense

source_name: 24h Methanol treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

label_protocol: 30 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of cyanine 3-dCTP (1 mM) or cyanine 5-dCTP (1 mM; Perkin Elmer-Cetus/NEN, Boston, MA, catalog # NEL999) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 30 min at 37°C. The labeled cDNAs were purified using CyScribe GFX Purification Kit (GE Healthcare Bio-Sciences Inc., Baie d'Urfé, QC, Canada) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using the TRIzol ® Reagent according to the manufacturer’s protocol (Invitrogen, Burlington, ON, Canada).

treatment_protocol: The self-incompatible wild potato species Solanum chacoense (2n=2x=24) was greenhouse grown with an average photoperiod of 14-16h per day. Plant material was collected from female progenitor, S. chacoense genotype G4 (S12 and S14 self-incompatibility alleles) (Van Sint Jan et al., 1996). For pollination-related events, different genotypes were used as pollen donor. For fully compatible pollinations, S. chacoense genotype V22 (S11 and S13 SI alleles) was used to pollinate S. chacoense genotype G4 (S12 and S14 SI alleles). For fully incompatible pollinations, S. chacoense G4 was selfed. For semi-compatible pollinations, S. chacoense PI230582 (S13 and S14 SI alleles) was used. For interspecific pollinations, pollen from the self-incompatible Solanum microdontum (PI500041 from NRSP-6 Potato Genebank) was used. Control pollinations to detect and eliminate touch-induced genes were accomplished by gently touching the stigmas with sterile 100 mm zirconia/silica beads (Biospec Products Inc., Bartlesville, OK, USA). For wounding experiments, the upper region of the style was slightly crushed with small forceps as described previously (Lantin et al., 1999). For methyl jasmonate treatment, MeJA was diluted in methanol (MeOH) to obtain a 0.1 M solution and 100 µl of the diluted compound (equivalent to 10 µl /l of air space) was added to a piece of Whatman paper suspended over the plant in a closed chamber. As controls, untreated plants in closed chambers and plants treated with 100 µl of MeOH were used (Lantin et al., 1999).

tag: sample type

value: ovule

source_name: Unpollinated ovules

value: Unpollinated ovules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9042

city: Seattle

first: Dan

last: Tenenbaum

state: WA

country: USA

institute: Institute for Systems Biology

description: Cells incubated under entrainment conditions

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org/Scientists_and_Research/Technology/ISB_Facilities/Microarray for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org/Scientists_and_Research/Technology/Data_Management/Microarray_Pipeline for more details.

label: Alexa 647

organism: Halobacterium salinarum

source_name: Halobacterium salinarum, hydrogen peroxide, recovery

growth_protocol: Standard mid-log phase (OD600 - 0.5-0.6) Halobacterium salinarum reference sample.

extract_protocol: Total DNA-free RNA prepared using the Absolutely RNA miniprep kit (Stratagene) and analyzed by PCR to rule out DNA contamination, with Agilent Bioanalyzer to verify integrity, and in the spectrophotometer for quantification.

tag: od

tag: time

value: 60 min.

tag: strain

tag: medium

value: CM

tag: agent

tag: time course

value: recovery

label: Alexa 546

source_name: Halobacterium standard reference sample


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10337

label_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

value: 10 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10334

value: 0 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10335


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10338

value: 20 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9044


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9041


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9043


title: 24h MeJa vs 24h Methanol (replica 4)

description:
24h MeJa (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: 24h Meja treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)

source_name: Methanol treated ovules


title: KAN_microdeletion_characterization

type: genomic

city: Paris

first: Eric

last: Pasmant

address: Faculté de Pharmacie de Paris, 4 avenue de l’Observatoire

country: France

institute: Paris Descartes University

description: Reference sample: Pool of six normal control DNAs from six healthy donors

hyb_protocol: Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Patient and normal control DNAs (reference) were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 24 hours. The sandwiched slides were hybridized for 24 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner (G2565BA).

data_processing:
Log2 ratios (contained in sample data table below) were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s CGH Analytics v3.5 software, and copy number aberrations were detected with the Aberration Detection Method 2 (ADM-2) algorithm using a threshold value of 6.0. This threshold value of the altered copy number was determined from the normal variation in the control hybridization.

A visual estimation of ADM-2 microdeletions length was obtained with the last proximal and distal non deleted probe locations using a *DNA analytics* (Agilent software) algorithm. The result of this analysis can be found in the 'microdeletion sub type' sample characteristic listed above.

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood leukocytes

label_protocol: 300 ng of genomic DNA from each sample was double digested with AluI and RsaI (Promega, Madison, WI) for 2 hours at 37°C. The digested DNAs were labeled by random priming with the Agilent Genomic DNA Labeling Kit Plus (Agilent technologies) for 2 hours at 37°C, according to the manufacturer’s instructions. Patients’ DNA and pooled normal control DNAs (reference) were labeled with Cy5-dUTP and Cy3-dUTP, respectively.

extract_protocol:
High-molecular-weight DNAs from patients and healthy donors were prepared by standard proteinase K digestion followed by phenol-chloroform extraction from whole blood leukocytes.
The quantity and quality of the DNA samples were assessed with Nanodrop technology (Coleman Technologies, Orlando, FL) and verified by electrophoresis through agarose gels and staining with ethidium bromide.

tag: cell type

value: whole blood leukocytes

tag: disease status

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years):

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: lisch nodules:

tag: scoliosis:

source_name: POOL

value: healthy controls


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10336

tag: od

tag: time

tag: strain


title: GUE_microdeletion_characterization

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: large café-au-lait macules (number):

tag: skin-fold freckling

value: Present

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: glioma

value: Absent

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue


title: 24h MeJa vs 24h Methanol (replica 3)

description:
24h MeJa (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

value: 24h Meja treated ovules from G4 genotype (S12 and S14 self-incompatibility alleles) ; greenhouse growth in closed chamber with an average photoperiod of 14-16h per day)


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9029

value: 50 min.

tag: medium

tag: agent

tag: time course


title: 24h MeJa vs 24h Methanol (replica 2)

description:
24h MeJa (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9028

tag: od

tag: time

tag: strain


title: DIE_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

value: Atypical

tag: age (years)

tag: nf1 inheritance

value: Inherited

tag: parental origin

value: Maternal

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling:

tag: lisch nodules:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:


title: 24h MeJa vs 24h Methanol (replica 1)

description:
24h MeJa (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue

value: ovule

value: Unpollinated ovules


title: VID_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: parental origin:

tag: little café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Unpollinated vs unpollinated  (replica 6)

description:
WT-unpollinated ovules (replica 6)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

source_name: Unpollinated ovules from G4 genotype (greenhouse growth with an average photoperiod of 14-16h per day)

tag: sample type

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9027

tag: od

tag: time

value: 40 min.

tag: strain

tag: medium

value: CM

tag: agent

tag: time course

value: recovery


title: YAH_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9026

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9025

value: 30 min.


title: Unpollinated vs unpollinated  (replica 5)

description:
WT-unpollinated ovules (replica 5)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue


title: TRI_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: large café-au-lait macules (number):

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9022

tag: od

tag: time

value: 10 min.

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9046

value: 20 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9024


title: DEN_microdeletion_characterization

tag: cell type

tag: disease status

value: neurofibromatosis type 1 (NF1)

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: de novo

tag: parental origin:

tag: weight (kg)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: glioma:

tag: tissue

value: healthy controls


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9023

tag: od

tag: time

tag: strain


title: Unpollinated vs unpollinated  (replica 4)

description:
WT-unpollinated ovules (replica 4)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9006

value: 0 min.

