title: SR-A mutant olfactory epithlium 16 hpO replicate3

status: Public on Oct 14 2006

type: RNA

city: Lexington

first: Marilyn

middle: L.

last: Getchell

state: KY

address: 800 South Limestone St.

department: Anatomy and Neurobiology

country: USA

institute: University of Kentucky

description: olfactory epithelium SR-A mutant mouse 16 hpO

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: olfactory epithelium

extract_protocol: Olfactory epithelium microdissected, frozen in liquid nitrogen;tissue pulverized in Tri-Reagent (Molecular Probes), processed through a QIAshredder column (Qiagen), total RNA extracted and purified with RNeasy Mini-Kit (Qiagen)

tag: SR-A mutant, 6 weeks old


title: SR-A mutant olfactory epithlium 16 hpO replicate2


title: SR-A mutant olfactory epithlium 48 hpO replicate2

description: olfactory epithelium SR-A mutant, mouse 48 hpO

tag: SR-A mutant,, 6 weeks old


title: Wild type olfactory epithlium 48 hpO replicate3

description: olfactory epithelium wild type mouse 48 hpO

tag: Wild type, 6 weeks old


title: SR-A mutant olfactory epithlium 2 hpO replicate3

description: olfactory epithelium SR-A mutant mouse 2 hpO


title: SR-A mutant olfactory epithelium 48 hpO replicate1


title: Wild type olfactory epithelium 16 hpO replicate1

description: olfactory epithelium wild type mouse 16 hpO


title: Wild type olfactory epithlium 8 hpO replicate2

description: olfactory epithelium wild type mouse 8 hpO


title: SR-A mutant olfactory epithelium 0 h replicate1

description: olfactory epithelium SR-A mutant mouse 0 h


title: SR-A mutant olfactory epithlium 0 h replicate2


title: SR-A mutant olfactory epithlium 0 h replicate3

description: olfactory epitheliumSR-A mutant mouse 0 h


title: SR-A mutant olfactory epithelium 16 hpO replicate1

description: olfactory epitheliumSR-A mutant mouse 16 hpO


title: SR-A mutant olfactory epithlium 8 hpO replicate3

description: olfactory epithelium SR-A mutant mouse 8 hpO


title: SR-A mutant olfactory epithelium 2 hpO replicate1


title: SR-A mutant olfactory epithlium 48 hpO replicate3


title: SR-A mutant olfactory epithlium 8 hpO replicate2

tag: SR-A mutant 6 weeks old


title: SR-A mutant olfactory epithelium 8 hpO replicate1


title: Wild type olfactory epithlium 0 h replicate2

description: olfactory epithelium wild type mouse 0 h


title: Wild type olfactory epithlium 8 hpO replicate3


title: Wild type olfactory epithelium 48 hpO replicate1


title: Wild type olfactory epithlium 48 hpO replicate2


title: Wild type olfactory epithlium 16 hpO replicate3


title: Wild type olfactory epithlium 2 hpO replicate2

description: olfactory epithelium wild type mouse 2 hpO


title: Wild type olfactory epithlium 16 hpO replicate2


title: mst1b2

status: Public on Oct 11 2006

city: Corvallis

first: Jingyi

last: Li

state: OR

institute: Oregon State University

description: female wild type poplar May shoot tip at age one

data_processing: GeneXp

organism:
Populus trichocarpa
Populus deltoides

source_name: female May shoot tip at age one

tag: May shoot tip at age one


title: jst5b1

description: female wild type poplar June shoot tip at age five

source_name: female June shoot tip at age five

tag: June shoot tip at age five


title: mst2b1

description: female wild type poplar May shoot tip at age two

source_name: female May shoot tip at age two

tag: May shoot tip at age two


title: Wild type olfactory epithelium 8 hpO replicate1


title: mst1b1


title: mst2a1


title: mst6b1

description: female wild type poplar May shoot tip at age six

source_name: female May shoot tip at age six

tag: May shoot tip at age six


title: mst6a1


title: mst6b2


title: SR-A mutant olfactory epithlium 2 hpO replicate2


title: Wild type olfactory epithlium 0 h replicate3


title: Wild type olfactory epithelium 2 hpO replicate1


title: Wild type olfactory epithlium 2 hpO replicate3


title: HaCaT_4 hours_EMF exposure_S1_Ctrl/EMF

status: Public on Oct 12 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: We applied loop design for our microarray experiments in order to reduce the systemic error.

hyb_protocol: Microarray was first blocked by 0.1 mg/ml BSA, 3xSSC, and 0.1% SDS mixed solution for 1 hours at 50 oC. Then dipped in ddH2O for four times. Labeled cDNA was pipetted onto the center of the microarray and a coverslip (large enough to cover the entire array surface) was placed over the probe. The microarray was transferred in a hybridization chamber and four 16μl drops of 3x SSC were pipetted around the slide to provide humidity in the hybridization chamber (Takara, Japan). Then, the hybridization chamber was submerged in a 65℃ water bath for 16 to 20 hours. After hybridization was complete, the microarray was washed in 2x SSC and 0.1% SDS at 42°C for 5 min, followed by additional 10 min wash steps in 0.1x SSC and 0.1% SDS, 1mim in 0.1x SSC for four times, and 10s in 0.01 x SSC, each at room temperature.

scan_protocol: barcode=12766767 "PMTGain=600	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.93	3.1" Temperature=28.81 "ScanPower=100	100"

data_processing: Data processing will be described in detail in our website http://140.114.106.30/publication/tjweng/

organism: Homo sapiens

source_name: Control samples

label_protocol: 60μg total RNA and 4.96ng spike RNA was annealed to oligo(dT) and reversely transcribed by Superscript II (Invitrogen, Carlsbad, CA) to single strand cDNA labeled with Cy5-labeled dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Reactions were terminated using 0.1 N NaOH and then neutralized by 0.1 N HCl. Labeled cDNA was purified by microcon YM-30 column (Qiagen, Inc., Valencia, CA) and blocked by adding 20μg of Cot1 human DNA (Invitrogen, Carlsbad, CA), 20μg ployA RNA (Invitrogen, Carlsbad, CA) and 20μg tRNA (Invitrogen, Carlsbad, CA).

growth_protocol: Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100μg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone). Cells were routinely split 1: 6 every 3 days and have a plating efficiency of approximately 10%. For microarray experiments, 2×106 cells were seed 48 hours before treatment.

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 1.5 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

treatment_protocol: No

tag: Cell line, Gender

value: male, Tissue:arm keratinocyte

source_name: Cells exposed to 15G ELF-EMF for 4hours

label_protocol: 60μg total RNA and 4.96ng spike RNA was annealed to oligo(dT) and reversely transcribed by Superscript II (Invitrogen, Carlsbad, CA) to single strand cDNA labeled with Cy3-labeled dUTP (Amersham Pharmacia Biotech, Piscataway, NJ). Reactions were terminated using 0.1 N NaOH and then neutralized by 0.1 N HCl. Labeled cDNA was purified by microcon YM-30 column (Qiagen, Inc., Valencia, CA) and blocked by adding 20μg of Cot1 human DNA (Invitrogen, Carlsbad, CA), 20μg ployA RNA (Invitrogen, Carlsbad, CA) and 20μg tRNA (Invitrogen, Carlsbad, CA).

treatment_protocol: Cells exposed to 15G ELF-EMF for 4hours


title: mst5b2

description: female wild type poplar May shoot tip at age five

source_name: female May shoot tip at age five

tag: May shoot tip at age five


title: jst5b2


title: mst6a2


title: Wild type olfactory epithlium 0 h replicate1


title: mst5b1


title: mst5a2


title: mst2b2


title: mst5a1


title: mst2a2


title: mst1a2


title: mbst5a2

description: female wild type poplar May basal shoot tip at age five

source_name: female May basal shoot tip at age five

tag: May basal shoot tip at age five


title: mbst6b1

description: female wild type poplar May basal shoot tip at agesix

source_name: female May basal shoot tip at age six

tag: May basal shoot tip at age six


title: mbst6a2


title: mbst5a1


title: mst1a1


title: jst6b1

description: female wild type poplar June shoot tip at age six

source_name: female June shoot tip at age six

tag: June shoot tip at age six


title: jst2b2

description: female wild type poplar June shoot tip at age two

source_name: female June shoot tip at age two

tag: June shoot tip at age two


title: mbst6a1


title: jst6b2


title: jst6a2


title: jst6a1


title: jst2a1


title: jst2a2


title: jst1b1

description: female wild type poplar June shoot tip at age one

source_name: female June shoot tip at age one

tag: June shoot tip at age one


title: jbs5b2

description: female wild type poplar June basal shoot tip at age five

source_name: female June basal shoot tip at age five

tag: June basal shoot tip at age five


title: jbst5b1


title: jbst6b1

description: female wild type poplar June basal shoot tip at age six

source_name: female June basal shoot tip at age six

tag: June basal shoot tip at age six


title: jbst5a2


title: mbst6b2


title: mbst5b2


title: jbst5a1


title: jst1a2


title: mbst5b1


title: jst1b2


title: jst2b1


title: jst1a1


title: 2fb6a1

description: male wild type poplar floral bud at age six

source_name: male floral bud from six year old poplar

tag: male floral bud at age six


title: 2lvb6a2

description: male wild type poplar lateral vegetative bud at age six

source_name: male lateral vegetative bud from six year old poplar

tag: male lateral vegetative bud at age six


title: 2fb6b1


title: jbst6b2


title: jbst6a2


title: jbst6a1


title: lvb5a2

description: wild type poplar lateral vegetative bud at age five

source_name: lateral vegetative bud from five year old poplar

tag: lateral vegetative bud at five year old


title: lvb2a1

description: wild type poplar lateral vegetative bud at age two

source_name: lateral vegetative bud from two year old poplar

tag: lateral vegetative bud at age two


title: lvb1b1

description: wild type poplar lateral vegetative bud at age one

source_name: lateral vegetative bud from one year old poplar

tag: lateral vegetative bud at age one


title: 2lvb6b1


title: 2lvb6a1


title: lvb1b2


title: 2lvb6b2


title: 2fb6b2


title: lvb6b2

description: wild type poplar lateral vegetative bud at age six

source_name: lateral vegetative bud from six year old poplar

tag: lateral vegetative bud at age six


title: 2fb6a2


title: lvb5a1


title: lvb2b1


title: lvb2a2


title: fb6b1

description: wild type poplar floral bud at age six

source_name: floral bud from six year old poplar

tag: floral bud at age six


title: lvb5b2


title: fb6a1

description: wild type poplar floral bud at age six


title: lvb6a1


title: lvb5b1


title: lvb6a2


title: Human Müller Cell Lines from diabetic donor of type II (HMCL-II)

