title: GA plus ABA treatment, biological rep3

city: Madison

first: Kegui

last: Chen

state: WI

address: 502 WALNUT STREET

department: Department of Agronomy

institute: University of Wisconsin

description: Gene expression data from aleurone treated with GA 1 μmol/L plus ABA 50 μmol/L

hyb_protocol: The labeled cRNA was purified, and 20 μg of the cRNA at a final concentration 0.5 µg/µL was fragmented. The fragmented cRNA (15 μg per hybridization) was used to make up the hybridization cocktail and 10 µg equivalents were hybridized to each GeneChip.

scan_protocol: The chips were washed and stained with streptavidin-phycoerythrin in the Affymetrix GeneChip fluidics station model 400. The stained chips were immediately scanned with an Agilent 2500A GeneArray scanner.

data_processing: The Microarray Suite (MAS) 5.0 (Affymetrix, Inc.) was used to assign present call (P<0.065) or absent call (P>0.065) for each probe sets.The trimmed mean target intensity of each array was arbitrarily set to 1000.  GeneChip RMA (GCRMA) provided in GeneSpring (Agilent Technologies, Palo Alto, CA) was chosen to determine the signal intensity for probe sets for further analysis.

organism: Hordeum vulgare

source_name: Department of Agronomy, Washington State University, Pullman, WA, USA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: The half-seeds without embryos were surface-sterilized and then imbibed in 10 mmol/L CaCl2-saturated paper tissues for three days in darkness at 25°C.To select sln1c homozygotes, the half-seeds with embryos were germinated and transferred to soil to identify the slender phenotype. The selected homozygous sln1c half-seeds without the embryo were imbibed in the same conditions as the wild type but with 5 μmol /L ABA. After imbibition for three days, the aleurones were isolated and washed 3-4 times with 10 mmol/L CaCl2.

extract_protocol: Total RNA was isolated according to a LiCl precipitation method.

treatment_protocol: The aleurones from the half-seeds were isolated and incubated in 10 mmol/L CaCl2 (control), or in the 10 mmol/L CaCl2 solution containing 1 μmol/L GA3 (GA treatment) or 50 μmol/L ABA (ABA treatment).  The isolated aleurones were treated in Petri dishes with continuously shaking (60 rpm) in darkness at 25°C, and harvested in 15 hours.

value: aleurone

tag: genome/variation

value: Himalaya

value: matured

tag: treatment group

value: GA 1 μmol/L plus ABA 50 μmol/L


title: GA plus ABA treatment, biological rep2

status: Public on Jan 01 2010

type: RNA

country: USA

label: biotin

molecule: total RNA

tag: tissue

tag: age


title: sln1 mutant, biological rep2

description: Gene expression data from aleurone treated without any hormone

value: Himalaya, sln1 mutant

value: untreated


title: sln1 mutant, biological rep1


title: sln1 mutant, biological rep3


title: 3days_vs_0day

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: 1.Used script to split 8-array imagene file of Cy3 intensity into eight separate Cy3 files.  2.Used script to split 8-array imagene file of Cy5 intensity into eight separate Cy5 files.  3.For each indidivual array, a merge file was produced consisting of merging the Cy3 and Cy5 intensity files created in step 1 and 2. The merged file is provided as supplementary file for each array.  4.Background correction (Mean values). Values below 0 (higher background than foreground) were disregarded 5. LOWESS normalization was performed using the BASE plugin 6. Normalised data was further processed using an R package (limma) to get to sample to sample comparisons with p-values (false discovery rate)