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11497

source_name: Halobacterium salinarum, hydrogen peroxide, constant stress

value: constant stress


title: Unpollinated vs unpollinated  (replica 3)

description:
WT-unpollinated ovules (replica 3)
Arrays containing 15,482 data points and are organized in 48 sub-arrays


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11496


title: GOD_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: height (cm)

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

value: Present

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

value: Absent

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9021

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 9045


title: Unpollinated vs unpollinated  (replica 2)

description:
WT-unpollinated ovules  (replica 2)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type

tag: tissue


title: NF00908_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11495

tag: time

tag: strain

tag: medium

tag: agent


title: LAP_microdeletion_characterization

tag: cell type

tag: little café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11493

tag: time course


title: Unpollinated vs unpollinated  (replica 1)

description:
WT-unpollinated ovules (replica 1)
Arrays containing 15,482 data points and are organized in 48 sub-arrays

tag: sample type


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11492

tag: time

tag: strain


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11494

tag: medium

tag: agent


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11489


title: NF00222_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: lisch nodules:


title: GEO_microdeletion_characterization

tag: nf1 inheritance:

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11486

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11488


title: wild type N2, biological rep1

city: Oslo

first: Jessica

middle: Margareta

last: Lindvall

address: Gaustadallee 24

country: Norway

institute: University of Oslo

hyb_protocol: hybridization protocol recommended by Affymetrix

scan_protocol: scanning protocol recommended by Affymetrix

data_processing: dChip was used for the processing of the data. The invariant set normalization method was used.

label: biotin

organism: Caenorhabditis elegans

source_name: wild type N2

label_protocol: biotin with GeneChip eukaryotic target labeling kit

extract_protocol: TRIZOL following RNA extraction with chloroform and isopropanol

tag: genotype/variation

value: wild type N2


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11484


title: RUA_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number):

tag: skin-fold freckling

tag: lisch nodules


title: OLI_microdeletion_characterization

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis

tag: tissue


title: ung-1, biological rep3

source_name: ung-1 mutant

tag: genotype/variation


title: wild type N2, biological rep2


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11482

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11481


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11483


title: wild type N2, biological rep3


title: NF01585_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: lisch nodules


title: ung-1, biological rep2

tag: genotype/variation


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11479

tag: time

tag: strain

tag: medium

tag: agent


title: DUB_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

value: Atypical

tag: age (years):

tag: weight (kg):

tag: height (cm):

tag: head circumference (cm):

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number):

tag: café-au-lait macules (number):

tag: skin-fold freckling:

tag: subcutaneous neurofibromas:

tag: cutaneous neurofibromas:

tag: plexiform neurofibromas:

tag: lisch nodules:

tag: glioma:

tag: learning disabilities:

tag: facial dysmorphism:

tag: scoliosis:

tag: tissue


title: ung-1, biological rep1

tag: genotype/variation


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11480

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11485


title: NF00596_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11478

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: NF01152_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: lisch nodules:

tag: glioma:

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11369

tag: time

tag: strain


title: NF01053_microdeletion_characterization

tag: nf1 inheritance

value: Inherited

tag: parental origin

value: Maternal

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism

tag: scoliosis


title: BW25113

city: Boulder

first: Amar

last: Singh

state: CO

address: 1111 Engineering Drive, UCB 424

department: Chemical & Biological Engineering

institute: University of Colorado

description: Gene expression data

hyb_protocol: Hybridized onto GeneChip Antisense Genome Array using Manufacturer's protocol

scan_protocol: Scanned using GeneArray Scanner (Affymetrix) using manufacturer's protocol

data_processing: Affymetrix MAS5 Normalization routine

organism: Escherichia coli

source_name: Microaerobic growth, M9 media, exponential phase

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

growth_protocol: E. coli BW25113 wild type and ldhA-pflB- double mutant growing microaerobically in M9 media containing 10 g/L Glucose were harvested in the mid-exponential phase

extract_protocol: Total RNA was isolated using Qiagen's RNeasy kit following manufacturer's protocol

tag: genotype/variation

value: Wild type


title: NF00085_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: lisch nodules:

tag: glioma:

tag: tissue


title: BW25113 ldhA-pflB-

description: Gene expression data

tag: strain

value: ldhA-pflB- double knockout


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11365

tag: time

tag: medium

value: CM

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11366


title: NF01510_microdeletion_characterization

tag: cell type

value: whole blood leukocytes

tag: disease status

tag: nf1 inheritance

tag: little café-au-lait macules (number):

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number):

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: glioma

tag: learning disabilities

tag: facial dysmorphism:

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11363

tag: time

tag: strain

tag: medium

tag: agent


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11361

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11528


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11360


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10544

tag: od


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10543


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10541


title: NF00573_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: facial dysmorphism

tag: tissue


title: NF01470_microdeletion_characterization

tag: parental origin

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules:

tag: glioma

tag: learning disabilities

tag: scoliosis


title: NF00437_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: lisch nodules


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11362

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10529

tag: od

value: 60 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10527

value: 30 min.


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10542


title: NF00398_microdeletion_characterization

value: neurofibromatosis type 1 (NF1)

tag: parental origin

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: glioma

tag: facial dysmorphism

tag: tissue


title: NF00358_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

value: Paternal

tag: weight (kg)

tag: lisch nodules

tag: glioma:

tag: learning disabilities

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10524

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10326


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11529


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10525


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10528


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10319


title: NF00234_microdeletion_characterization

value: de novo

tag: parental origin:

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: glioma

tag: facial dysmorphism

tag: tissue

value: healthy controls


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10318

tag: od

tag: time

tag: strain

value: constant stress


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11368

tag: medium

tag: agent

tag: time course


title: NF01507_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance

tag: parental origin:

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

value: Present

tag: lisch nodules

tag: learning disabilities

tag: scoliosis


title: NF00759_microdeletion_characterization

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

value: Absent

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: glioma

tag: facial dysmorphism

tag: tissue


title: NF00886_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance:

tag: parental origin:

tag: lisch nodules:


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10315

tag: od

tag: time

tag: strain

tag: medium

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10314


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10313


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10317


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10312

value: 0 min.


title: NF01465_microdeletion_characterization

tag: nf1 inheritance

tag: weight (kg)

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules

tag: learning disabilities

tag: scoliosis


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10311

tag: od

tag: time

tag: strain

tag: medium


title: NF00663_microdeletion_characterization

tag: cell type

tag: disease status

tag: microdeletion sub-type

tag: age (years)

tag: nf1 inheritance:

tag: parental origin:

tag: weight (kg)

tag: glioma

tag: facial dysmorphism

tag: tissue


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10526

tag: agent

tag: time course


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 10316


title: NF00028_microdeletion_characterization

value: Atypical

tag: nf1 inheritance

tag: parental origin

tag: height (cm)

tag: head circumference (cm)

tag: little café-au-lait macules (number)

tag: large café-au-lait macules (number)

tag: café-au-lait macules (number)

tag: skin-fold freckling

tag: subcutaneous neurofibromas

tag: cutaneous neurofibromas

tag: plexiform neurofibromas

tag: lisch nodules:

tag: learning disabilities

tag: scoliosis


title: HUVEC at 340 min., exposed to insulin

city: Padova

first: Tiziana

last: Sanavia

address: Gradenigo, 6/B

country: Italy

institute: University of Padova

description: Gene expression data from HUVEC

hyb_protocol: Hybridization were performed using protocols described in the Affymetrix GeneChip expression analysis technical manual.

scan_protocol: Image quantification was performed using GeneChip (Affymetrix, SantaClara, CA) scanner and software.

data_processing: Preprocessing steps such as background substraction, probe cell normalization and expression level calculations, were performed using quantile normalization and Robust Microarray Analysis (RMA) software.

source_name: HUVEC at 340 min., exposed to insulin

label_protocol: Sample labeling was performed using protocolos described in the Affymetrix GeneChip expression analysis tecnical manual.

growth_protocol: Cells were cultured in Endothelial Cell Growth Medium (Promocell), supplemented with 10% fetal bovine serum (FBS) (Sigma Aldrich, Saint Louis, USA), 0.02% Supplement Mix/ Endothelial Cell Growth Medium (PromoCell), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma Aldrich).

extract_protocol: Total RNA was extracted using commercially available kit (TRIzol Reagent, Invitrogen) and stored at -80°C.  The samples were further purified using RNeasy mini kit (Qiagen, Milan, Italy) following manufacturer's recommendations. The quality and quantity of total RNA was measured using the Agilent test on a Bioanalyzer (Agilent Technologies, PAlo Alto, CA).

treatment_protocol: HUVECs were seeded onto six well plates at a density of 2X105 per well; 1 ml of quiescent medium, in absence or presence of 1 mU/ml (7 nM) insulin (Calbiochem-Inalco Spa), was added to each well.

tag: cell type

value: Normal Human Umbilical Vein Endothelial Cells (HUVEC)

value: insulin

tag: time point

value: 340 min


title: HUVEC at 40 min., exposed to insulin

description: Gene expression data from HUVEC

source_name: HUVEC at 40 min., exposed to insulin

tag: agent

value: 40 min


title: HUVEC at 440 min., exposed to insulin

description: Gene expression data from HUVEC

source_name: HUVEC at 440 min., exposed to insulin

value: 440 min


title: tc252.normoxia.spheroid

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: Ewing's sarcoma cell line cell line grown as spheroids and under normoxia

hyb_protocol: Following RNA purification, 20µg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with 200µl hybridization buffer containing hybridization controls and hybridized to U133-A microarrays. The arrays were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm.