status: Public on Aug 12 2006

type: SAGE

anchor: NlaIII

city: Ste-Foy

first: Caroline

last: Lupien

state: Québec

address: 2705, boul. Laurier

department: Centre de Recherche du CHUL

country: Canada

institute: Université Laval

description: Bolduc et al., 2004, J. Mol. End., 33: 429-444

molecule: polyA RNA

source_name: human Müller cells from diabetic donor of type II

tag: gender

value: female

tag: age

value: 69 years

tag: diabetes

value: type 2


title: lvb1a2


title: lvb2b2


title: lvb1a1


title: fb6a2

description: wild type poplar floral bud at age six


title: lvb6b1


title: Human retinal Müller cells library

source_name: human retinal Müller cells

tag: pooled cells


title: fb6b2

description: wild type poplar floral bud at age six


title: Human Müller Cell Lines from diabetic donor of type I (HMCL-I)

source_name: human Müller cells from diabetic donor of type I

value: male

value: 34 years

value: type 1


title: Control versus SA C

status: Public on Jul 22 2006

city: Waterloo

first: Barbara

last: Moffatt

state: Ontario

address: 200 University Ave West

department: Biology

institute: University of Waterloo

description: Three biological replicates with dye swap as technical replicate were performed

hyb_protocol: Microarrays were prehybridized, hybridized and washed according to the protocol provided by the MicroArray Lab at Biotechnology Research Institute, Montreal. (http://www.bri.nrc.gc.ca/pdf/microarray_Direct_Incorporation_Labeling%20_Protocol_e.doc). An extra step of dipping the slides in isopropanol was performed

scan_protocol: ScanArray confocal scanning system and QuantArray data acquisition software (Perkin Elmer, Boston, MA) were used according to the manufacturer’s instruction

data_processing: Joint Lowess used for data normalization; an algorithm that used a Bayesian approach to assess the significance of each treatment for each gene was used [Labbe, A (2005) Multiple testing using the posterior probability of half-space : application to gene expression data. PhD thesis. University of Waterloo, Waterloo, ON, Canada]

organism: Eutrema

source_name: Control (Yukon ecotype of Thellungiella)

label_protocol: Forty ug of total RNA was reverse transcribed to synthesize aminoally-labeled cDNA followed by coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules using protocol from the Institute of Genome Research (TIGR; http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml)

growth_protocol: Plants of the Yukon ecotype of Thellungiella salsuginea (Pall.) O.E. Schulz (Al-Shehbaz et al., 1999; Cody, 2000) were grown in controlled environments with an irradiance of 250 mmol photons m-2 s-1; a 21 h daylength, and a day/night temperature of regime of 22/10°C

extract_protocol: Total RNA was extracted from only above ground tissues as described by Danyluk and Sarhan (1990)

tag: Leaves from control plants

source_name: SA (Yukon ecotype of Thellungiella)

treatment_protocol: In order to have plants acclimated to high salinity, plants were watered with NaCl solutions at concentrations that increased by 50 mM increment every 3 days until the final concentration reached 300 mM; tissues were harvested 3 days later

tag: Leaves from SA-plants


title: Dr versus RW A (dye reverse)

source_name: Dr (Yukon ecotype of Thellungiella)

treatment_protocol: or the drought treatment, water was withheld from one-month-old plants until they wilted visibly (about three days)

tag: Leaves from droughted plants

source_name: RW (Yukon ecotype of Thellungiella)

treatment_protocol: plants were droughted for 3 days, and then re-watered and allowed to recover for 2 days

tag: leaves from re-watered plants after 3 days of drought


title: Dr versus RW C

tag: Leaves from re-watered plants after drought


title: Control versus SA C (dye reverse)


title: Control versus Dr C (Dye reverse)

tag: Leave from control plants

growth_protocol: Plants of the Yukon ecotype of Thellungiella salsuginea (Pall.) O.E. Schulz (Al-Shehbaz et al., 1999; Cody, 2000) were grown in controlled environments with an irradiance of 250 mmol photons m-2 s-1; a 21 h daylength, and a day/night temperature regime of 22/10°C. When the plants were four-week-old, water was withheld from one-month-old plants until they wilted visibly (about three days)

treatment_protocol: For the drought treatment, water was withheld from one-month-old plants until they wilted visibly (about three days)

tag: Leaves from 3-day droughted plants


title: Control versus SA B (dye reverse)

tag: leaves from control plants


title: Drought (Dr) versus Re-watering (RW) A

source_name: Drought (Yukon ecotype of Thellungiella)

tag: Leaves from re-watered plants after 3-day drought


title: Dr versus RW B (Dye reverse)

tag: leaves from droughted plants


title: Control versus Salt-acclimated (SA) A (Dye reverse)

tag: Leaves from 300mM NaCl-acclimated plants


title: Dr versus RW B


title: Control versus Cold 3-week A (Dye Reverse)

description: Three biological replicates with dye swap as technical replicate were examined for all experimental conditions

hyb_protocol: Microarrays were prehybridized, hybridized and washed according to the protocol provided by the MicroArray Lab at Biotechnology Research Institute, Montreal. (http://www.bri.nrc.gc.ca/pdf/microarray_Direct_Incorporation_Labeling%20_Protocol_e.doc).  An extra step of dipping the slides in isopropanol was performed prior to air-drying the slides.

scan_protocol: ScanArray confocal scanning system and QuantArray data acquisition software (Perkin Elmer, Boston, MA) were used according to the manufacturer’s instructions to capture the data.

data_processing: Data transformed using Joint Lowess method

source_name: 3-week cold lacclimated leaves (Yukon ecotype of Thellungiella)

growth_protocol: Plants of the Yukon ecotype of Thellungiella salsuginea (Pall.) O.E. Schulz (Al-Shehbaz et al., 1999; Cody, 2000) were grown in controlled environments with an irradiance of 250 mmol photons m-2 s-1; a 21 h daylength, and a day/night temperature regime of 22/10°C

tag: Leaves harvested from 3-week cold acclimated plants

source_name: Control leaves (Yukon ecotype of Thellungiella)

treatment_protocol: For cold treatment, 4-week-old plants were shifted to a day/night temperature regime of 5/4oC with a 21 h daylength and leaves were sampled after 3 weeks.

tag: Leaves harvested from control plants


title: Control versus Dr C


title: Control versus 3-week salt acclimated (SA) A

tag: Leaves from 3-week 300mM NaCl-acclimated plants


title: Control versus Cold 3-week C (dye replicate)

hyb_protocol: Microarrays were prehybridized, hybridized and washed according to the protocol provided by the MicroArray Lab at Biotechnology Research Institute, Montreal. (http://www.bri.nrc.gc.ca/pdf/microarray_Direct_Incorporation_Labeling%20_Protocol_e.doc). An extra step of dipping the slides in isopropanol was performed prior to air-drying the slides.

data_processing: Joint Lowess used for data normalization

tag: Leaves harvested from untreated control plants

source_name: Cold 3-week (Yukon ecotype of Thellungiella)

growth_protocol: For cold treatment, 4-week-old plants were shifted to a day/night temperature regime of 5/4oC with a 21 h daylength and leaves were sampled after 3 weeks.


title: Control versus Cold 3-week B


title: Control Versus Drought (Dr) A (dye reverse)


title: Control versus 3-week Cold B (Dye reverse)


title: Control versus Salt-acclimated (SA) B


title: Control Versus Dr B (Dye Reverse)

tag: Leaves from Control plants

tag: Leaves harvested from 3-day droughted plants


title: Control versus Cold 3-Week A

data_processing: a data transformation method called the Joint Lowess

label_protocol: Forty mg of total RNA was reverse transcribed to synthesize aminoally-labeled cDNA followed by coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules using protocol from the Institute of Genome Research (TIGR; http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml)

tag: Leaves harvested from untreated plants

tag: Leaves harvested from 3 week cold-acclimated plants


title: left ventricular- 10 months old- obese 2

status: Public on Jul 05 2006

city: Toulouse

first: Philippe

middle: V

last: Rouet

address: 1 Ave Jean Poulhes

department: Cardiology

country: France

institute: INSERM U1048

description: no functional leptin receptor

hyb_protocol: Using one nylon membrane per animal for the hybridization (kit Array-Advantage GF, Ambion)

scan_protocol: Exposition of each membrane during 24 hours (Storage Phosphor Screen, Molecular Dynamics). Revelation with Scan Typhoon 9400 (resolution at 50 µm per pixel). Analysis of images by Image Quant 5.1

data_processing: background subtraction, log transformation, normalization by total mean, exponential (back from log), scaling by a factor 10000.

organism: Rattus norvegicus

source_name: 10 months old SHHF obese rat, left ventricular

label_protocol: Reverse Transcription of 3 µg total RNA from each left ventricular with Superscript enzyme (Invitrogen). Purification of cDNA labelled with 33P with NucleoSpin Extract (Macherey-Nagel)

growth_protocol: Animals were lodged in the Zootechnic service of the Louis Bugnard Institute. A veterinary oversees animal health and management. Temperature : 22 +/- 1 degrees. Cycles nights/days : 12 hours. Food : Teklad Global 16% Protein Rodent Diet (Harlan)

extract_protocol: General anesthesia by Isoflurane 4%. Heart extraction. Isolation of total RNA from left ventricular by : TRIzol (Invitrogen), homogeneisor Ika Ultra-Thurax T 25 (Janke and Kunkel), DNAfree (Ambion). Quality and quantity were determined by capillary electrophoresis (Agilent).

tag: Strain

value: SHHF, Gender:Male, Age:10 months, Tissue:left ventricular, Other:hypertension, metabolic syndrom, dilated cardiomyopathy starting from 10 months


title: left ventricular- 10 months old- obese 5

description: no functional leptin receptor


title: left ventricular- 10 months old - obese 3

description: no functional leptin receptor


title: Dr versus RW C (dye reverse)

tag: Leaves from control plants


title: Control versus Dr A


title: left ventricular- 10 months old- obese 3

description: no functional leptin receptor


title: Control Versus Drought (Dr) B

data_processing: Joint Lowess used for data normalization; an algorithm that used a Bayesian approach to assess the significance of each treatment for each gene was used (Labbe, A (2005) Multiple testing using the posterior probability of half-space : application to gene expression data. PhD thesis. University of Waterloo, Waterloo, ON, Canada)


title: left ventricular- 10 months old - lean 5

description: Lean rats can be homozygous or heterozygous for the leptin receptor gene (+/+ or cp/+, cp means corpulent allele and is a recessive autosomic one, + means wild type)

source_name: 10 months old SHHF lean rat, left ventricular

value: SHHF, Gender:Male,

tag: Age

value: 10 months, Tissue:left ventricular, Other:hypertension, dilated cardiomyopathy starting from 14 months


title: left ventricular- 10 months old- obese 1

description: no functional leptin receptor


title: CLIP93667 - replicate #3

status: Public on Jul 03 2006

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

description: see above.