organism: Lactiplantibacillus plantarum

source_name: 0 day in retentostat. Specific growth rate: 0.0250 h-1

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Lactobacillus plantarum WCFS1 was cultivated in a chemically defined medium (Teusink et al. 2006. J. Biol. Chem. 281:40041-40048) containing 25 mM glucose at 30°C. A 2.0-liter fermentor (Applikon Biotechnology, The Netherlands) with 1.5 liter working volume was inoculated with 30 ml of an exponentially growing preculture. The fermentor was operated under anaerobic conditions (nitrogen atmosphere) at a stirring speed of 200 rpm, and pH was regulated at 5.5 with NaOH 5M. At an OD600nm of 0.7, the feed pump was switched on and the fermentor was operated in chemostat mode (dilution rate D=0.025 h-1) until steady-state was achieved (6 volume changes, as judged by constant OD600nm). The culture was then switched to retentostat conditions, while keeping the dilution rate constant, i.e. the spent medium was eliminated through a 0.22 µm polypropylene filter (Applikon Biotechnology, The Netherlands) fully immerged in the culture medium, in order to retain the biomass inside the fermentor. To ensure a constant working volume in the fermentor, a conductivity contact positioned at the surface of the liquid triggered a peristaltic pump, which removed the filtrate at a rate equivalent to the dilution rate.

extract_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer  1.For each sample prepare a tube with Extraction Mixture  2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture  3.Mix and store the sample at -40°C  4.Centrifuge cells at -20°C at 9000 rpm for 10 minutes (Centrifuge RC5B)  5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture  6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand  7.Freeze the tube immediately in liquid nitrogen  8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  12.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  13.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   14.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

tag: strain

tag: time point

value: 0 day in retentostat

tag: specific growth rate

source_name: 3 days in retentostat. Specific growth rate: 0.0074 h-1

value: 3 days in retentostat


title: 17days_vs_3days

source_name: 17 days in retentostat. Specific growth rate: 0.0009 h-1

value: 17 days in retentostat


title: 31days_vs_17days

source_name: 31 days in retentostat. Specific growth rate: 0.0002 h-1

value: 31 days in retentostat


title: 31days_vs_0day


title: reactor B (nitrate) vs reactor 4 (citrate)

description: Each slide contains 8 arrays, these are numbered 1-8 as follows: 1 (1st row left-column), 2 (1st row right-column), 3 (2nd row left-column) 4 (2nd row right-column), 5 (3rd row left-column), 6 (3rd row right-column) 7 (4th row left-column), 8 (4th row right-column)

source_name: L. plantarum Reactor B nitrate

growth_protocol: pH controlled anaerobic Batch cultivation CDM with mannitol

treatment_protocol: heme +K2 +nitrate

tag: agent

value: heme +K2 +nitrate

source_name: L. plantarum Reactor 4 citrate

treatment_protocol: citrate

value: citrate


title: 0day_vs_17days


title: GA treatment, biological rep3

description: Gene expression data from aleurone treated with GA 1 μmol/L

value: GA 1 μmol/L


title: control, biological rep3


title: reactor C (nitrate) vs reactor 3 (citrate)

source_name: L. plantarum Reactor C nitrate

source_name: L. plantarum Reactor 3 citrate


title: reactor D (nitrate) vs reactor 1 (citrate)

source_name: L. plantarum Reactor D nitrate

source_name: L. plantarum Reactor 1 citrate


title: control, biological rep1


title: ABA treatment, biological rep3

description: Gene expression data from aleurone treated with ABA 50 μmol/L

value: ABA 50 μmol/L


title: reactor 3 (citrate) vs reactor D (nitrate)


title: GA treatment, biological rep2


title: ABA treatment, biological rep2


title: reactor 4 (citrate) vs reactor A (nitrate)

source_name: L. plantarum Reactor A nitrate


title: reactor C (nitrate) vs reactor B (nitrate)


title: reactor 1 (citrate) vs reactor C (nitrate)


title: GA plus ABA treatment, biological rep1


title: reactor 4 (citrate) vs reactor D (nitrate)


title: reactor A (nitrate) vs reactor 2 (citrate)

source_name: L. plantarum Reactor 2 citrate


title: control, biological rep2


title: GA treatment, biological rep1


title: reactor 3 (citrate) vs reactor 4 (citrate)


title: reactor 2 (citrate) vs reactor B (nitrate)


title: reactor B (nitrate) vs reactor A (nitrate)


title: reactor A (nitrate) vs reactor 1 (citrate)


title: ABA treatment, biological rep1


title: reactor 1 (citrate) vs reactor 2 (citrate)