label_protocol: 1.5µg total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer's protocols (Gene Expression Analysis, Technical Manual, Revison #4; Eukaryotic Target Preparation, Revison #3).

growth_protocol: multicellular spheroids: confluent monolayers of different ESFT cells were trypsinized, resuspended as single cells, and replated at a concentration of 1.0 X 105 cells/ml on tissue culture dishes that had been coated with sterile 1.4% agar for anchorage-independence. Cells were allowed to recover for 18 h before hypoxia/normoxia treatment.

extract_protocol: RNA was extrated using the Qiagen RNA extrction kit according to the manufacturer's instructions.

treatment_protocol: For incubations under normoxia (21% O2), cells were placed in a Thermo-CO2 incubator and grown in a humidified atmosphere containing 5% CO2 (Thermo Electron Corp., Asheville, NC). treatment was applied for 24h.

tag: disease status

value: Ewing's sarcoma

tag: cell line

tag: genome/variation

value: EWS-FLI1 fusion type 1

tag: p53 status

value: wild type

tag: culture conditions

value: spheroid, normoxia


title: tc252.hypoxia.spheroid

description: Ewing's sarcoma cell line cell line grown as spheroids and under hypoxia

treatment_protocol: Hypoxic treatment of cells was achieved by incubating cells in a PROOX model 110 chamber (Biospherix, Redfield, NY) flushed with a gas mixture of 5% CO2/95% N2. Oxygen concentration within the chamber was maintained at 1% using a ProOx 110 oxygen regulator (Biospherix, USA).  treatment was applied for 24h.

value: spheroid, hypoxia


title: HUVEC at 200 min., control

description: Gene expression data from HUVEC

source_name: HUVEC at 200 min., non exposed to insulin

value: 200 min


title: HUVEC at 0 min., control, biological replicate 2

description: Gene expression data from HUVEC

source_name: HUVEC at 0 min., non exposed to insulin, biological replicate 2

value: 0 min


title: HUVEC at 100 min., control

description: Gene expression data from HUVEC

source_name: HUVEC at 100 min., non exposed to insulin

value: 100 min


title: HUVEC at 200 min., exposed to insulin

description: Gene expression data from HUVEC

source_name: HUVEC at 200 min., exposed to insulin


title: sknmc.hypoxia.spheroid

source_name: Ewing's sarcoma cell line cell line grown as spheroids and under hypoxia

value: SK-N-MC

value: mutant


title: sknmc.normoxia.spheroid

source_name: Ewing's sarcoma cell line cell line grown as spheroids and under normoxia


title: HUVEC at 40 min., control

description: Gene expression data from HUVEC

source_name: HUVEC at 40 min., non exposed to insulin


title: FFT ToR G1 phase vs. S phase DNA rep2

status: Public on May 25 2010

city: Jerusalem

first: Itamar

last: Simon

address: Ein Karem Campus

country: Israel

institute: The Hebrew university

description: G1/S FFT rep2 LogRatio

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent  scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software, Data obtained from log10 of processed Red signal/processed Green signal.

source_name: FFT (foreskin fibroblasts) cells,  G1 phase DNA, replicate 2

label_protocol: 250-1000 ng DNA was labeled with either dUTP-cy3 or dUTP-cy5 by direct labeling using Agilent labeling kit

extract_protocol: DNA was extracted using a strandard protocol - incubation with lysis buffer that included ProteinaseK, that was followed by phenol-chlorophorm extraction, sonication of the DNA to smaller fragments (300-1000bp) and Ethanol precipitationand purification using QIAGEN PCR purification kit.

value: FFT (foreskin fibroblasts)

source_name: FFT cells,  S phase DNA, replicate 2


title: MOLT4 ToR G1 phase vs. S phase DNA rep2

description: G1/S Molt-4 rep2 LogRatio

source_name: MOLT4 cells, G1 phase DNA , replicate 2

value: MOLT4  (human lymphoblasts cell line)

source_name: MOLT4 cells, S phase DNA , replicate 2


title: HUVEC at 440 min., control

description: Gene expression data from HUVEC

source_name: HUVEC at 440 min., non exposed to insulin

value: Normal Human Umbilical Vein Endothelial Cells (HUVEC)


title: HUVEC at 340 min., control

description: Gene expression data from HUVEC

source_name: HUVEC at 340 min., non exposed to insulin


title: FFT ToR G1 phase vs. S phase DNA rep1

description: G1/S FFT rep1 LogRatio

source_name: FFT (foreskin fibroblasts) cells,  G1 phase DNA, replicate 1

source_name: FFT cells,  S phase DNA, replicate 1


title: HUVEC at 100 min., exposed to insulin

description: Gene expression data from HUVEC

source_name: HUVEC at 100 min., exposed to insulin

value: insulin


title: Coordination of frontline defense mechanisms under severe oxidative stress. Array 11487

source_name: Halobacterium salinarum, hydrogen peroxide, constant stress

tag: time

tag: strain

tag: medium

value: CM

tag: time course

value: constant stress

source_name: Halobacterium standard reference sample


title: MOLT4 ToR G1 phase vs. S phase DNA rep1

description: G1/S Molt-4 rep1 LogRatio

source_name: MOLT4 cells, G1 phase DNA , replicate 1

source_name: MOLT4 cells, S phase DNA , replicate 1


title: calorically restricted, old, poor performing, rat CA3, replicate 2

city: Jupiter

first: Zane

last: Zeier

state: FL

address: 130 Scripps Way

department: Neuroscience

institute: Scripps

description: Neuro-Foster-49 CRO PP CA3 R6-RAE230_2

hyb_protocol: Purified RNA was labeled and hybridized to RAE 230 V2.0 gene chips (one chip per region per animal) by the NIH core facility.

scan_protocol: The chips were scanned with an Affymtrix GeneChip Scanner 3000, and the raw data (available at the nih neuorscience microarray consortium, http://arrayconsortium.tgen.org/np2/viewProject.do?action=viewProject&projectId=522821) were processed with Affymetrix GCOS software.

data_processing: Normalization and computation of gene expression values were performed using the perfect-match-only method by inputting data (.cel files) into dChip (Li and Wong, 2001); subsequent statistical and GO analyses were performed in BRB array tools.

organism: Rattus norvegicus

extract_protocol:
Brains were quickly removed and placed on an ice-cold petridish then bisected by making a vertical incision along the midline such that the two hemispheres were separated. The neocortex of each hemisphere was then resected in order to expose and remove the hippocampi using forceps and a spatula. The CA1, CA3, and dentate gyrus (DG) regions were then separated using a curved razor blade to make a lateral incision along the ventral side of the hippocampus in order to separate the CA3 region. Next, the remaining hippocampi was rotated 90 degrees and a dorsal-ventral oriented incision was made in order to separate the DG and CA1 regions. Tissue from each region was immediately snap-frozen in liquid nitrogen upon dissection.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Ad libitum (AL) fed and calorie restricted (CR) male F344xBN rats aged 18 or 28 months were obtained from the National Institute on Aging (NIA) rodent colony. Reduction of calorie intake began at 14 weeks of age starting with 10%, 25%, and finally 40% restriction at 17 weeks until the end of the experiment.

tag: tissue

value: Hippocampus

tag: tissue region

tag: diet

value: calorically restricted

tag: behavioral performance

value: poor performers

tag: age (months)


title: calorically restricted, old, poor performing, rat CA1, replicate 1

description: Neuro-Foster-46 CRO PP CA1 R6-RAE230_2

label_protocol: Purified RNA was labeled and hybridized to RAE 230 V2.0 gene chips (one chip per region per animal) by the NIH core facility.