hyb_protocol: Macroarrays were pre-hybridized in roller bottles with 10 ml of a hybridization solution containing 5X SSPE (1X SSPE is 0.18 M NaCl, 10 mM NaH2PO4 and 1 mM EDTA pH7.7), 2% SDS, 1X Denhardt’s reagent (Sigma), 100 ug/ml of sonicated salmon sperm DNA for 1h at 65oC. Hybridizations were performed overnight at 65oC with 5 ml of fresh hybridization solution containing the labeled cDNA. After hybridization macroarrays were washed twice for 5 min at room temperature and twice for 20 min at 65oC with a washing solution (0.5X SSPE, 0.2% SDS).

scan_protocol: The macroarrays were then exposed to a phosphoimager screen and scanned with the Typhoon phosphoimager (Pharmacia-Amersham). Two hybridizations for each independent RNA extraction were performed. In total, a set of 4 macroarrays was used for each strain. Hybridized arrays were scanned using the Typhoon 9400 phosphoimager (Amersham Biosciences). The signal intensity was quantified using the ArrayVision software (Imaging Research). The intensity was measured in arbitrary units using the ARMdens measure.

data_processing: Normalized by a multiplicative constant. The correction factor is obtained setting arbitrarily the median of log10(intensities) to ZERO.

organism: Listeria monocytogenes

label_protocol: Total RNA (1ug) was mixed with 6 ul of 5X AMV reverse transcriptase buffer (Roche), 3 ul of a mixture of dATP, dGTP, dTTP (10 mM), 5 ug of random hexamers (Primer Random p(dN)6, Roche) and DEPC-treated water to a final volume of 21 ul. The mixture was heated at 90oC for 2 min and cooled to 42oC before addition of 3 ul of alpha-33P dCTP (20 uCi) and 2 ul (50U/ul) of AMV reverse transcriptase (Roche). The mixture was incubated for 2 h at 42oC. A column was used for the removal of unincorporated nucleotides according to the manufacturer’s instructions (QIAquick Nucleotide Removal Kit, QIAgen). The obtained cDNA was denaturated by heating at 99oC for 5 min just before hybridization.

growth_protocol: All strains were grown until late exponential phase (OD600 0.9) in the defined rich medium MCDB 202 (CryoBioSystem), at 37oC. Pulsed Field Gel Electrophoresis was performed for molecular characterization of the strains. Bacterial cells were grown overnight in BHI medium (Difco) and inoculated (10%) in 10 ml MCDB 202 medium for total RNA extraction. For each strain, two overnight cultures were used.

extract_protocol: Cells were harvested by centrifugation at 12000 g for 4 min at 4oC, and immediately frozen. Pellets were resuspended in 400 ul of buffer (10% glucose, 12.5 mM Tris pH 7.6, 5 mM EDTA) and 60 ul of EDTA 0.5 M, and cells were mechanically disrupted in a FastPrep apparatus after the addition of 500 ul of acid phenol (pH 4.5) and 0.4 g of glass beads (Sigma). After a centrifugation step, the aqueous phase was transferred to new tubes, 1 ml of Trizol (Invitrogen) was added and samples were incubated for 5 min at room temperature. 200 ul of chlorophorm/isoamylic alcohol were added to each sample, followed by centrifugation for 5 min. This step was repeated twice and to the final aqueous supernatant 500 ul of 2-propanol were added for total RNA precipitation. The mixture was left at -20oC for 15 min and centrifuged for 30 min at 4oC. Pellets were then washed with 70% ethanol and dried at room temperature prior to being dissolved in 50 ul of diethylpyocarbonate (DEPC)-treated water. The RNA concentration was estimated using a spectrophotometer and RNA quality was checked on agarose gel containing ethidium bromide.


title: CLIP93667 - replicate #1

description: see above.


title: CLIP93667 - replicate #2

description: see above.


title: CLIP93649 - replicate #4

description: see above.


title: CLIP93666 - replicate #3

description: see above.


title: left ventricular-4 months old- lean 1

data_processing: background subtraction, log transformation, normalization by total mean, exponential (back from log), scaling by a factor 10000

source_name: 4 months old SHHF lean rat, left ventricular

value: 4 months, Tissue:left ventricular, Other:hypertension, dilated cardiomyopathy starting from 14 months old


title: left ventricular- 4 months old- lean 2


title: CLIP93666 - replicate #2

description: see above.


title: left ventricular- 4 months old- lean 4


title: left ventricular- 10 months old- lean 3


title: left ventricular- 4 months old- obese 4

description: no functional leptin receptor

source_name: 4 months old SHHF obese rat, left ventricular

value: 4 months, Tissue:left ventricular, Other :hypertension, metabolic syndrom, dilated cardiomyopathy starting from 10 months old


title: left ventricular- 4 months old- obese 3

description: no functional leptin receptor

value: SHHF, Gender:Male, Age:4 months, Tissue:left ventricular, Other:hypertension, metabolic syndrom, dilated cardiomyopathy starting from 10 months old


title: left ventricular-4 months old- obese 2

description: no functional leptin receptor


title: left ventricular- 4 months old- lean 3


title: CLIP93665 - replicate #4

description: see above.


title: left ventricular- 4 months old- obese 5

description: no functional leptin receptor

value: 4 months, Tissue:left ventricular, Other:hypertension, metabolic syndrom, dilated cardiomyopathy starting from 10 months old


title: CLIP93665 - replicate #3

description: see above.


title: CLIP93665 - replicate #2

description: see above.


title: CLIP93649 - replicate #3

description: see above.


title: CLIP93665 - replicate #1

description: see above.


title: CLIP93649 - replicate #2

description: see above.


title: CLIP93666 - replicate #4

description: see above.


title: Control versus Cold 3-week C


title: CLIP93649 - replicate #1

description: see above.


title: CLIP93666 - replicate #1

description: see above.


title: CLIP90602 - replicate #4

description: see above.


title: CLIP90602 - replicate #1

description: see above.


title: CLIP93667 - replicate #4

description: see above.


title: CLIP90602 - replicate #2

description: see above.


title: left ventricular- 10 months old- lean 4


title: CLIP80459 - replicate #3

description: see above.


title: CLIP90602 - replicate #3

description: see above.


title: CLIP80459 - replicate #2

description: see above.


title: CLIP80459 - replicate #1

description: see above.


title: CLIP80459 - replicate #4

description: see above.

label_protocol: Total RNA (1ug) was mixed with 6 ul of 5X AMV reverse transcriptase buffer (Roche), 3 ul of a mixture of dATP, dGTP, dTTP (10 mM), 5 ug of random hexamers  (Primer Random p(dN)6, Roche) and DEPC-treated water to a final volume of 21 ul. The mixture was heated at 90oC for 2 min and cooled to 42oC before addition of 3 ul of alpha-33P dCTP (20 uCi) and 2 ul (50U/ul) of AMV reverse transcriptase (Roche). The mixture was incubated for 2 h at 42oC. A column was used for the removal of unincorporated nucleotides according to the manufacturer’s instructions (QIAquick Nucleotide Removal Kit, QIAgen). The obtained cDNA was denaturated by heating at 99oC for 5 min just before hybridization.


title: left ventricular- 10 months old-lean 1

label_protocol:
Reverse Transcription of 3 µg total RNA from each left ventricular with Superscript enzyme (Invitrogen).
Purification of cDNA labelled with 33P with NucleoSpin Extract (Macherey-Nagel)


title: left ventricular- 4 months old- lean 5


title: Gene expression profiling of FSHMD1A muscle (11c)

status: Public on Jun 16 2006

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: We compared the transcription profiles of FSHMD1A deltoideous muscles with a pool of 10 human deltoideous muscles obtained from normal donors, in a microarray competitive hybridization.

hyb_protocol: Microarray hybridization was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 ul of 3 x SSC. Labeled cDNA was dissolved in 40 ul of hybridization buffer, denatured at 90°C for 2 min and applied directly to the slides. Hybridization was performed overnight at 42°C by immersion in a water bath (W28, Grant, Cambridge, UK). The following post-hybridization washes were performed: 1XSSC, 0.1% SDS for 4 min at 42°C, 0,1X SSC, 0.1% SDS for 4 min at room temperature and 0,2X SSC for 2 min at room temperature.

scan_protocol: Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.

source_name: FSHMD1A deltoid muscle n°11(c)

label_protocol: Linear amplification of mRNA was carried on using the Message-Amp-aRNA kit (Ambion, TX, USA) with two consecutive amplification steps, according to the manufacturer’s recommendations. Fluorescent cDNA targets were prepared by direct labelling 1.5 ug of aRNA from each sample.

extract_protocol: Total RNA was isolated using the TRIZOL reagent (Invitrogen/Life Technologies) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany).