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_JunB_RNAi_4

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 performed microarray hybridizations with either RNA from muscles transfected with control, non targeting scramble construct or RNA from muscles transfected with a specifc RNAi vector against JunB.

hyb_protocol: Microarray hybridization was carried on overnight at 42°C by submerging microarrays closed in a sealed chamber (HybChamber, GeneMachines, San Carlos, CA, USA) in a high-precision water bath (W28 Grant, Cambridge, UK). Post-hybridization washing was performed according to the protocol suggested in the One Color Microarray Based Gene Expression kit (Agilent).

scan_protocol: Fluorescence signals were detected by analyzing the microarrays in an Agilent scanner.

data_processing: Data were normalized between experiments with quantile method.

organism: Mus musculus

source_name: Mouse tibialis anterior muscle

label_protocol: 1 μg of total RNA was amplified using the One Color Microarray Based Gene Expression kit (Agilent) manufacturer's protocol.

extract_protocol: Total RNA from muscles was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

value: tibialis anterior muscle

tag: sex

value: male

tag: transfection protocol

value: electroporated with JunB RNAi for 12 days


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_JunB_RNAi_3


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_JunB_RNAi_2


title: reactor 2 (citrate) vs reactor 3 (citrate)


title: reactor D (nitrate) vs reactor C (nitrate)


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_control 2

value: electroporated with control, non targeting scramble construct for 12 days


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_JunB_RNAi_1


title: LSK control 2

city: Bronx

first: Ulrich

last: Steidl

state: NY

address: 1300 Morris Park Ave., Chanin #606

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

description: Total RNA from FACS-sorted LSK cells was amplified by 2 rounds of RT and T7 promoter-based in-vitro transcription and the resultant biotinylated cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Array data were analyzed with the dChip software. After smoothing spline normalization, expression values were calculated applying the perfect-match/mismatch difference model algorithm (dChip).

label: biotin/SAPE

source_name: Bone Marrow LSK cells

label_protocol: Amplification of RNA by 2 rounds of reverse transcription followed by T7 promoter-dependent in-vitro transcription (see Steidl et al., Nat Genet 2006; 38:1269-77). Then standard labeling according to Affymetrix protocols.

extract_protocol: RNeasy Micro

tag: cell type

value: FACS-sorted Lin-, c-kit+, Sca-1+ (LSK) bone marrow cells

tag: mouse type

value: control


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_control 4

value: electroporated with control, non targeting scramble construct 12 days


title: LSK dtg 2

value: CLtTAxBCR-ABL double transgenic (dtg) mice


title: Control animals vs. glucose-fed animals replicate 6

city: POHANG

first: SEUNG-JAE

last: LEE

state: GYEONGBUK

address: SAN 31 HYOJA-DONG, NAM-GU

department: LIFE SCEICNE

country: South Korea

institute: POHANG UNIVERSITY OF SCIENCE AND TECHNOLOGY

description: Biological replicate 6 of 6. Control vs. glucose-fed adult C. elegans

hyb_protocol: Oligoarray control targets and hybridization buffer (3XSSC, 20mM HEPES pH 7.0, 0.2% SDS) were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization for at least 6 hours at 63 centidegree, slides were washed sequentially.

scan_protocol: Scanned on an Axon Gene Pix scanner. Images were quantified using Gene Pix Pro version 4.4 (Molecular Devices)

data_processing: Data were normalized using Acuity version 4.0 (Molecular Devices)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Control animals

label_protocol: 5 µg of poly A RNA was reversed transcribed at 42°C for 2 hours in the presence of 200 U SuperScript II Reverse Transcriptase (Invitrogen), random hexamer primers and each dATP, dTTP, dGTP, dCTP, with aa-dUTP. The cDNA was then cleaned up, labeled with Cy3 or Cy5, and quenched and cleaned up again.