title: calorically restricted, old, good performing, rat CA3, replicate 3

description: Neuro-Foster-42 CRO GP CA3 R5-RAE230_2

value: good performers


title: ad libatum, old, poor performing, rat dentate gyrus, replicate 2

description: Neuro-Foster-35 ALO PP DG R8a-RAE230_2

value: DG

value: ad libatum


title: calorically restricted, old, poor performing, rat dentate gyrus, replicate 3

description: Neuro-Foster-54 CRO PP DG R12-RAE230_2


title: calorically restricted, old, poor performing, rat CA3, replicate 4

description: Neuro-Foster-51 CRO PP CA3 R12-RAE230_2


title: calorically restricted, old, good performing, rat CA1, replicate 3

description: Neuro-Foster-39 CRO GP CA1 R5-RAE230_2


title: calorically restricted, old, good performing, rat dentate gyrus, replicate 3

description: Neuro-Foster-45 CRO GP DG R5-RAE230_2


title: calorically restricted, old, poor performing, rat CA1, replicate 3

description: Neuro-Foster-48 CRO PP CA1 R12-RAE230_2


title: ad libatum, old, poor performing, rat dentate gyrus, replicate 3

description: Neuro-Foster-36 ALO PP DG R11a-RAE230_2


title: calorically restricted, old, poor performing, rat dentate gyrus, replicate 1

description: Neuro-Foster-52 CRO PP DG R6-RAE230_2


title: calorically restricted, old, good performing, rat dentate gyrus, replicate 2

description: Neuro-Foster-44 CRO PP DG R3-RAE230_2


title: calorically restricted, old, good performing, rat CA1, replicate 1

description: Neuro-Foster-37 CRO GP CA1 R1-RAE230_2


title: calorically restricted, old, poor performing, rat dentate gyrus, replicate 2

description: Neuro-Foster-53 CRO PP DG R7a-RAE230_2


title: calorically restricted, old, good performing, rat CA3, replicate 2

description: Neuro-Foster-41 CRO GP CA3 R3-RAE230_2


title: calorically restricted, old, poor performing, rat CA3, replicate 3

description: Neuro-Foster-50 CRO PP CA3 R7-RAE230_2


title: calorically restricted, old, good performing, rat CA1, replicate 2

description: Neuro-Foster-38 CRO GP CA1 R3-RAE230_2


title: calorically restricted, old, good performing, rat CA3, replicate 1

description: Neuro-Foster-40 CRO GP CA3 R1-RAE230_2


title: ad libatum, old, poor performing, rat CA3, replicate 4

description: Neuro-Foster-33 ALO PP CA3 R11a-RAE230_2


title: HUVEC at 0 min., control, biological replicate 1

description: Gene expression data from HUVEC

source_name: HUVEC at 0 min., non exposed to insulin, biological replicate 1

tag: cell type


title: calorically restricted, old, good performing, rat dentate gyrus, replicate 1

description: Neuro-Foster-43 CRO GP DG R1-RAE230_2


title: calorically restricted, old, poor performing, rat CA1, replicate 2

description: Neuro-Foster-47 CRO PP CA1 R7-RAE230_2


title: ad libatum, old, poor performing, rat dentate gyrus, replicate 1

description: Neuro-Foster-34 ALO PP DG R5a-RAE230_2


title: ad libatum, old, poor performing, rat CA3, replicate 3

description: Neuro-Foster-32 ALO PP CA3 R8-RAE230_2


title: ad libatum, old, poor performing, rat CA3, replicate 2

description: Neuro-Foster-31 ALO PP CA3 R5-RAE230_2


title: ad libatum, old, poor performing, rat CA1, replicate 3

description: Neuro-Foster-30 ALO PP CA1 R11-RAE230_2


title: ad libatum, old, poor performing, rat CA1, replicate 2

description: Neuro-Foster-29 ALO PP CA1 R8-RAE230_2


title: ad libatum, old, good performing, rat dentate gyrus, replicate 3

description: Neuro-Foster-27 ALO GP DG R10-RAE230_2


title: ad libatum, old, poor performing, rat CA1, replicate 1

description: Neuro-Foster-28 ALO PP CA1 R5-RAE230_2


title: ad libatum, old, good performing, rat dentate gyrus, replicate 2

description: Neuro-Foster-26 ALO GP DG R9-RAE230_2


title: ad libatum, old, good performing, rat CA3, replicate 2

description: Neuro-Foster-23 ALO GP CA3 R9-RAE230_2


title: SJ 716

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description:
ejection fraction (EF): 30
group: A

hyb_protocol: Agilent : 750.0 ng at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Lowess non linear normalization

label: Cy3, Cy5

source_name: Ref

label_protocol: Ambion

extract_protocol: Trizol

value: Trizol

value: REF

value: Ref

tag: Tissue

value: blood

extract_protocol: Qiagen

tag: Labeling_reference:SJ 716

value: PAXgene

value: Blood


title: GG 721

description:
ejection fraction (EF): 25
group: A


title: ad libatum middle aged rat dentat gyrus, replicate 1

description: Neuro-Foster-7 ALMA DG R1-RAE230_2

value: not applicable


title: ad libatum, old, good performing, rat CA3, replicate 3

description: Neuro-Foster-24 ALO GP CA3 R10-RAE230_2


title: L65 NM

description:
ejection fraction (EF): 20
group: A


title: L52 GH

description:
ejection fraction (EF): 30
group: A

source_name: L52 GH

tag: Labeling_reference:L52 GH

value: L52 GH


title: ad libatum, old, good performing, rat CA1, replicate 2

description: Neuro-Foster-20 ALO GP CA1 R9-RAE230_2


title: L14 ST

description:
ejection fraction (EF): 20
group: A

source_name: L14 ST

tag: Labeling_reference:L14 ST

value: L14 ST


title: ad libatum middle aged rat dentat gyrus, replicate 3

description: Neuro-Foster-9 ALMA DG R6-RAE230_2


title: ad libatum middle aged rat CA1, replicate 2

description: Neuro-Foster-2 ALMA CA1 R4-RAE230_2


title: ad libatum middle aged rat CA3, replicate 1

description: Neuro-Foster-4 ALMA CA3 R1-RAE230_2


title: ad libatum middle aged rat dentat gyrus, replicate 2

description: Neuro-Foster-8 ALMA DG R4-RAE230_2


title: ad libatum middle aged rat CA3, replicate 3

description: Neuro-Foster-6 ALMA CA3 R6-RAE230_2


title: ad libatum, old, good performing, rat dentate gyrus, replicate 1

description: Neuro-Foster-25 ALO GP DG R1-RAE230_2


title: ad libatum middle aged rat CA3, replicate 2

description: Neuro-Foster-5 ALMA CA3 R1-RAE230_2


title: ad libatum, old, good performing, rat CA3, replicate 1

description: Neuro-Foster-22 ALO GP CA3 R1-RAE230_2


title: L62 VN

description:
ejection fraction (EF): 30
group: A

value: trizol

value: ref

source_name: L62 VN

tag: Labeling_reference:L62 VN

value: L62 VN


title: L120 KN

description:
ejection fraction (EF): 31
group: A


title: ZE 738

description:
ejection fraction (EF): 35
group: A

tag: Labeling_reference:ZE 738


title: ad libatum, old, good performing, rat CA1, replicate 1

description: Neuro-Foster-19 ALO GP CA1 R1-RAE230_2

value: Hippocampus


title: ad libatum middle aged rat CA1, replicate 1

description: Neuro-Foster-1 ALMA CA1 R1-RAE230_2


title: L19 BJ

description:
ejection fraction (EF): 36
group: A


title: L17 RR

description:
ejection fraction (EF): 40
group: A

source_name: L17 RR

tag: Labeling_reference:L17 RR

value: L17 RR


title: L4 SM

description:
ejection fraction (EF): 35
group: A


title: L43 LP

description:
ejection fraction (EF): 40
group: A

source_name: L43 LP

tag: Labeling_reference:L43 LP

value: L43 LP


title: L20 AG

description:
ejection fraction (EF): 45
group: B

source_name: L20 AG

tag: Labeling_reference:L20 AG

value: L20 AG


title: L63 DA

description:
ejection fraction (EF): 38
group: A


title: L16 JA

description:
ejection fraction (EF): 45
group: B


title: RH 712

description:
ejection fraction (EF): 50
group: B

value: Réf


title: L11 BA

description:
ejection fraction (EF): 65
group: B

value: Trizol


title: HJ 687

description:
ejection fraction (EF): 55
group:  B

value: sang


title: L13 VJ

description:
ejection fraction (EF): 40
group: A

source_name: L13 VJ

tag: Labeling_reference:L13 VJ

value: L13 VJ

value: REF

value: Ref


title: MJ 697

description:
ejection fraction (EF): 65
group: B

value: blood

tag: Labeling_reference:MJ 697

value: PAXgene

value: Blood


title: L30 CM

description:
ejection fraction (EF): 61
group: B

source_name: L30 CM

tag: Labeling_reference:L30 CM

value: L30 CM


title: L45 ME

description:
ejection fraction (EF): 45
group: B

value: R


title: L38 DP

description:
ejection fraction (EF): 71
group: B

source_name: L38 DP

tag: Labeling_reference:L38 DP

value: L38 DP


title: KF 692

description:
ejection fraction (EF): 70
group: B

tag: Labeling_reference:KF 692


title: BL 708

description:
ejection fraction (EF): 60
group: B

tag: Labeling_reference:BL 708


title: Mutant strain on nitrogen limitation with ethanol as carbon source_02

city: Göteborg

first: Goutham

middle: N

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description:
Gene expression from steady-state.
Mutant, N-Lim (Eth)02

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G.

data_processing: Only the S. cerevisiae genes were analyzed. Control probes and S. pombe genes were eliminated from the dataset.  The data were analyzed with BioConductor suite:  GCRMA (background correction), qspline (normalization).