tag: - Sex

value: M

tag: - Age (years)

tag: - EcoR1 Fragment length (Kb)

tag: - Clinical severity

value: high

tag: - Inflammation signs

tag: - Regenerating fibres

tag: - Ragged-red-fibres

tag: - Myopatic features

value: minimal

source_name: normal deltoid control

tag: Pool of ten human deltoideous normal muscles


title: Gene expression profiling of FSHMD1A muscle (11b)

source_name: FSHMD1A deltoid muscle n°11(b)


title: Gene expression profiling of FSHMD1A muscle (8a)

source_name: FSHMD1A deltoid muscle n°8(a)

value: mild


title: Gene expression profiling of FSHMD1A muscle (9b)

source_name: FSHMD1A deltoid muscle n°9(b)


title: Gene expression profiling of FSHMD1A muscle (11a)

source_name: FSHMD1A deltoid muscle n°11(a)


title: Gene expression profiling of FSHMD1A muscle (10)

source_name: FSHMD1A deltoid muscle n°10

value: F

value: rare


title: left ventricular- 4 months old- obese 1

description: no functional leptin receptor


title: Gene expression profiling of FSHMD1A muscle (8c)

source_name: FSHMD1A deltoid muscle n°8(c)


title: Gene expression profiling of FSHMD1A muscle (9a)

source_name: FSHMD1A deltoid muscle n°9(a)


title: Gene expression profiling of FSHMD1A muscle (8b)

source_name: FSHMD1A deltoid muscle n°8(b)


title: Gene expression profiling of FSHMD1A muscle (6a)

source_name: FSHMD1A deltoid muscle n°6(a)

value: intermediate


title: Gene expression profiling of FSHMD1A muscle (4a)

source_name: FSHMD1A deltoid muscle n°4(a)


title: Gene expression profiling of FSHMD1A muscle (5b)

source_name: FSHMD1A deltoid muscle n°5(b)

value: low

value: some


title: Gene expression profiling of FSHMD1A muscle (3a)

source_name: FSHMD1A deltoid muscle n°3(a)


title: Gene expression profiling of FSHMD1A muscle (4b)

source_name: FSHMD1A deltoid muscle n°4(b)


title: Gene expression profiling of FSHMD1A muscle (7a)

source_name: FSHMD1A deltoid muscle n°7(a)


title: Gene expression profiling of FSHMD1A muscle (7b)

source_name: FSHMD1A deltoid muscle n°7(b)


title: Gene expression profiling of FSHMD1A muscle (6b)

source_name: FSHMD1A deltoid muscle n°6(b)


title: Gene expression profiling of FSHMD1A muscle (5a)

source_name: FSHMD1A deltoid muscle n°5(a)

source_name: normal deltoid control


title: HDDP_rotator_rep2

status: Public on Jun 15 2006

type: genomic

city: New Orleans

first: Timothy

last: Hammond

state: LA

address: 1430 Tulane Ave

department: Department of Medicine, Nephrology Section, SL-45

institute: Tulane University Health Sciences Center

description: Saccharomyces cerevisiae homozygous diploid deletion pool grown in a rotating wall vessel (RWV) for 18 hours on a rotator

hyb_protocol: 1.2 ug of the uptag and downtag products were combined with 200 uM unlabeled primers (U1, U2, D1, D2) and hybridized to a TAG 3 array. The sample volume was brought to 200 l in 6× SSPE-T, boiled for 2 min, and then allowed to cool on ice. Before hybridization, the TAG 3 chip was washed for 10 min with 6× SSPE-T. The sample was then hybridized to the chip for 16 h at 42°C. Following hybridization, the chip was washed two times with six changes of 6× SSPE-T, then stained with streptavidin–phycoerythrein for 10 min at 42°C, and washed two times with five changes of 6× SSPE-T

scan_protocol: Chip was scanned at 560 nm using a GeneChip scanner (Affymetrix, Santa Clara, Calif.). The hybridization intensities for each of the array elements were determined using Affymetrix GeneChip software.

data_processing: Affymetrix GeneChip software

label: Biotin

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Homozygous diploid deletion pool, grown on rotator

label_protocol: The uptag and downtag barcodes from all deletion cassettes were amplified from the genomic DNA of the homozygous deletion pool, using biotinylated primers specific to the universal sequences at the end of each unique barcode region. The four primer sequences were U1 (GATGTCCACGAGGTCTCT), U2 (CGTACGCTGCAGGTCGAC), D1 (CGGTGTCGGTCTCGTAG), and D2 (ATCGATGAATTCGAGCTCG).

growth_protocol: Culture was grown for 18 hours at 30 C in a rotating wall vessel placed on a rotator set at 30 rpm

extract_protocol: Genomic DNA was prepared from yeast cultures using the MasterPure yeast DNA purification kit (Gentra Systems, Minneapolis, Mass.)

tag: A pool of all homozygous diploid deletion strains, derived from the parental strain BY4743 (MAT a/alpha his3D1, leu2D, met15D ura3D)


title: HDDP_static_rep2

description: Saccharomyces cerevisiae homozygous diploid deletion pool grown in a rotating wall vessel (RWV) for 18 hours in a static position

source_name: Homozygous diploid deletion pool, grown static

growth_protocol: Culture was grown for 18 hours at 30 C in a rotating wall vessel placed in a horizontal static position


title: HDDP_static_rep1

label_protocol:
The uptag and downtag barcodes from all deletion cassettes were amplified from the genomic DNA of the homozygous deletion pool, using biotinylated primers specific to the universal sequences at the end of each unique barcode region. The four primer sequences were U1 (GATGTCCACGAGGTCTCT), U2 (CGTACGCTGCAGGTCGAC), D1 (CGGTGTCGGTCTCGTAG), and D2 (ATCGATGAATTCGAGCTCG).
The resulting PCR products were purified using Microcon YM-10 centrifugal filter devices (Amicon Bioseparation–Millipore, Minneapolis, Minn.)


title: Gastric_cancer_patient_66_dye_swap

status: Public on Jun 01 2006

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing: log2 ratio of Cy3/Cy5

source_name: Gastric tissue normal region

tag: normal

source_name: Gastric tissue tumor region

tag: tumor stage

value: IA, IB, II, IIIA, IIIB, or IV=IV

tag: Sex

value: female, male:male

tag: tumor depth

value: early gastric cancer or advanced gastric cancer=advanced gastric cancer

tag: tumor histology

value: moderately differentiated or poorly differentiated=poorly differentiated

tag: Lauren's t ype

value: intestinal type, diffuse type, mixed type, or not determined=diffuse type


title: Gene expression profiling of FSHMD1A muscle (2c)

source_name: FSHMD1A deltoid muscle n°2(c)


title: Gene expression profiling of FSHMD1A muscle (2b)

source_name: FSHMD1A deltoid muscle n°2(b)


title: Gene expression profiling of FSHMD1A muscle (3b)

source_name: FSHMD1A deltoid muscle n°3(b)


title: HDDP_rotator_rep1


title: Gastric_cancer_patient_64_dye_swap


title: Gene expression profiling of FSHMD1A muscle (1b)

source_name: FSHMD1A deltoid muscle n°1(b)

source_name: normal deltoid muscle


title: Gene expression profiling of FSHMD1A muscle (2a)

source_name: FSHMD1A deltoid muscle n°2(a)


title: Gene expression profiling of FSHMD1A muscle (1a)

description: We compared the transcription profiles of FSHMD1A deltoideous muscles with a pool of 10 human deltoideous muscles obtained from normal donors in a microarray competitive hybridization.

hyb_protocol: Microarray hybridization was carried out in a dual slide chamber (HybChamber, Gene Machines, San Carlos, CA, USA) humidified with 100 µl of 3 x SSC. Labeled cDNA was dissolved in 40 µl of hybridization buffer, denatured at 90°C for 2 min and applied directly to the slides. Hybridization was performed overnight at 42°C by immersion in a water bath (W28, Grant, Cambridge, UK). The following post-hybridization washes were performed: 1XSSC, 0.1% SDS for 4 min at 42°C, 0,1X SSC, 0.1% SDS for 4 min at room temperature and 0,2X SSC for 2 min at room temperature.

source_name: FSHMD1A deltoid muscle n°1(a)

tag: - EcoR1 Fragment Length (Kb)

tag: Pool of ten human deltoideous muscles


title: HDDP_shaker_rep1

description: Saccharomyces cerevisiae homozygous diploid deletion pool grown in a rotating wall vessel (RWV) for 18 hours in a shaker

source_name: Homozygous diploid deletion pool, grown in shaker

growth_protocol: Culture was grown for 18 hours at 30 C in a rotating wall vessel placed in a gyrorotatory shaker set at 90 rpm


title: HDDP_shaker_rep2


title: Gastric_cancer_patient_70_dye_swap

value: female, male:female


title: Gastric_cancer_patient_55_dye_swap

value: IA, IB, II, IIIA, IIIB, or IV=IIIB


title: Gastric_cancer_patient_69_dye_swap


title: Gastric_cancer_patient_58_dye_swap

value: intestinal type, diffuse type, mixed type, or not determined=intestinal type


title: Gastric_cancer_patient_67_dye_swap


title: Gastric_cancer_patient_68_dye_swap

value: intestinal type, diffuse type, mixed type, or not determined=mixed type


title: left ventricular- 10 months old- lean 2

source_name: 10 months old SHHF lean rat, left ventricular

tag: Strain

value: SHHF, Gender:Male,

tag: Age

value: 10 months, Tissue:left ventricular, Other:hypertension, dilated cardiomyopathy starting from 14 months


title: Gastric_cancer_patient_53_dye_swap


title: Gastric_cancer_patient_63_dye_swap

value: female, male:NA

value: intestinal type, diffuse type, mixed type, or not determined=not determined


title: Gastric_cancer_patient_60_dye_swap


title: Gastric_cancer_patient_45_dye_swap

value: IA, IB, II, IIIA, IIIB, or IV=IIIA


title: Gastric_cancer_patient_46_dye_swap


title: Gastric_cancer_patient_65_dye_swap


title: Gastric_cancer_patient_62_dye_swap


title: Gastric_cancer_patient_33_dye_swap

value: IA, IB, II, IIIA, IIIB, or IV=II


title: Gastric_cancer_patient_56_dye_swap


title: Gastric_cancer_patient_314_dye_swap


title: Gastric_cancer_patient_61_dye_swap


title: Gastric_cancer_patient_32_dye_swap


title: Gastric_cancer_patient_57_dye_swap


title: Gastric_cancer_patient_54_dye_swap


title: Gastric_cancer_patient_59_dye_swap


title: Gastric_cancer_patient_51_dye_swap


title: Gastric_cancer_patient_52_dye_swap


title: Gastric_cancer_patient_44_dye_swap


title: Gastric_cancer_patient_27_dye_swap

value: IA, IB, II, IIIA, IIIB, or IV=IB


title: Gastric_cancer_patient_412_dye_swap


title: Gastric_cancer_patient_23_dye_swap

value: moderately differentiated or poorly differentiated=moderately differentiated