growth_protocol: Cultured on OP50-seeded agar plates at 20 centidegree

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

treatment_protocol: Control OP50 culture

tag: developmental stage

value: adult

tag: gender

value: hermaphrodite

source_name: glucose-fed animals

treatment_protocol: OP50 + 2% glucose culture

tag: development


title: PNRA820211G

city: Saint-Gilles

first: Isabelle

last: Luron

state: Rennes

address: Domaine de la Prise

department: Human Nutrition Division

country: France

institute: National Institute for Agronomical Research (INRA)

description: Hybridization OK

hyb_protocol: Hybridizations were performed in a Discovery XT System hybridization robot using the ChipMap 80 kit (Ventana Medical Systems, Tucson, AZ, USA) at INRA SCRIBE transcriptomic facilities (IFR 140 GFAS, Rennes, France). Prehybridization and hybridization were performed using INRA SCRIBE dedicated protocol. Briefly, prehybridization was performed in 2 ml of ChipSpread buffer containing 4X SSC and 0.2 % SDS (1 h, 42 °C). Before hybridization, target cDNAs labelled with either Cy5 or Cy3 were mixed and hybridized (6h, 42 °C). Microarrays were then washed manually at room temperature in 1X SSC.

scan_protocol: Images of the microarrays were generated with a Genepix 4000B scanner and Genepix Pro analysis software v6.0 (Axon Instruments, Molecular Devices Co., Sunnyvale, CA, USA).

data_processing: Analysed with R software and the package Limma (Smyth 2004). Aberrant spots (flag value < -49) were removed. Median values were background corrected with the “normexp” procedure (Ritchie et al. 2007, offset =35)  then loess normalized (Colantuoni et al. 2002) then Gquantile normalized (Yang and Thorne 2003). A linear model applied to perform the differential analysis considering animals pairing.

organism: Sus scrofa

source_name: high protein, 28 days old

label_protocol: Five micrograms of RNA samples were labelled with Cy5 and hybridized against a common reference (5 microg of a mix of all RNA samples used in the experiment) labelled with Cy3 using the ChipShotTM Direct Labeling and Clean-Up system (Promega) according to the manufacturer instructions for total RNA labeling.

extract_protocol: Total RNA was extracted from individual frozen samples of distal small intestine and colonic segments collected from each pig, as previously described (Chomczynski and Sacchi 1987). RNA was quantified by absorbance at 260 nm (Multiskan Spectrum, Thermo Labsystems) and its integrity was estimated using RNA 6000 nano (LabChip® kit in 2100 Bioanalyser, Agilent, France).

tag: deathweight

tag: birthweight

value: Female

tag: diet

value: high protein

tag: site

value: distal small intestine

value: 28 days

tag: batch

value: IUGR

tag: birth date

tag: pair

source_name: Pool of equal amount of all tissue with prefix=PNRA

tag: number of samples in the pool


title: PNRA830238G

description: Hybridization OK

source_name: normal protein, 28 days old

value: Male

value: normal protein

tag: age


title: LSK control 3


title: PNRA721616G

description: Hybridization OK


title: PNRA830079G

description: Hybridization OK


title: PNRA721840G

description: Hybridization OK

source_name: normal protein, 7 days old

value: 7 days


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_control 1

tag: tissue

value: tibialis anterior muscle

value: male

tag: strain


title: LSK control 1


title: PNRA820170G

description: Hybridization OK

source_name: high protein, 7 days old

tag: sex


title: LSK dtg 1

tag: cell type


title: PNRA820212G

description: Hybridization OK


title: Control animals vs. glucose-fed animals replicate 5

description: Biological replicate 5 of 6. Control vs. glucose-fed adult C. elegans


title: PNRA820171G

description: Hybridization OK


title: PNRA830085G

description: Hybridization OK


title: PNRA721619G

description: Hybridization OK


title: Down-regulation of JunB by RNAi in mouse muscles in vivo_control 3

tag: transfection protocol

value: electroporated with control, non targeting scramble construct for 12 days


title: PNRA732378G

description: Hybridization OK


title: LSK dtg 3

value: FACS-sorted Lin-, c-kit+, Sca-1+ (LSK) bone marrow cells

tag: mouse type


title: PNRA732385G

description: Hybridization OK


title: Control animals vs. glucose-fed animals replicate 4

description: Biological replicate 4 of 6. Control vs. glucose-fed adult C. elegans