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Steady-state sample from chemostat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microgram total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Yeast cells were growth to a steady-state using appropriate nutrient limitations in a chemostat

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit and treated with DNase afterwards

treatment_protocol: Biomass was quenched on ice, separated from the growth medium and flash frozen in liquid nitrogen until subsequent use

tag: strain

value: SCE088 (mutant)

tag: treatment protocol


title: DA 706

description:
ejection fraction (EF): 63
group: B

tag: Tissue

tag: Labeling_reference:DA 706


title: NA 735

description:
ejection fraction (EF): 40
group: A

tag: Labeling_reference:NA 735


title: Mutant strain on nitrogen limitation with glucose as carbon source_02

description:
Gene expression from steady-state.
Mutant, N-Lim (Glu)02


title: Mutant strain on nitrogen limitation with ethanol as carbon source_01

description:
Gene expression from steady-state.
Mutant, N-Lim (Eth)01


title: Mutant strain on ethanol limitation_01

description:
Gene expression from steady-state.
Mutant, Eth-Lim01

value: ethanol limitation


title: L67 SR

description:
ejection fraction (EF): 73
group: B


title: L140 RM

description:
ejection fraction (EF): 70
group: B


title: L88 TG

description:
ejection fraction (EF): 73
group: B


title: L23 FS

description:
ejection fraction (EF): 40
group: A

source_name: L23 FS

tag: Labeling_reference:L23 FS

value: L23 FS


title: ad libatum, old, good performing, rat CA1, replicate 3

description: Neuro-Foster-21 ALO GP CA1 R10-RAE230_2

tag: tissue

value: Hippocampus

tag: tissue region

tag: diet

value: ad libatum

tag: behavioral performance

value: good performers

tag: age (months)


title: FC 732

description:
ejection fraction (EF): 63
group: B

value: Trizol

tag: Labeling_reference:FC 732


title: Mutant strain on glucose limitation_02

description:
Gene expression from steady-state.
Mutant, Glu-Lim02

value: glucose limitation


title: Mutant strain on nitrogen limitation with glucose as carbon source_01

description:
Gene expression from steady-state.
Mutant, N-Lim (Glu)01


title: Reference strain on glucose limitation_01

description:
Gene expression from steady-state.
Reference, Glu-Lim02

value: SCE090 (reference)


title: Reference strain on ethanol limitation_02

description:
Gene expression from steady-state.
Reference, Eth-Lim02


title: Reference strain on nitrogen limitation with ethanol as carbon source_01

description:
Gene expression from steady-state.
Reference, N-Lim (Eth)01


title: Reference strain on nitrogen limitation with glucose as carbon source_02

description:
Gene expression from steady-state.
Reference, N-Lim (Glu)02


title: Reference strain on ethanol limitation_01

description:
Gene expression from steady-state.
Reference, Eth-Lim01


title: Mutant strain on glucose limitation_01

description:
Gene expression from steady-state.
Mutant, Glu-Lim01


title: Reference strain on glucose limitation_02

description:
Gene expression from steady-state.
Reference, Glu-Lim01


title: Reference strain on nitrogen limitation with ethanol as carbon source_02

description:
Gene expression from steady-state.
Reference, N-Lim (Eth)02


title: ad libatum middle aged rat CA1, replicate 3

description: Neuro-Foster-3 ALMA CA1 R6-RAE230_2

value: not applicable


title: Root Col(0) replica 3

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

description: Gene expression in 18 days old roots

hyb_protocol: 15 µg of labeled cRNA was used for each hybridization. After 16 hours of hybridization at 45C the arrays were processed through the washing and staining procedures according to the manufacturer instructions (Affymetrics).

scan_protocol: The GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: The microarray data were preprocessed using the Robust Multichip Average (RMA) package (Irizarry RA et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.) using R. The data were normalized using quantile normalization, and expression measures were produced by fitting the RMA robust linear model.

organism: Arabidopsis thaliana

source_name: Col(0), roots

label_protocol: To prepare the samples for microarray experiments the “GeneChip Expression Analysis” procedure of Affymetrix (Santa Clara, USA) was followed. Briefly, 10 µg total RNA was processed through a one-cycle cDNA synthesis procedure, the resulting double-stranded cDNA was cleaned up and submitted to the synthesis of biotin-labelled cRNA. This biotin-labelled cRNA was then cleaned up, quantified and fragmented.

growth_protocol: Wild-type Col-0 and mutant glu1-2 seeds were surface sterilised and sown on solid in vitro cultivation medium consisting of 1x Murashige and Skoog basal salt mixture, 3% sucrose, 0.75% phytoagar (w/v), pH5.7. This medium contains 1650 mg ammonium nitrate/L. Seeds were stratified for 3 days at 4°C before being transferred to a controlled growth chamber under a 16 hour photoperiod (light intensity: 75 µmol.m-2.sec-1) at 21-23°C. Leaves and roots of 18 day old in vitro grown plantlets were harvested separately and immediately flash-frozen in liquid N2. Harvesting of tissue was performed two hours after onset of the 16 hour light period. The harvested tissue was stored at -80°C until further processing.

extract_protocol: Total RNA was extracted from plant tissue (300 mg roots, 500 mg leaves) using the RNeasy Midi kit (Qiagen, Hilden, Germany) following the supplier’s instructions. Total RNA was consentrated using Microcon YM30 columns (Amicon). RNasin (Promega , Madison, USA) was added to the RNA to the final concentration of 1 U/µl. RNA quality was assessed by standard denaturing agarose gel electrophoresis and RNA concentration was measured with a NanoDrop ND-1000 (Nanodrop, Delaware, USA).

value: roots

tag: stage

value: 18 days after germination


title: Reference strain on nitrogen limitation with glucose as carbon source_01

description:
Gene expression from steady-state.
Reference, N-Lim (Glu)01


title: Sea Acclimated penguin 1

city: Bremerhaven

first: Cyril

last: Degletagne

address: Am Handelshafen

department: Functional Ecology

country: Germany

institute: Alfred Wegener Institute

description: Gene expression data in pectoralis muscle from a sea acclimated penguin

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Arrays in a Genechip hybridization oven 640 (Affymetrix). GeneChips were washed and stained with streptavidin-phycoerythrin (Invitrogen Corporation, CA, USA) in a fluidic 450 (Affymetrix) according to the manufacturer’s instruction.

scan_protocol: The arrays were scanned with a confocal laser (Genechip scanner 3000, Affymetrix).

data_processing: The data were analyzed with the MAXRS method dedicated to heterologous hybridization analysis on high density microarrays (Degletagne et al., submitted). They were then normalized by using the quantile method implemented in the limma Bioconductor package.

organism: Aptenodytes patagonicus

source_name: Muscle sample biopsy from juvenile penguin that had completly accomplished its acclimation to marine life

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Four penguins were captured just before they undergone their first immersion to cold sea water and three penguins were captured after they had completely accomplished their acclimation to marine life.

extract_protocol: Total RNA was extracted using TriReagent procedure (Invitrogen, Cergy Pontoise, France) following the manufacturer's instructions.

treatment_protocol: Penguins were anaesthetized by isoflurane inhalation, and approximately 100mg of pectoralis muscle was surgically excised, frozen in liquid nitrogen and kept at -80°C until molecular analysis.

tag: gender

value: female

tag: developmental stage

value: juvenile

value: pectoralis muscle


title: Control 25

city: Zurich

first: Leah

last: Cueni

address: Wolfgang Pauli-Str. 10

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

description: comparative transcriptional profiling

hyb_protocol: Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using the Applied Biosystems Chemiluminescence Detection Kit (PN 4342142) and the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer according to the manufacturer’s protocol. 20 µg labeled cRNA were applied per array.

scan_protocol: Scanning was performed according to the Chemiluminescent Detection Kit (PN 4339627) and Chemiluminescent Microarray Analyzer User Guide (PN 4338852).

data_processing: The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.  Quantile normalization of the raw signals was performed using R software version 2.3.1 (The R Foundation for Statistical Computing).

label: Digoxigenin-UTP

organism:
Homo sapiens
Mus musculus

source_name: MCF7 breast carcinoma xenograft, empty vector transfected, cell clone 25

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 1 µg of total RNA for each sample using the Applied Biosystems NanoAmp RT-IVT Labeling Kit (PN 4365715) according to the manufacturer’s protocol.

growth_protocol: 15 mio. MCF7 human breast carcinoma cells, in a 1:1 mixture of serum-free DMEM and Cultrex basement membrane extract (R&D), were injected bilaterally into the mammary fatpad of 7 to 9 weeks old female BALB/cA nude mice (Taconic). The total injection volume was 0.2 ml. At the same time mice were implanted s.c. in the interscapular region with 0.72 mg, 60-day release 17β-estradiol pellets (Innovative Research of America). Each cell clone was injected into five mice and tumors were grown for 24 days before mice were euthanized and tumors harvested.

extract_protocol: Total RNA was isolated from approximately 25 mg RNAlater (Ambion)-stabilized tumor tissue using the EZ1 RNA Universal Tissue Kit and the BioRobot EZ1 (Qiagen), according to the manufacturer’s instructions, including DNase digestion. Equal amounts of RNA of each tumor derived from the same MCF7 cell clone (10 tumors per cell clone) were pooled into one sample for labeling and hybridization.