title: Gastric_cancer_patient_34_dye_swap


title: Gastric_cancer_patient_18_dye_swap


title: Gastric_cancer_patient_40_dye_swap


title: Gastric_cancer_patient_21_dye_swap


title: Gastric_cancer_patient_14_dye_swap

value: IA, IB, II, IIIA, IIIB, or IV=IA

value: early gastric cancer or advanced gastric cancer=early gastric cancer


title: Gastric_cancer_patient_36_dye_swap

value: female, male:male

value: early gastric cancer or advanced gastric cancer=advanced gastric cancer


title: Gastric_cancer_patient_15_dye_swap

value: moderately differentiated or poorly differentiated=poorly differentiated

value: intestinal type, diffuse type, mixed type, or not determined=diffuse type


title: Gastric_cancer_patient_25_dye_swap


title: Gastric_cancer_patient_31_dye_swap

value: female, male:female


title: Gastric_cancer_patient_26_dye_swap


title: Gastric_cancer_patient_5_dye_swap

value: intestinal type, diffuse type, mixed type, or not determined=intestinal type


title: Gastric_cancer_patient_313_dye_swap


title: Gastric_cancer_patient_22_dye_swap

tag: age:


title: Gastric_cancer_patient_311_dye_swap


title: Gastric_cancer_patient_3_dye_swap


title: Gastric_cancer_patient_9_dye_swap


title: Gastric_cancer_patient_12_dye_swap


title: Gastric_cancer_patient_8_dye_swap


title: Gastric_cancer_patient_69

value: IA, IB, II, IIIA, IIIB, or IV=IV


title: Gastric_cancer_patient_1_dye_swap


title: Gastric_cancer_patient_2_dye_swap


title: Gastric_cancer_patient_66


title: Gastric_cancer_patient_67


title: Gastric_cancer_patient_70


title: Gastric_cancer_patient_68

value: intestinal type, diffuse type, mixed type, or not determined=mixed type


title: Gastric_cancer_patient_60

value: IA, IB, II, IIIA, IIIB, or IV=IIIB


title: Gastric_cancer_patient_61


title: Gastric_cancer_patient_65


title: Gastric_cancer_patient_62


title: Gastric_cancer_patient_64


title: Gastric_cancer_patient_63

value: female, male:NA


title: Gastric_cancer_patient_59


title: Gastric_cancer_patient_53


title: Gastric_cancer_patient_54


title: Gastric_cancer_patient_55


title: Gastric_cancer_patient_58


title: Gastric_cancer_patient_56


title: Gastric_cancer_patient_57


title: Gastric_cancer_patient_32


title: Gastric_cancer_patient_34


title: Gastric_cancer_patient_40


title: Gastric_cancer_patient_314


title: Gastric_cancer_patient_313


title: Gastric_cancer_patient_52


title: Gastric_cancer_patient_51


title: Gastric_cancer_patient_412


title: Gastric_cancer_patient_27


title: Gastric_cancer_patient_44


title: Gastric_cancer_patient_36


title: Gastric_cancer_patient_33


title: Gastric_cancer_patient_26


title: Gastric_cancer_patient_45


title: Gastric_cancer_patient_46


title: Gastric_cancer_patient_311


title: Gastric_cancer_patient_28

value: intestinal type, diffuse type, mixed type, or not determined=not determined


title: Gastric_cancer_patient_31


title: Gastric_cancer_patient_25


title: Gastric_cancer_patient_12


title: Gastric_cancer_patient_23


title: Gastric_cancer_patient_22


title: Gastric_cancer_patient_1


title: Gastric_cancer_patient_21


title: Maf1-ChID-rapa30

status: Public on Apr 30 2006

city: Gif Sur Yvette

first: Michel

last: Werner

department: Biologie Joliot-Curie

institute: Commissariat à L'Energie Atomique-Saclay

description: Competitive Hybridization between DNA before and after Maf1 immunodepletion of the crosslinked chromatin. Mean of 3 replicates after normalization to GeneList1

data_processing: Depletion ratio between DNA before Maf1 IP and DNA after Maf1 IP

source_name: Maf1-myc immunodepleted Chromatin

label_protocol: indirect aa-dUTP

treatment_protocol: 30 min rapamycin 0.2 ng/ul

tag: strain  MW671-Cmyc

source_name: Maf1-myc input Chromatin


title: Maf1-ChID-rapa120

treatment_protocol: 120 min rapamycin 0.2 ng/ul


title: Gastric_cancer_patient_18


title: Gastric_cancer_patient_9


title: Gastric_cancer_patient_14


title: Gastric_cancer_patient_3


title: Maf1-ChID-rapa0

treatment_protocol: No treatment


title: Gastric_cancer_patient_8


title: Gastric_cancer_patient_2


title: Gastric_cancer_patient_5


title: Smad4 positive sample in medium containing 10ng/ml TGF-ß for 12 hours.

status: Public on Apr 25 2006

city: Berlin

first: xiaoqing

last: wu

state: Berlin

address: Robert-Roessle-strasse 10

department: Molecular Cell biolgoy

country: Germany

institute: Institute for biology

description:
mRNA extracted from the stable clone K3 cells derived from MDA-MB-468 breast adenocarcinoma cell line. The MDA-MB-468 cells were transfected with a plasmid construct encoding the wild-type Smad4 gene (pBK-CMV-Smad4) and selected with 400µg/ml geneticin (G418).
Keywords = Smad4
Keywords = tumor suppressor gene
Keywords = TGF-ß
Keywords = serpins
Keywords = invasion
Keywords = microarray analysis

source_name: Smad4 positive, with TGF-ß treatment for 12 hours.


title: Smad4 positive sample in medium containing 10ng/ml TGF-ß for 20 minutes.

source_name: Smad4 positive, with TGF-ß treatment for 20 minutes


title: Smad4 positive sample only in medium

source_name: Smad4 positive, without TGF-ß treatment


title: Bdp1-rapa30

description: The IP-DNA of two different IP were labeled and hybridized in the same slide. The quality of the IP was verified independently by Q-PCR.

data_processing: Each Channel Intensiy was normalized a priori to GeneList1 (Intergenic element known to be not bound by the Pol III transcription machinery according to Harismendy et al., 2003) giving an enrichment ratio for each channel. The mean of this enrichment of several replicates (at least 2) experiments is reported

source_name: Bdp1-ChIP inWT context 30min rapamycin

label_protocol: indirect via aa-dUTP

tag: strain MW4035

source_name: Bdp1-ChIP inDmaf1 context 30min rapamycin

treatment_protocol: 30 min rapammycin 0.2 ng/ul

tag: strain yDO4


title: BRF1-rapa0

source_name: BRF1-ChIP inWT context 0min rapamycin

tag: strain MW4034

source_name: BRF1-ChIP inDmaf1 context 0min rapamycin

tag: strain yDO5


title: Smad4 positive sample in medium containing 10ng/ml TGF-ß for 4 hours.

source_name: Smad4 positive, with TGF-ß treatment for 4 hours.


title: BRF1-rapa30

source_name: BRF1-ChIP inWT context 30min rapamycin

source_name: BRF1-ChIP inDmaf1 context 30min rapamycin


title: Smad4 positive sample in medium containing 10ng/ml TGF-ß for 1 hour.

source_name: Smad4 positive, with TGF-ß treatment for 1 hour


title: control sample in medium containing 10ng/ml TGF-ß for 12 hours.

description:
mRNA extracted from the stable clone A26 cells derived from MDA-MB-468 breast adenocarcinoma cell line. The MDA-MB-468 cells were transfected with a plasmid construct encoding a ß-galactosidase gene (pBK-CMV-ßgal) and selected with 400µg/ml geneticin (G418).
Keywords = Smad4
Keywords = tumor suppressor gene
Keywords = TGF-ß
Keywords = serpins
Keywords = invasion
Keywords = microarray analysis

source_name: Smad4 negative, with TGF-ß treatment for 12 hours


title: Tau95-rapa30

source_name: Tau95-ChIP inWT context 30min rapamycin

tag: strain yOH1

source_name: Tau95-ChIP inDmaf1 context 30min rapamycin

tag: strain yDO3


title: control sample in medium containing 10ng/ml TGF-ß for 1 hour.

source_name: Smad4 negative, with TGF-ß treatment for 1 hour


title: control sample in medium containing 10ng/ml TGF-ß for 4 hours

source_name: Smad4 negative, with TGF-ß treatment for 4 hours


title: control sample in medium containing 10ng/ml TGF-ß f0r 20 minutes.

source_name: Smad4 negative, with TGF-ß treatment for 20 minutes


title: C160-rapa0

source_name: C160-ChIP inWT context 0min rapamycin

tag: strain MW671

source_name: C160-ChIP inDmaf1 context 0min rapamycin

tag: strain yDO1


title: Tau95-rapa0

source_name: Tau95-ChIP inWT context 0min rapamycin

source_name: Tau95-ChIP inDmaf1 context 0min rapamycin


title: C160-rapa30

source_name: C160-ChIP inWT context 30min rapamycin

source_name: C160-ChIP inDmaf1 context 30min rapamycin


title: Bdp1-rapa0

source_name: Bdp1-ChIP inWT context 0min rapamycin

source_name: Bdp1-ChIP inDmaf1 context 0min rapamycin


title: juv 011905 cr6 3-2

status: Public on Mar 31 2006

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

description: Whole juvenile mummichogs (Fundulus heteroclitus)

hyb_protocol: Probes are heated to 100C for 10 minutes, and then chilled on ice. Arrays are prehybridized with 5 mL of ExpressHyb Hybridization Solution (Clontech, Palo Alto, CA) and 1 mg sheared salmon sperm (denatured at 95C for 10 minutes then chilled on ice) at 68C for greater than 4 hours. Arrays were hybridized overnight at 68C. The blots were washed four times for 15 minutes at 64C using 2x SSC/0.5% SDS, then four times for 15 minutes at 64C using 0.5x SSC/0.5% SDS.

scan_protocol: Blots are wrapped in plastic wrap and exposed to a phosphoscreen at room temperature, visualized on BioRad FX Imager (Hercules, CA), and quantified with Invitrogen ResGen Pathways software (Carlsbad, CA).

data_processing: Data normalized to immediate background using ResGen Pathways software.

label: radioactive phosphorus 33 - [33P] dATP

organism: Fundulus heteroclitus

source_name: whole juvenile Fundulus heteroclitus

label_protocol: 2 ug RNA is diluted into 10 uL of DEPC water. 10 uL of 0.5 uM poly T primers are added and incubated at 65C for 5 minutes and cooled to room temperature for two minutes. Radiolabelled cDNA is made by adding 30 uL of a mix containing 10 uL 5x reverse transcription buffer, 6 uL 10 mM dNTPs (without dATP), 10 uCi [33P]dATP, and 200 units MMLV-RT and incubating for 2 hours at 37C. Probes are cleaned of short nucleotide sequences through ProbeQuant G-50 Micro Columns (Amersham Biosciences, Piscataway, NJ) and counted on scintillation counter.