tag: developmental stage

tag: gender


title: PNRA722449G

description: Hybridization OK

tag: deathweight


title: PNRA722445G

description: Hybridization OK

tag: birthweight


title: PNRA722300G

description: Hybridization OK

tag: diet


title: Control animals vs. glucose-fed animals replicate 3

description: Biological replicate 3 of 6. Control vs. glucose-fed adult C. elegans

tag: development


title: Control animals vs. glucose-fed animals replicate 1

description: Biological replicate 1 of 6. Control vs. glucose-fed adult C. elegans


title: PNRA721842G

description: Hybridization OK

tag: site

tag: batch


title: CIN730279G

description: Hybridization OK

data_processing: Analysed with R software and the package Limma (Smyth 2004). Aberrant spots (flag value < -49) were removed. Median values were background corrected with the "normexp" procedure (Ritchie et al. 2007, offset =35)  then loess normalized (Colantuoni et al. 2002) then Gquantile normalized (Yang and Thorne 2003). A linear model applied to perform the differential analysis considering animals pairing.

source_name: 100 mg slice of distal small intestine

tag: birth date

tag: pair

value: suckling

value: CONTROL

source_name: Pool of equal amount of all tissue samples with prefix = CIN


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 8

description: Biological replicate 8 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

growth_protocol: Culture on daf-16 or empty vector RNAi-expressing bacteria-seeded agar plates (20 centidegree)

treatment_protocol: daf-2 mutant animals treated with daf-16 RNAi feeding

source_name: daf-2 mutant animals treated with empty vector RNAi


title: PNRA722120G

description: Hybridization OK

tag: age

tag: number of samples in the pool


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 7

description: Biological replicate 7 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

source_name: daf-2 mutant animals treated with daf-16 RNAi

tag: strain

treatment_protocol: daf-2 mutant animals treated with empty vector RNAi


title: PNRA830543G

description: Hybridization OK

tag: sex


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 6

description: Biological replicate 6 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi


title: PNRA830551G

description: Hybridization OK


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 5

description: Biological replicate 5 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi


title: PNRA722119G

description: Hybridization OK


title: PNRA830245G

description: Hybridization OK


title: CIN730278G

description: Hybridization OK


title: Control animals vs. glucose-fed animals replicate 2

description: Biological replicate 2 of 6. Control vs. glucose-fed adult C. elegans


title: CIN720844C

description: Hybridization OK

source_name: 100 mg slice of colon

value: colon


title: CIN730279C

description: Hybridization OK


title: CIN720840C

description: Hybridization OK


title: PNRA722301G

description: Hybridization OK


title: CIN632340G

description: Hybridization OK


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 3

description: Biological replicate 3 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

value: adult


title: CIN730278C

description: Hybridization OK


title: CIN720840G

description: Hybridization OK


title: CIN632341G

description: Hybridization OK


title: CIN632259G

description: Hybridization OK


title: CIN632341C

description: Hybridization OK


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 2

description: Biological replicate 2 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi

value: hermaphrodite


title: CIN632340C

description: Hybridization OK


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 4

description: Biological replicate 4 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi


title: daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi replicate 1

description: Biological replicate 1 of 8. daf-2 mutants treated with daf-16 RNAi vs. daf-2 mutants treated with empty vector RNAi