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech), xenografted into BALB/cA nude mice. Cell clone control 25.


title: Podoplanin 14

description: comparative transcriptional profiling

source_name: MCF7 breast carcinoma xenograft, human podoplanin transfected, cell clone 14

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech) containing full-length cDNA of human podoplanin (transcript variant 1, GenBank Accession number NM_006474), xenografted into BALB/cA nude mice. Cell clone podoplanin 14.


title: Never Immersed penguin 4

description: Gene expression data in pectoralis muscle from a never immersed penguin

source_name: Muscle sample biopsy from juvenile penguin captured just before it undergone its first immersion to cold water

value: male


title: Never Immersed penguin 2


title: Never Immersed penguin 3


title: Podoplanin 11

description: comparative transcriptional profiling

source_name: MCF7 breast carcinoma xenograft, human podoplanin transfected, cell clone 11

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech) containing full-length cDNA of human podoplanin (transcript variant 1, GenBank Accession number NM_006474), xenografted into BALB/cA nude mice. Cell clone podoplanin 11.


title: Cells were treated with GDC-0941 at a concentration of 1mM for 6 hours, Replicate 3

city: South San Francisco

first: Debraj

last: GuhaThakurta

state: CA

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech Inc

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133P 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene chips were scanned using a Hewlett-Packard G2500A

data_processing: The data were analyzed with standard RMA normalization in BioConductor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: DMEM media supplemented  10% Fetal bovine serum, non-essential amino acids and 2mmol/L L-glutamine

extract_protocol: Qiagen RNAeasy Midi kits

tag: cell line

value: T47D breast cancer cell

tag: agent

value: GDC-0941 at a concentration of 1mM


title: Sea Acclimated penguin 2


title: Sea Acclimated penguin 3


title: Cells were treated with GDC-0941 at a concentration of 1mM for 6 hours, Replicate 2


title: Control. Replicate 1

description: Control. Replicate 1

source_name: Control


title: Mutant strain on ethanol limitation_02

description:
Gene expression from steady-state.
Mutant, Eth-Lim02

tag: strain

value: SCE088 (mutant)

tag: treatment protocol

value: ethanol limitation


title: Control 9

description: comparative transcriptional profiling

source_name: MCF7 breast carcinoma xenograft, empty vector transfected, cell clone 9

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech), xenografted into BALB/cA nude mice. Cell clone control 9.


title: Control. Replicate 2

description: Control. Replicate 2


title: Cells were treated with GDC-0941 at a concentration of 1mM for 6 hours, Replicate 1


title: KTPC_pCAR1_Pmr_His_4h

city: Tokyo

first: Hideaki

last: NOJIRI

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: Pmr binding sites detection on the pCAR1

hyb_protocol: Labeled DNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of the hybridization  to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using KT2440b520511FF-3; Bandwidth: 300, Threshold: 0, MaxGap: 30, MinRun, 30.
bar files are generated by Affymetrix Tiling Analysis Software v1.1.  File KT2440_p_value20.bed and pCAR1_p_value20.bed contains all Pmr binding sites represented in this paper

organism: Pseudomonas putida

source_name: His-tag ChIP DNA in P.putida KT2440 (pCAR1); Pmr-His

label_protocol: Samples were enzymatically fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: An overnight culture of KT2440(pCAR1) derivative expressing 6 × His-tagged Pmr in LB at 30˚C was inoculated into 200 ml of NMM-4 supplemented with 0.1 % (v/w) succinate to obtain an initial turbidity (600 nm) at 0.05, and then incubated at 30˚C in a rotating shaker at 120 rpm for 4 h to turbidity (600 nm) at 0.20-0.30.

extract_protocol: The His-tagged Pmr and DNA in the cells were in vivo cross-linked by addition of formaldehyde to a final concentration of 1 % for 15 min while shaking at 30˚C. The cross-linking reaction was quenched by addition of glycine to a final concentration of 125 mM for 5 min, then cells were washed twice with chilled TE buffer (pH 8.0). The resultant harvested cells were disrupted by sonication on ice in 2.4 mL of QuickPick IMAC (Bio-Nobile, Truku, Finland) wash buffer. After centrifugation at 17,000×g for 20 min, the supernatant was affinity-purified using the QuickPick IMAC metal affinity kit to yield 6 × His-tagged Pmr complex according to the manufacturer’s instructions. Cross-links were dissociated by heating at 65˚C for 4 h and the resultant DNA was purified using Qiaquick (QIAGEN) according to the manufacturer's instructions.

tag: antibody

value: Anti His-tag

tag: antibody manufacturer

value: GE Healthcare Bio-Sciences, NJ, USA

tag: antibody catalog number

source_name: Input DNA from P.putida KT2440 (pCAR1); Pmr-His

tag: fraction

value: input


title: Control. Replicate 3

description: Control. Replicate 3


title: KTPCdpmr_KT_02

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of hybridization to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using each forward and reverse bpmap files; Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
The BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 and pCAR1 chromosome.

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)deltaPmr

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: 100 ml of NMM-4 (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 1.0 mg ml-1 sodium succinate was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).


title: KTPCdpmr_pCAR1_02

description: This is an Affymetrix custom-commercial tiling array that covers the plasmid pCAR1 (RefSeq: AB088420) at 11-bp density.


title: KTPCdpmr_pCAR1_01


title: KTPCdpmr_KT_01


title: Podoplanin 6

description: comparative transcriptional profiling

source_name: MCF7 breast carcinoma xenograft, human podoplanin transfected, cell clone 6

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech) containing full-length cDNA of human podoplanin (transcript variant 1, GenBank Accession number NM_006474), xenografted into BALB/cA nude mice. Cell clone podoplanin 6.


title: Control 4

description: comparative transcriptional profiling

source_name: MCF7 breast carcinoma xenograft, empty vector transfected, cell clone 4

tag: MCF7 human breast carcinoma cells, stably transfected with the pTet-Off regulator plasmid and the pTRE2hyg response plasmid (Clontech), xenografted into BALB/cA nude mice. Cell clone control 4.


title: Podoplanin 14

description: comparative transcriptional profiling


title: Never Immersed penguin 1

tag: tissue


title: Podoplanin 11

description: comparative transcriptional profiling


title: Control 25

description: comparative transcriptional profiling


title: AWRIB563_versus_AWRIB515

status: Public on May 24 2010

city: Urrbrae

first: Anthony

middle: R

last: Borneman

state: South Australia

address: Paratoo Rd

country: Australia

institute: The Australian Wine Research Institute

description: CGH anlysis of strain AWRIB563

hyb_protocol: 16hrs at 60°C in Agilent hybridization buffer using MAUI hybridization chamber. Washed using 2XSSC, 0.1% SDS for 10mins at 60°C, 0.1XSSC, 0.1%SDS for 19mins at RT, and four washes of 0.1XSSC for 1min at RT.

scan_protocol: Axon Genepix

data_processing: .gpr files were converted to .mev format using "express converter v1.8". Files were normalized using Midas v2.19 using Lowess normalization.

organism: Oenococcus oeni

label_protocol: 200ng DNA was random primer labeled using klenow (Bioprime) with amino-allyl dUTP and coupled to Amersham dye.