growth_protocol: During breeding times, eggs were collected.  Eggs were then removed and kept moist until hatching.

extract_protocol: RNA isolation performed into TriReagent according to manufacture’s protocols, followed by DNAse treatment.

treatment_protocol: Juvenile fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish are fed freshly hatched Artemia daily. Hatchlings less than 48 hours old were randomly divided and exposed to potassium chromate at 3 mg/L Cr(VI) for 30 days with static renewal water exchanges every other day. 24 fish were divided into 4 tanks of 500mL volume (6 fish/tank) per treatment group. At the conclusion of the exposure, half the fish from each tank were used for whole body RNA isolation. The other half were used for determining chromium body burden.

tag: Laboratory reared whole juvenile mummichog (30-32 days old)


title: juv 011905 cr6 15-3

treatment_protocol: Juvenile fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish are fed freshly hatched Artemia daily. Hatchlings less than 48 hours old were randomly divided and exposed to potassium chromate at 1.5 mg/L Cr(VI) for 30 days with static renewal water exchanges every other day. 24 fish were divided into 4 tanks of 500mL volume (6 fish/tank) per treatment group. At the conclusion of the exposure, half the fish from each tank were used for whole body RNA isolation. The other half were used for determining chromium body burden.


title: juv 011905 cr6 3-3


title: reversible and irreversible Thy-1 nephritis at day 42

status: Public on Apr 01 2006

city: Tokyo

first: Toshiaki

last: Monkawa

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Internal Medicine

country: Japan

institute: Keio University School of Medicine

description: Total RNA from whole kidney was isolated with TRIzol Reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s protocol. Poly (A)+ RNA was purified with an Oligotex DT-30 super mRNA purification kit (Takara Shuzo, Shiga, Japan). cDNA probes were synthesized from 2.0 microgram of the purified poly (A)+ RNA by a two-step procedure using the CyScribe Post-Labeling Kit (Amersham Biosciences Corp., Piscataway, NJ, USA). In the first step, amino allyl-dUTP (AA-dUTP) was incorporated into first-strand cDNA during reverse transcription. In the second step the amino allyl modified cDNA was chemically labeled with CyDyeTM NHS-esters (either Cy3 or Cy5 signal). The Cy3- or Cy5-labeled cDNA probes were then combined and diluted in 30 microlitter of ArrayHyb Low Temp Hybridization Buffer (Sigma, St. Louis, MO, USA).

data_processing: Data obtained from GenePix Pro 3.0 was imported into Microsoft Excel for further statistical analysis. The ratio of the Cy3 to Cy5 signal intensity (Cy3/Cy5) was calculated for each spot and log2-transformed, and each log2(Cy3/Cy5) value was normalized by subtracting the average of the log2(Cy3/Cy5) values for the GAPDH genes.

label: Cy3 or Cy5

source_name: irreversible Thy-1 nephritis at day 42

tag: RNA from whole kidney of irreversible Thy-1 nephritis at day 42

source_name: reversible Thy-1 nephritis at day 42

tag: RNA from whole kidney of reversible Thy-1 nephritis at day 42


title: juv 011905 cr6 15-4


title: reversible and irreversible Thy-1 nephritis at day 7

description: Total RNA from whole kidney was isolated with TRIzol Reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s protocol. Poly (A)+ RNA was purified with an Oligotex DT-30 super mRNA purification kit (Takara Shuzo, Shiga, Japan). cDNA probes were synthesized from 2.0 ?g of the purified poly (A)+ RNA by a two-step procedure using the CyScribe Post-Labeling Kit (Amersham Biosciences Corp., Piscataway, NJ, USA). In the first step, amino allyl-dUTP (AA-dUTP) was incorporated into first-strand cDNA during reverse transcription. In the second step the amino allyl modified cDNA was chemically labeled with CyDyeTM NHS-esters (either Cy3 or Cy5 signal). The Cy3- or Cy5-labeled cDNA probes were then combined and diluted in 30 ?l of ArrayHyb?? Low Temp Hybridization Buffer (Sigma, St. Louis, MO, USA).

source_name: irreversible Thy-1 nephritis at day 7

tag: RNA from whole kidney of irreversible Thy-1 nephritis at day 7

source_name: reversible Thy-1 nephritis at day 7

tag: RNA from whole kidney of reversible Thy-1 nephritis at day 7


title: reversible and irreversible Thy-1 nephritis at day 4

description:
Total RNA from whole kidney was isolated with TRIzol Reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s protocol. Poly (A)+ RNA was purified with an Oligotex DT-30 super mRNA purification kit (Takara Shuzo, Shiga, Japan). cDNA probes were synthesized from 2.0 ?g of the purified poly (A)+ RNA by a two-step procedure using the CyScribe Post-Labeling Kit (Amersham Biosciences Corp., Piscataway, NJ, USA). In the first step, amino allyl-dUTP (AA-dUTP) was incorporated into first-strand cDNA during reverse transcription. In the second step the amino allyl modified cDNA was chemically labeled with CyDyeTM NHS-esters (either Cy3 or Cy5 signal). The Cy3- or Cy5-labeled cDNA probes were then combined and diluted in 30 ?l of ArrayHyb?? Low Temp Hybridization Buffer (Sigma, St. Louis, MO, USA).
Oligonucleotide microarrays with approximately 4854 rat genes (DNA chip consortium, SIGMA Genosys Japan) were used to analyze mRNA expression at the designated times. Microarray slides were incubated at 42?C in prehybridization buffer (5x SSC, 0.1%SDS, 1%BSA-0.2?m filtered) for 1 hour. Labeled cDNA probes were hybridized with the cDNA microarray slides by overnight incubation at 42?C. The slides were washed with wash buffer 1 (1x SSC, 0.03% SDS) at 42?C for 4 min, then with wash buffer 2 (0.2x SSC) at room temperature for 4 min, and finally with wash buffer 3 (0.05x SSC) at room temperature for 4 min. Hybridization images were scanned with a GenePix 4000A scanner (Axon Instrument Inc., Foster City, CA, USA), and the fluorescence intensity of the Cy3 and Cy5 was quantitated with GenePix Pro 3.0 software (Axon Instrument Inc). To avoid the effect of putative artificial signals caused by non-specific dye-cDNA interactions, each hybridization was performed twice, where the second experiment was performed with a reversed Cy-dye assignment (the so called “dye flip”). At least four hybridizations were performed at each time point.

source_name: irreversible Thy-1 nephritis at day 4

tag: RNA from whole kidney of irreversible Thy-1 nephritis at day 4

source_name: reversible Thy-1 nephritis at day 4

tag: RNA from whole kidney of reversible Thy-1 nephritis at day 4


title: control sample only in medium

source_name: Smad4 negative, without TGF-ß treatment


title: Gastric_cancer_patient_15

source_name: Gastric tissue tumor region

tag: tumor stage

tag: Sex

tag: tumor depth

tag: tumor histology

tag: Lauren's t ype

source_name: Gastric tissue normal region

tag: normal


title: WT vs pilR gdn17

status: Public on Apr 18 2006

city: Melbourne

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

country: Australia

institute: Monash University

description: RNA was extracted using Trizol and 5ug was converted to cDNA with amino allyl dUTP, which was then coupled to cy dyes.

hyb_protocol: Slides were prepared for hybridisation by incubation at 42C for 45 min in 30 ul of prehybridisation solution (25% (v/v) formamide, 5 x SSC, 0.1% (v/v) SDS, 10 mg per ml BSA, 1 mg per ml salmon sperm DNA) under a coverslip in a humidified chamber.  The coverslip was removed in ddH2O before drying by centrifugation for 10 min at 1,000 x g using a Clements GS200 centrifuge.  Hybridisation solution (25% (v/v) formamide, 5 x SSC (v/v), 0.1% SDS (v/v), 1 mg per ml salmon sperm DNA) was added to 15 ul of probe to make a final volume of 30.75 ul.  The probe solution was heated for 5 min at 95C, cooled slightly, and applied to the array slide.  A coverslip was lowered on top of the slide before placing the slide in a humidified CMT-hybridisation chamber (Corning) and incubated at 42C overnight.  The coverslip was removed using 2 x SSC-0.1% (v/v) SDS at 42C before washing the slide in a fresh solution of 2 x SSC-0.1% SDS at 42C for 5 min.  The slide was then washed in 0.1 x SSC-0.1% SDS for 10 min at room temperature before four-30 s rinses in 0.1 x SSC.  The slide was rinsed once in ddH2O, dried by centrifugation and then scanned.

scan_protocol: Slides were scanned using a GMS 418 microarray scanner (Genetic Microsystems) and the cy3 and cy5 channels were combined and quantified using ImaGene version 5.1 (Biodiscovery).

data_processing: Expression and p-values are attached to series file

organism: Dichelobacter nodosus

source_name: pilR mutant

label_protocol: Labelled cDNA was synthesised using amino allyl-dUTP (aa-dUTP) at a 3:2 ratio with dTTP.  Random hexamers (6 ug) were annealed to 5 ug of RNA in RT reactions that contained 20U of RNasin (Promega), 10 mM DTT, 400U Superscript II (Invitrogen), 500 uM dATP, dCTP, dGTP, 200 uM dTTP and 300 uM aa-dUTP.  Reactions were allowed to incubate overnight at 42C.  RNA was hydrolysed at 65C for 15 min in the presence of 200 mM NaOH and 100 mM EDTA before neutralisation in 300 mM Tris-HCl pH 7.4.  Reactions were purified with Microcon columns (Millipore) and dried using a Speedvac SVC (Savant).  The amino-allyl labelled cDNA was coupled to monoreactive cy3 or cy5 dyes (Amersham Biosciences) for 2 h at room temperature, in the dark in 50 mM sodium bicarbonate buffer pH 9 and 50% DMSO, before purification using Microcon columns and drying under vacuum.  Typically, 15 ug of labelled cDNA (cy3 and cy5 cDNA probes) was hybridised to the slides.

growth_protocol: 24h EYE broth culture

extract_protocol: Trizol extraction with multiple DNaseI treatments

tag: D. nodosus pilR mutant JIR3772

source_name: Wild-type D. nodosus

tag: Wild-type D. nodosus VCS1703A


title: WT vs rpoN gdn7

description:
RNA was extracted using Trizol and 5ug was converted to cDNA with amino allyl dUTP, which was then coupled to cy dyes.