extract_protocol: phenol/chloroform DNA extraction


title: AWRIB421_versus_AWRIB515

description: CGH anlysis of strain AWRIB421


title: AWRIB202_versus_AWRIB515

description: CGH anlysis of strain AWRIB202


title: AWRIB418_versus_AWRIB515

description: CGH anlysis of strain AWRIB418


title: AWRIB429_versus_AWRIB515

description: CGH anlysis of strain AWRIB429


title: AWRIB423_versus_AWRIB515

description: CGH anlysis of strain AWRIB423


title: AWRIB552_versus_AWRIB515

description: CGH anlysis of strain AWRIB552


title: AWRIB553_versus_AWRIB515

description: CGH anlysis of strain AWRIB553


title: AWRIB422_versus_AWRIB515

description: CGH anlysis of strain AWRIB422


title: AWRIB304_versus_AWRIB515

description: CGH anlysis of strain AWRIB304


title: AWRIB419_versus_AWRIB515

description: CGH anlysis of strain AWRIB419


title: KTPC_KT_Pmr_His_4h

description: Pmr binding sites detection on the KT2440 chromosome


title: Podoplanin 6

description: comparative transcriptional profiling


title: renal allograft biopsy,  (Minnesota) 518A1AGX7

city: Edmonton

first: Jeff

last: Reeve

state: Alberta

address: 250 HMRC University of Alberta

institute: University of Alberta

description: Samples with the same initial numbers in the sample names are replicates from the same patient. For the main analysis, only the earliest biopsy per patient was used, and only in those patients with a biopsy taken > 1 year post-transplant

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU133 Plus 2.0 Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Gene Array Scanner (Affymetrix) and processed with GeneChip Operating Software Version 1.4.0 (Affynetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: renal allograft biopsy

label_protocol: RNA (1-2ug) was labeled using GeneChip HT One-Cycle Target Labeling and Control kit. Quality of labeled cRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to HGU133Plus2.0. GeneChip (Affymetrix, Santa Clara, CA).

growth_protocol: All human renal allograft biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Following homogenization of the tissue in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA), total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 4ug/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: failed=1/non failed=0

tag: time of biopsy post transplant (days)

tag: time from biopsy to failure/censoring (days)

tag: rejection/non rejection

value: nonrej

tag: sample included in the main analysis- the first biopsy per patient from the 105 late (> 1 year) patients


title: renal allograft biopsy,  (Minnesota) 497A3AGX7


title: renal allograft biopsy,  (Minnesota) 532A1AGX7


title: renal allograft biopsy,  (Minnesota) 464A1AGX7


title: renal allograft biopsy,  (Minnesota) 492A2AGX7


title: renal allograft biopsy,  (Minnesota) 503A1AGX7


title: renal allograft biopsy,  (Minnesota) 446A1AGX7


title: renal allograft biopsy,  (Minnesota) 435A1AGX7


title: renal allograft biopsy,  (Minnesota) 437A1AGX7


title: renal allograft biopsy,  (Minnesota) 453A1AGX7


title: renal allograft biopsy,  (Minnesota) 428A1AGX7


title: renal allograft biopsy,  (Minnesota) 526A1AGX7

value: rej


title: renal allograft biopsy,  (Minnesota) 529A1AGX7


title: renal allograft biopsy,  (Minnesota) 544A1AGX7


title: renal allograft biopsy,  (Minnesota) 445A1AGX7


title: renal allograft biopsy,  (Minnesota) 438A2AGX7


title: renal allograft biopsy,  (Minnesota) 467A2AGX7


title: renal allograft biopsy,  (Minnesota) 479A1AGX7


title: renal allograft biopsy,  (Minnesota) 427A1AGX7


title: renal allograft biopsy,  (Minnesota) 395A1AGX7


title: renal allograft biopsy,  (Minnesota) 396A1AGX7


title: renal allograft biopsy,  (Minnesota) 385A2AGX7


title: renal allograft biopsy,  (Minnesota) 413A2AGX7


title: renal allograft biopsy,  (Minnesota) 525A1AGX7


title: renal allograft biopsy,  (Minnesota) 398A1AGX7


title: renal allograft biopsy,  (Minnesota) 373A1AGX7


title: renal allograft biopsy,  (Minnesota) 382A1AGX7


title: renal allograft biopsy,  (Minnesota) 370A1AGX7


title: renal allograft biopsy,  (Minnesota) 367A1AGX7


title: HBx versus Control Biological repeat 3 (no UV)

type: other

city: Singapore

first: Yu

last: Wang

address: 11 Hospital Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: Biological repeat 3

hyb_protocol: The Cy-5 and Cy-3 labeled samples were then mixed in equal amount and hybridized onto the mirVana™ bioarrays at 42 °C overnight.

scan_protocol: Scanned on an Axon 4000B scanner and signal quantified with GenePix Pro 6.0.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used. This study focuses only on human sequences. Only those human miRNAs with foreground signal more than 3X background signal are considered significant.

molecule: other

source_name: Control 3

label_protocol: Small RNA from 20ug of total RNA from HBx cells were labelled with Cy-5 and that from control cells were labelled Cy-3 with Kreatech ULS™ Small RNA Labeling Kit

growth_protocol: The human hepatocellular carcinoma HepG2 cells were cultured in Dulbecco’s modified Eagle’s media (DMEM) supplemented with 10% fetal calf serumand 25mM HEPES. The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol: Total RNA including low molecular weight RNA were extracted with Ambion MirVana™  MiRNA Isolation Kit and small RNA of <40 nt were enriched with FlashPage Fractionator

treatment_protocol: HepG2 cells were transduced with either HBx-expressing recombinant adenovirus (HBx) or control adenovirus (Control).Cells were harvested 72 hours post transduction for microarray analysis.

tag: cell line

tag: treatment

value: Control adenovirus transduced, not UV treated

source_name: HBx-expressing HepG2_3

value: HBx adenovirus transduced, not UV treated


title: renal allograft biopsy,  (Minnesota) 316A1AGX7


title: renal allograft biopsy,  (Minnesota) 301A1AGX7


title: renal allograft biopsy,  (Minnesota) 313A1AGX7


title: renal allograft biopsy,  (Minnesota) 307A1AGX7


title: HBx versus Control Biological repeat 1 (no UV)

description: Biological repeat 1

source_name: Control 1

source_name: HBx-expressing HepG2_1


title: renal allograft biopsy,  (Minnesota) 315A1AGX7


title: renal allograft biopsy,  (Minnesota) 317A1AGX7


title: renal allograft biopsy,  (Minnesota) 325A1AGX7


title: renal allograft biopsy,  (Minnesota) 334A1AGX7


title: renal allograft biopsy,  (Minnesota) 305A1AGX7


title: renal allograft biopsy,  (Minnesota) 296A1AGX7


title: renal allograft biopsy,  (Minnesota) 277A1AGX7


title: renal allograft biopsy,  (Minnesota) 276A1AGX7


title: renal allograft biopsy,  (Minnesota) 290A1AGX7


title: renal allograft biopsy,  (Minnesota) 387A1AGX7


title: renal allograft biopsy,  (Minnesota) 254A3AGX7


title: renal allograft biopsy,  (Minnesota) 286A1AGX8


title: renal allograft biopsy,  (Minnesota) 285A2AGX7


title: renal allograft biopsy,  (Minnesota) 236A4AGX7


title: HBx versus Control Biological repeat 2 (no UV)

description: Biological repeat 2

source_name: Control 2

source_name: HBx-expressing HepG2_2


title: renal allograft biopsy,  (Minnesota) 266A1AGX7


title: West Nile Virus NY99 (10^6 Copies, 200ng Human Lung RNA) 05

city: New York

first: Omar

last: Jabado

state: NY

address: 722 W 168 Street 17th Fl

department: Epidemiology

institute: Columbia University

description:
Table 1
West Nile Virus New York 1999

hyb_protocol: 65C overnight hybridization on a Agilent rotating incubator

scan_protocol: Agilent scanner 5um

data_processing: Cy3 Median Signal - Background; gMedianSignal - gBGMedianSignal (Agilent data labels).  No further processing, since non-parametric methods were used to analyze the data.

organism: West Nile virus

source_name: WNV RNA from infected tissue culture, quantified by TaqMan Real-Time PCR

label_protocol: Total RNA conversion to cDNA with degenerate oligonucleotide primers containing a known sequence tag, then amplification using primers specific to the tag that incorporate a Genisphere 3DNA-Cy3 binding sequence

growth_protocol: infection of permissive tissue culture cell lines until cytopathic effect was observed

extract_protocol: Trizol RNA extraction followed by isopropanol precipitation

treatment_protocol: viral infection

tag: target

tag: virus accession number

tag: virus taxon id

tag: experiment type

value: Known Input Virus Hybridization

tag: sample type


title: West Nile Virus NY99 (10^6 Copies, no Human Lung RNA) 09

description:
Table 1
West Nile Virus New York 1999

value: WNV RNA from infected tissue culture, quantified by TaqMan Real-Time PCR


title: West Nile Virus NY99 (10^6 Copies, 200ng Human Lung RNA) 07

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, no  Human Lung RNA) 08

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, no Human Lung RNA) 11

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, no Human Lung RNA) 10

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, 10ng Human Lung RNA) 02

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, 200ng Human Lung RNA) 06

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, 200ng Human Lung RNA) 04

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, 10ng Human Lung RNA) 03

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^4 Copies, no Human Lung RNA) 11

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^6 Copies, 10ng Human Lung RNA) 01

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^4 Copies, no Human Lung RNA) 12

description:
Table 1
West Nile Virus New York 1999


title: AL1115 Biological Replicate 2

city: St Lucia

first: Jason

last: Steen

address: Carmody Road

department: IMB

institute: University of Queensland

description: Parent, casulated strain

hyb_protocol: Combimatrix chips were hybridised as per manufacturers instructions.

scan_protocol: Hybridised arrays were scanned on a Genepix 4000b.  PMT used was max PMT with less than 20 saturated spots.

data_processing: Raw spot intensities were extracted using Microarray Imager V5.9.3 (combimatrix).  Background correction was performed using the LIMMA normexp method, and the log2 values calculated. Between-array quantile normalization was then applied to the log intensities. Spots from duplicate probes were averaged, and the averaged probe intensities analyzed using the LIMMA software package. A moderated t-test on the normalized log intensities was performed to identify significantly differing probe intensities. Probes were sorted by significance, and the False Discovery Rate used to control for multiple testing.

organism: Pasteurella multocida

source_name: Total Bacteria

label_protocol: 5ug total RNA was Reverse transcribed to cDNA with random hexamers and SuperScriptIII RT.  cDNA was NaOH treated to remove RNA contamination, and purified using Qiagen minElute columns.  2ug purified cDNA was labelled with KREAtech Cy-3-ULS.

growth_protocol: Bacteria were grown in BHI broth to OD600=~0.6

extract_protocol: Bacteria were pelleted by centrifugation, and Total RNA extracted using TRIzol.  Total RNA was DNAse treated and further purified on Rneasy mini columns

tag: capsule

value: Positive

tag: strain


title: AL1115 Biological Replicate 3

description: Parent, casulated strain


title: Psoriasis BDCA+ P4

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Psoriasis BDCA+

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: group

tag: patient


title: West Nile Virus NY99 (10^4 Copies, no Human Lung RNA) 10

description:
Table 1
West Nile Virus New York 1999


title: AL1115 Biological Replicate 1

description: Parent, capsulated strain


title: Psoriasis BDCA+ P2

label_protocol: GeneChip Two-Cycle cDNA Synthesis  Kit (Affymetrix )


title: West Nile Virus NY99 (10^4 Copies, no  Human Lung RNA) 09

description:
Table 1
West Nile Virus New York 1999


title: AL1114 Biological Replicate 3

description: acapasular strain, SNP in Fis results in L28S

value: Negative


title: AL1114 Biological Replicate 1


title: Psoriasis BDCA- P4

source_name: Psoriasis BDCA-


title: Psoriasis BDCA- P3


title: Psoriasis BDCA+ P1


title: Psoriasis BDCA- P2


title: West Nile Virus NY99 (10^4 Copies, 200ng Human Lung RNA) 08

description:
Table 1
West Nile Virus New York 1999


title: Psoriasis BDCA- P1


title: Zaire ebolavirus (ZEBOV)

description:
Table 3, Table 4
Zaire ebolavirus

organism: Zaire ebolavirus

source_name: ZEBOV RNA from infected tissue culture cells

value: Zaire ebolavirus (ZEBOV)

value: Virus Hybridization

value: Zaire ebolavirus


title: West Nile Virus NY99 (10^4 Copies, 200ng Human Lung RNA) 06

description:
Table 1
West Nile Virus New York 1999


title: Aerobic hydrogen peroxide chemostat culture 3. Slide 1

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description: no additional information

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample and re-suspended in 120 ml salt-based hybridisation buffer (supplied with the microarray slides).  This was heated at 95 oC for 3 min then cooled on ice for 3 min.  The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated for 18 h at 42 °C.  Following hybridization, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 °C) SSC buffers for 5 min each at 37oC: 1× SSC/0.1 % SDS, 1× SSC, 0.2× SSC and 0.01× SSC.  Microarray slides were dried by centrifugation at 500 × g for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner.  The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 3.5).

data_processing: Spots automatically flagged as bad, negative or poor in the Imagene software were removed before the statistical analysis was carried out in GeneSight.  The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values.  The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

source_name: Steady-state continuous cultured control aerobic samples in absence of hydrogen peroxide

label_protocol:
The labelling procedure uses equal quantities of RNA from adequate hydrogen peroxide and control samples
Approximately 9 µg RNA was annealed to 4.5 µg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65 oC for 10 min, followed by 10 min at 22 oC and cooling on ice for 2 min. This was supplemented with 6 ml of 5× First-strand buffer (Invitrogen), 2.5 ml dNTP mixture (5 mM each dATP, dTTP, dGTP and 2 mM dCTP), 3 ml 0.1 M DTT, 2 ml 1 mM Cy5 (Perkin Elmer) and 1.5 ml Superscript III reverse transcriptase (200 U) (Invitrogen).  This was incubated at 42 oC for 3 hours.  The reaction was terminated by the addition of NaOH (7.5 ml of 1M) and HCl (7.5 ml of 1M) before the addition of TE buffer (300 ml).  Labelled cDNA was purified using a Qiaquick purification kit (Qiagen).

growth_protocol: Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 2 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 1 litre, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 1 l/min, and the dissolved oxygen tension was maintained at 40% air saturation

extract_protocol: Samples (10 ml) were harvested directly into RNA Protect (Qiagen) to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.  RNA was quantified using a BioPhotometer (Eppendorf).

treatment_protocol: At steady-state, hydrogen peroxide was added to the chemostat culture and to the nutrient feed at a final concentration of 300 uM. Samples were removed immediately prior to and 5 minutes after injection of hydrogen peroxide

tag: stress

value: control

value: Wild type strain MG1655

source_name: Steady-state continuous cultured control aerobic samples in presence of 300uM hydrogen peroxide for 5 minutes

value: 300uM hydrogen peroxide


title: Aerobic hydrogen peroxide chemostat culture 3. Slide 2

description: no additional information


title: Aerobic hydrogen peroxide chemostat culture 2. Slide 2

description: no additional information


title: Aerobic hydrogen peroxide chemostat culture 2. Slide 1

description: no additional information


title: West Nile Virus NY99 (10^4 Copies, 10ng Human Lung RNA) 03

description:
Table 1
West Nile Virus New York 1999


title: Vesicular stomatitis virus Indiana (VSV)

description:
Table 3, Table 4
Vesicular stomatitis virus strain Indiana

organism: Vesicular stomatitis Indiana virus

source_name: VSV RNA from infected tissue culture cells


title: West Nile Virus NY99 (10^4 Copies, 10ng Human Lung RNA) 02

description:
Table 1
West Nile Virus New York 1999


title: West Nile Virus NY99 (10^4 Copies, 200ng Human Lung RNA) 05

description:
Table 1
West Nile Virus New York 1999


title: Negative Control (Vero cell tissue culture supernatant) 02

description:
Table 3
Monkey

organism: Chlorocebus aethiops

source_name: RNA extracted from vero cell tissue culture

value: Negative Control

value: Monkey


title: Aerobic hydrogen peroxide chemostat culture 1. Slide 2

description: no additional information


title: West Nile Virus NY99 (10^4 Copies, 10ng Human Lung RNA) 01

description:
Table 1
West Nile Virus New York 1999


title: Aerobic peroxynitrite chemostat culture 3. Slide 2

description: no additional information

source_name: Steady-state continuous cultured control aerobic samples in presence of 300uM peroxynitrite for 5 minutes

treatment_protocol: At steady-state, peroxynitrite was added to the chemostat culture and to the nutrient feed at a final concentration of 300 uM. Samples were removed immediately prior to and 5 minutes after injection of peroxynitrite

value: 300uM peroxynitrite

source_name: Steady-state continuous cultured control aerobic samples in absence of peroxynitrite


title: Aerobic hydrogen peroxide chemostat culture 1. Slide 1

description: no additional information