Slide data was obtained using IMAGENE and normalised and analysed using BASE

data_processing: Actual expression ratios are in series table analysed using BASE

source_name: rpoN mutant

label_protocol: Labelled cDNA was synthesised using amino allyl-dUTP (aa-dUTP) at a 3:2 ratio with dTTP.  Random hexamers (6 ug) were annealed to 5 ug of RNA in RT reactions that contained 20U of RNasin (Promega), 10 mM DTT, 400U Superscript II (Invitrogen), 500 uM dATP, dCTP, dGTP, 200 uM dTTP and 300 uM aa-dUTP.  Reactions were allowed to incubate overnight at 42C.  RNA was hydrolysed at 65C for 15 min in the presence of 200 mM NaOH and 100 mM EDTA before neutralisation in 300 mM Tris-HCl pH 7.4.  Reactions were purified with Microcon columns (Millipore) and dried using a Speedvac SVC (Savant).  The amino-allyl labelled cDNA was coupled to monoreactive cy3 or cy5 dyes (Amersham Biosciences) for 2 h at room temperature, in the dark in 50 mM sodium bicarbonate buffer pH 9 and 50% DMSO, before purification using Microcon columns and drying under vacuum.  Typically, 15 ug of labelled cDNA (cy3 and cy5 cDNA probes) was hybridised to the slides.

growth_protocol: 24h EYE broth cultures

extract_protocol: Trizol with multiple DNaseI treatments

tag: D. nodosus rpoN mutant JIR3887

tag: Wild type VCS1703A


title: juv 011905 cr6 0-4

treatment_protocol: Juvenile fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish are fed freshly hatched Artemia daily. Hatchlings less than 48 hours old were randomly divided and exposed to potassium chromate at 0 mg/L Cr(VI) for 30 days with static renewal water exchanges every other day. 24 fish were divided into 4 tanks of 500mL volume (6 fish/tank) per treatment group. At the conclusion of the exposure, half the fish from each tank were used for whole body RNA isolation. The other half were used for determining chromium body burden.

tag: Laboratory reared whole juvenile mummichog (30-32 days old)


title: WT vs pilR gdn18

source_name: Wild-type


title: juv 011805 cr6 0-3


title: WT vs pilR gdn16


title: reversible and irreversible Thy-1 nephritis at day 14

source_name: irreversible Thy-1 nephritis at day 14

tag: RNA from whole kidney of irreversible Thy-1 nephritis at day 14

source_name: reversible Thy-1 nephritis at day 14

tag: RNA from whole kidney of reversible Thy-1 nephritis at day 14


title: juv 011905 cr6 0-2


title: reversible and irreversible Thy-1 nephritis at day 56

source_name: irreversible Thy-1 nephritis at day 56

tag: RNA from whole kidney of irreversible Thy-1 nephritis at day 56

source_name: reversible Thy-1 nephritis at day 56

tag: RNA from whole kidney of reversible Thy-1 nephritis at day 56


title: juv 011905 cr6 3-4

source_name: whole juvenile Fundulus heteroclitus


title: juv 011905 cr6 3-1


title: adult 091404 Cr6 15-12

description: liver from adult male Fundulus heteroclitus

source_name: Fundulus heteroclitus adult male liver

extract_protocol: RNA isolation performed by TriReagent according to manufacture’s protocols, followed by DNAse treatment.

treatment_protocol: Laboratory acclimated fish were exposed in individual tanks to potassium chromate at 1.5 mg/L Cr(VI) for 7 days with water exchanges every other day. Fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish were fed daily Tetramin flake fish food. At the conclusion of the exposure, livers were excised and frozen at -80C.

tag: Adult (>4cm in length) male liver excised immediately upon euthanasia


title: WT vs rpoN gdn15

hyb_protocol: Slides were prepared for hybridisation by incubation at 42C for 45 min in 30 µl of prehybridisation solution (25% (v/v) formamide, 5 x SSC, 0.1% (v/v) SDS, 10 mg per ml BSA, 1 mg per ml salmon sperm DNA) under a coverslip in a humidified chamber.  The coverslip was removed in ddH2O before drying by centrifugation for 10 min at 1,000 x g using a Clements GS200 centrifuge.  Hybridisation solution (25% (v/v) formamide, 5 x SSC (v/v), 0.1% SDS (v/v), 1 mg per ml salmon sperm DNA) was added to 15 µl of probe to make a final volume of 30.75 µl.  The probe solution was heated for 5 min at 95C, cooled slightly, and applied to the array slide.  A coverslip was lowered on top of the slide before placing the slide in a humidified CMT-hybridisation chamber (Corning) and incubated at 42C overnight.  The coverslip was removed using 2 x SSC-0.1% (v/v) SDS at 42C before washing the slide in a fresh solution of 2 x SSC-0.1% SDS at 42C for 5 min.  The slide was then washed in 0.1 x SSC-0.1% SDS for 10 min at room temperature before four-30 s rinses in 0.1 x SSC.  The slide was rinsed once in ddH2O, dried by centrifugation and then scanned.


title: WT vs rpoN gdn13

hyb_protocol: Slides were prepared for hybridisation by incubation at 42C for 45 min in 30 µl of prehybridisation solution (25% (v/v) formamide, 5 x SSC, 0.1% (v/v) SDS, 10 mg per ml BSA, 1 mg per ml salmon sperm DNA) under a coverslip in a humidified chamber.  The coverslip was removed in ddH2O before drying by centrifugation for 10 min at 1,000 x g using a Clements GS200 centrifuge.  Hybridisation solution (25% (v/v) formamide, 5 x SSC (v/v), 0.1% SDS (v/v), 1 mg per ml salmon sperm DNA) was added to 15 µl of probe to make a final volume of 30.75 µl.  The probe solution was heated for 5 min at 95C, cooled slightly, and applied to the array slide.  A coverslip was lowered on top of the slide before placing the slide in a humidified CMT-hybridisation chamber (Corning) and incubated at 42C overnight.  The coverslip was removed using 2 x SSC-0.1% (v/v) SDS at 42C before washing the slide in a fresh solution of 2 x SSC-0.1% SDS at 42C for 5 min.  The slide was then washed in 0.1 x SSC-0.1% SDS for 10 min at room temperature before four-30 s rinses in 0.1 x SSC.  The slide was rinsed once in ddH2O, dried by centrifugation and then scanned.


title: adult 072704 cr6 3-2

treatment_protocol: Laboratory acclimated fish were exposed in individual tanks to potassium chromate at 3.0 mg/L Cr(VI) for 7 days with water exchanges every other day. Fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish were fed daily Tetramin flake fish food. At the conclusion of the exposure, livers were excised and frozen at -80C.


title: WT vs rpoN gdn8

hyb_protocol: Slides were prepared for hybridisation by incubation at 42C for 45 min in 30 µl of prehybridisation solution (25% (v/v) formamide, 5 x SSC, 0.1% (v/v) SDS, 10 mg per ml BSA, 1 mg per ml salmon sperm DNA) under a coverslip in a humidified chamber.  The coverslip was removed in ddH2O before drying by centrifugation for 10 min at 1,000 x g using a Clements GS200 centrifuge.  Hybridisation solution (25% (v/v) formamide, 5 x SSC (v/v), 0.1% SDS (v/v), 1 mg per ml salmon sperm DNA) was added to 15 µl of probe to make a final volume of 30.75 µl.  The probe solution was heated for 5 min at 95C, cooled slightly, and applied to the array slide.  A coverslip was lowered on top of the slide before placing the slide in a humidified CMT-hybridisation chamber (Corning) and incubated at 42C overnight.  The coverslip was removed using 2 x SSC-0.1% (v/v) SDS at 42C before washing the slide in a fresh solution of 2 x SSC-0.1% SDS at 42C for 5 min.  The slide was then washed in 0.1 x SSC-0.1% SDS for 10 min at room temperature before four-30 s rinses in 0.1 x SSC.  The slide was rinsed once in ddH2O, dried by centrifugation and then scanned.

tag: WT D. nodosus VCS1703A


title: juv 011905 cr6 15-2


title: juv 011905 cr6 15-1


title: adult 091404 Cr6 3-11


title: juv 011905 cr6 0-1


title: adult 091404 Cr6 3-9


title: adult 081304 cr6 15-2


title: adult 091504 Cr6 0-8

treatment_protocol: Laboratory acclimated fish were exposed in individual tanks to potassium chromate at 0 mg/L Cr(VI) for 7 days with water exchanges every other day. Fish maintained at a 14:10 light:dark cycle at 25C in salinity of 18 parts per thousand. Fish were fed daily Tetramin flake fish food. At the conclusion of the exposure, livers were excised and frozen at -80C.


title: adult 081304 cr6 15-4


title: adult 081304 cr6 3-5


title: adult 091404 Cr6 3-8


title: adult 091404 Cr6 15-5


title: adult 081304 cr6 15-3


title: adult 091504 Cr6 15-6


title: adult 081304 cr6 0-9


title: adult 072704 cr6 0-2


title: adult 091404 Cr6 0-7


title: adult 091504 Cr6 0-5


title: adult 081304 cr6 0-12


title: Sa_24h_2

status: Public on Mar 22 2006

city: Tsukuba

first: Shoshi

last: Kikuchi

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

institute: National Institute of Agrobiological Sciences

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the salt stress treatment, seedlings by adding 150 mM sodium chloride to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.
Keywords = Rice
Keywords = Salt stress
Lot batch = US22502511_16011538011045_S01_A01

organism: Oryza sativa

source_name: Sa_24h treated sample labeled by green (Cy3)

source_name: Untreated sample labeled by red (Cy5)


title: Cold_24h_2

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the cold stress treatment, seedlings with planter boxes were incubation at 10 °C for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.
Keywords = Rice
Keywords = Cold stress
Lot batch = US22502511_16011538011053_S01_A01

source_name: Cold_24h treated sample labeled by green (Cy3)


title: Os_24h_1

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the osmotic stress treatment, seedlings by adding 260 mM mannitol to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Osmotic stress
Lot batch = US22502511_16011538011042_S01_A01

source_name: Untreated sample labeled by green (Cy3)

source_name: Os_24h treated sample labeled by red (Cy5)


title: Os_24h_2

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the osmotic stress treatment, seedlings by adding 260 mM mannitol to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.
Keywords = Rice
Keywords = Osmotic stress
Lot batch = US22502511_16011538011043_S01_A01

source_name: Os_24h treated sample labeled by green (Cy3)


title: Cold_24h_1

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the cold stress treatment, seedlings with planter boxes were incubation at 10 °C for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Cold stress
Lot batch = US22502511_16011538011054_S01_A01

source_name: Cold_24h treated sample labeled by red (Cy5)


title: FS_24h_2

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the flooded standing (FS) treatment, seedlings with planter boxes were submerged vertically. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Flooded standing stress
Lot batch = US22502511_16011538011503_S01_A01

source_name: FS_24h treated sample labeled by green (Cy3)


title: GM1

city: Riverside

first: Stephen

middle: R.

last: Spindler

state: CA

department: Biochemistry

institute: University of California, Riverside

description:
Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.  Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), GLIP plus MET (GM), rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.
Measurement of specific mRNA levels.  Liver total RNA was isolated as described from livers of pathology-free mice in each group (n=4 per group) (13). mRNA levels were measured using Affymetrix mouse U74Av2 arrays according to standard Affymetrix protocols (Affymetrix).
Probe set expression measurement and normalization.  After hybridization and scanning, raw image files were converted to probe set data (*.CEL files) using Microarray Suite (MAS 5.0). Probe set data from all 32 arrays were simultaneously analyzed with the Robust multichip Average (RMA) method to generate normalized expression measures for each probe set (Fig. 2; Ref. 24)  The data were further filtered to exclude probe data sets that were “Absent” across all 32 arrays according to the MAS 5.0 detection algorithm (1,47).
Keywords = CR mimetics
Keywords = microarray profiling
Keywords = drug discovery
Keywords = gene-expression biomarkers

source_name: liver


title: CR8-3

description:
Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.  Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), MET plus GLIP, rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.
Measurement of specific mRNA levels.  Liver total RNA was isolated as described from livers of pathology-free mice in each group (n=4 per group) (13). mRNA levels were measured using Affymetrix mouse U74Av2 arrays according to standard Affymetrix protocols (Affymetrix).
Probe set expression measurement and normalization.  After hybridization and scanning, raw image files were converted to probe set data (*.CEL files) using Microarray Suite (MAS 5.0). Probe set data from all 32 arrays were simultaneously analyzed with the Robust multichip Average (RMA) method to generate normalized expression measures for each probe set (Fig. 2; Ref. 24)  The data were further filtered to exclude probe data sets that were “Absent” across all 32 arrays according to the MAS 5.0 detection algorithm (1,47).
Keywords = CR mimetics
Keywords = microarray profiling
Keywords = drug discovery
Keywords = gene-expression biomarkers


title: FD_24h_1

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours (stress treated sample). In the flooded lying down (FD) treatment, seedlings without planter boxes were submerged in the horizontal direction. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Flooded lying down stress
Lot batch = US22502511_16011538011495_S01_A01

source_name: FD_24h treated sample labeled by red (Cy5)


title: FS_24h_1

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the flooded standing (FS) treatment, seedlings with planter boxes were submerged vertically. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Flooded standing stress
Lot batch = US22502511_16011538011502_S01_A01

source_name: FS_24h treated sample labeled by red (Cy5)


title: Dr_24h_2

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the drought stress treatment, seedlings by adding 25% polyethylene glycol 6000 to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.
Keywords = Rice
Keywords = Drought stress
Lot batch = US22502511_16011538011565_S01_A01

source_name: Dr_24h treated sample labeled by green (Cy3)


title: FD_24h_2

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours (stress treated sample). In the flooded lying down (FD) treatment, seedlings without planter boxes were submerged in the horizontal direction. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.
Keywords = Rice
Keywords = Flooded lying down stress
Lot batch = US22502511_16011538011496_S01_A01

source_name: FD_24h treated sample labeled by green (Cy3)


title: Sa_24h_1

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the salt stress treatment, seedlings by adding 150 mM sodium chloride to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Salt stress
Lot batch = US22502511_16011538011044_S01_A01

source_name: Sa_24h treated sample labeled by red (Cy5)


title: CON 2

description:
Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.
Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), MET plus GLIP, rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.
Measurement of specific mRNA levels.  Liver total RNA was isolated as described from livers of pathology-free mice in each group (n=4 per group) (13). mRNA levels were measured using Affymetrix mouse U74Av2 arrays according to standard Affymetrix protocols (Affymetrix).
Probe set expression measurement and normalization.  After hybridization and scanning, raw image files were converted to probe set data (*.CEL files) using Microarray Suite (MAS 5.0). Probe set data from all 32 arrays were simultaneously analyzed with the Robust multichip Average (RMA) method to generate normalized expression measures for each probe set (Fig. 2; Ref. 24)  The data were further filtered to exclude probe data sets that were “Absent” across all 32 arrays according to the MAS 5.0 detection algorithm (1,47).
Keywords = CR mimetics
Keywords = microarray profiling
Keywords = drug discovery
Keywords = gene-expression biomarkers


title: SRYU_RDE2_14028s _M9_OD 0.30_Anaerob__pH7.0_Glc_Temp.37_5D742_2

status: Public on Mar 04 2006

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description:
Salmonella typhimurium 14028s Expression at the early exponential phase (OD600»0.3)
User - GYun
Date_of_Scan = 02/14/2005

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: 14028s gDNA


title: SRYU_RDE2_14028s _M9_OD 0.30_Anaerob__pH7.0_Glc_Temp.37_5D742_3


title: Dr_24h_1

description:
The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the drought stress treatment, seedlings by adding 25% polyethylene glycol 6000 to the planter box were grown for 24 h. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Drought stress
Lot batch = US22502511_16011538011564_S01_A01

source_name: Dr_24h treated sample labeled by red (Cy5)


title: GD10:00_heart_FolR1neo/neo

status: Public on Feb 20 2006

city: Houston

first: Huiping

last: Zhu

state: TX

address: 2121 W. Holcombe Blvd

department: Center for Environmental and Genetic Medicine

institute: Institute of Biosciences and Technology, TAMUSHSC

description: The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of FolR1 gene ablation on embryonic heart development

data_processing: R 2.0.0, scaled to 1.0

label: Fluor 647-streptavidin

tag: LmBc_FolR1neo/neo, gestational day

value: GD10:00, tissue:heart


title: GD10:00_heart_FolR1(wt)

tag: LmBc_FolR1 wild type, gestational day


title: GD9:00_heart tube_FolR1neo/neo_c

description: The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of FolR1 gene ablation on embryonic heart development during heart looping stage

source_name: GD11:12_heart tube_FolR1neo/neo

value: GD9:00, tissue:heart


title: GD10:00_heart_FolR1neo/neo_b


title: SRYU_RDE2_14028s _M9 _OD 0.3_Anaerob_pH7.0_Glc_Temp.37_5D741_3


title: GD10:00_heart_FolR1(wt)_b


title: GD10:00_heart_FolR1(wt)_c


title: SRYU_RDE2_14028s _M9_OD 0.30_Anaerob__pH7.0_Glc_Temp.37_5D742_1


title: GD9:00_heart tube_FolR1neo/neo_b


title: SRYU_RDE2_14028s _M9 _OD 0.3_Anaerob_pH7.0_Glc_Temp.37_5D741_1


title: SRYU_RDE2_14028s _M9 _OD 0.3_Anaerob_pH7.0_Glc_Temp.37_5D741_2


title: GD10:00_heart_FolR1neo/neo_c


title: GD11:12_conotruncus_FolR1neo/neo_b

description: The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of FolR1 gene ablation on embryonic

value: GD11:12, tissue:conotruncus


title: n6t0n

status: Public on Feb 15 2006

city: Bethesda

first: Robert

middle: L

last: Danner

state: MD

address: 10 Center Drive

department: Critical Care Medicine Department

institute: Clinical Center

description: Naïve cells (RPMI 1640 for 48 h).  Total RNA was isolated using RNeasy Mini Kit and Qiashredder column.  Targets were produced using standard Affymetrix procedures from 10 micrograms of total RNA.

source_name: U937 cells; Human monoblastoid line devoid of guanylate cyclase


title: GD9:00_heart tube_FolR1(wt)_c

source_name: GD11:12_heart tube_FolR1(wt)


title: GD11:12_conotruncus_FolR1neo/neo_c

description: The median of the expression values for each sample at the specified timepoint was used to generate the effective expression ratios representing the impact of FolR1 gene ablation on embryonic development in mice during the critical phase of aorticopulmonary septation.


title: n2t0n


title: GD9:00_heart tube_FolR1neo/neo

source_name: GD9:00_heart tube_FolR1neo/neo


title: n7t0n


title: GD11:12_conotruncus_FolR1(wt)


title: n4t0n


title: GD11:12_conotruncus_FolR1(wt)_b


title: GD11:12_conotruncus_FolR1neo/neo

treatment_protocol: maternal supplementation with s-folinic acid,  6.25mg/kg/day P.O.


title: GD9:00_heart tube_FolR1(wt)_b


title: GD9:00_heart tube_FolR1(wt)

source_name: GD9:00_heart tube_FolR1(wt)


title: GSG37

status: Public on Feb 01 2006

city: Leiden

first: Rolf

last: Turk

address: Wassenaarseweg 72

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

description: Genepix

hyb_protocol: SSC/SDS 55C

scan_protocol: Agilent

data_processing: VSN

source_name: GSG - 14

label_protocol: Aminoallyl-UTP labeled cRNA

tag: Gamma-SG deficient

tag: Male

tag: 14 wk

tag: Hindlimb muscle

source_name: GSG - 12

tag: 12 wk


title: n1t0n


title: GSG32

description: Genepix

source_name: GSG -4

tag: 4 wk


title: GSG38

description: Genepix

source_name: GSG - 20

tag: 20 wk


title: GSG29

description: Genepix

source_name: GSG - 1

tag: 1 wk


title: GSG39

description: Genepix


title: GSG34

description: Genepix

source_name: GSG - 8

tag: 8 wk

source_name: GSG - 6

tag: 6 wk


title: GSG35

description: Genepix

source_name: GSG - 10

tag: 10 wk


title: n3t0n


title: GSG31

description: Genepix


title: BSG18

description: Genepix

source_name: BSG -20

tag: Beta-SG deficient

source_name: BSG - 14


title: BSG17

description: Genepix

source_name: BSG - 12


title: GSG22

description: Genepix

source_name: GSG - 4


title: GSG28

description: Genepix


title: GSG27

description: Genepix


title: BSG19

description: Genepix

source_name: BSG - 1

source_name: BSG - 20


title: GSG24

description: Genepix


title: GSG21

description: Genepix


title: BSG16

description: Genepix

source_name: BSG - 10


title: GSG33

description: Genepix


title: GSG36

description: Genepix