title: CIN632259C

description: Hybridization OK

value: Female


title: CIN632253G

description: Hybridization OK


title: CIN632249G

description: Hybridization OK


title: CIN632231G

description: Hybridization OK


title: CIN632245C

description: Hybridization OK


title: CIN632238C

description: Hybridization OK


title: CIN632228C

description: Hybridization OK


title: CIN632227G

description: Hybridization OK


title: CIN622664G

description: Hybridization OK


title: CIN632231C

description: Hybridization OK


title: CIN632245G

description: Hybridization OK


title: CIN632238G

description: Hybridization OK


title: CIN622633C

description: Hybridization OK


title: CIN622627C

description: Hybridization OK


title: CIN622633G

description: Hybridization OK


title: CIN622592G

description: Hybridization OK


title: CIN622593C

description: Hybridization OK


title: CIN632236G

description: Hybridization OK


title: CIN632216G

description: Hybridization OK


title: CIN622593G

description: Hybridization OK


title: CIN632249C

description: Hybridization OK


title: CIN622627G

description: Hybridization OK


title: CIN632253C

description: Hybridization OK


title: CIN632228G

description: Hybridization OK


title: CIN622663G

description: Hybridization OK


title: CIN622547G

description: Hybridization OK


title: CIN622541G

description: Hybridization OK


title: CIN622547C

description: Hybridization OK


title: CIN622592C

description: Hybridization OK


title: CIN622531G

description: Hybridization OK


title: CIN622541C

description: Hybridization OK


title: CIN632236C

description: Hybridization OK


title: CIN622489G

description: Hybridization OK


title: CIN622489C

description: Hybridization OK


title: CIN622530G

description: Hybridization OK


title: CIN622474G

description: Hybridization OK


title: CIN622206G

description: Hybridization OK


title: CIN622476C

description: Hybridization OK


title: CIN622531C

description: Hybridization OK


title: CIN622474C

description: Hybridization OK


title: CIN622491G

description: Hybridization OK


title: CIN622490G

description: Hybridization OK


title: CIN622475G

description: Hybridization OK


title: CIN622003G

description: Hybridization OK


title: CIN622005C

description: Hybridization OK


title: CIN622206C

description: Hybridization OK


title: CIN622205C

description: Hybridization OK


title: CIN622475C

description: Hybridization OK


title: CIN622205G

description: Hybridization OK


title: CIN622530C

description: Hybridization OK


title: CIN622003C

description: Hybridization OK


title: CIN720844G

description: Hybridization OK


title: CIN720833G

description: Hybridization OK


title: CIN632237C

description: Hybridization OK


title: CIN622476G

description: Hybridization OK


title: CIN730768C

description: Hybridization OK


title: N2 S L1 CTD110.6

type: genomic

city: Bethesda

first: Michael

last: Krause

state: MD

address: 5 Center Drive

department: LMB/NIDDK

institute: NIH

description:
N2 S L1 CTD110.6 ChIP
N2 S L1 Input Chromatin

hyb_protocol: Labeled DNAs were hybridized to Affymetrix C. elegans GeneChip Tiling 1.0 arrays at 45o C overnight.

scan_protocol: Arrays were washed and scanned.

data_processing:
The resulting CEL files were analyzed using Affymetrix TAS software.
Thresholds were selected, and the resulting BED files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals). To determine genes most strongly linked to O-GlcNAc associated (RL-2 reactive) chromatin regions, the input-normalized ChIP signal intensity for each probe from mutants unable to O-GlcNAcylate protein substrates (ogt-1(ok430)) was subtracted from that of mutants that are unable to remove GlcNAc from substrates (oga-1(ok1207)).  A value at, or above, 2.2 was used to threshold resulting data in order to determine O-GlcNAc peaks.  Bioinformatic analysis (GenPathway) was used to identify genes associated with RL2 peaks above threshold and located within 2 kb of the transcriptional start site (genome version, WS195).  Application of these criteria resulted in the identification of 828 genes associated with O-GlcNAc-positive chromatin.

The .bar files are two-column text files that list the chromosomal location and signal intensity for each probe on the array.

molecule: genomic DNA

source_name: wild type ChIP

label_protocol: ChIP and input DNAs were amplified by whole-genome amplification (WGA) using the GenomePlex WGA Kit (Sigma). The resulting amplified DNAs were purified, quantified, and tested by qPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions.  Amplified DNAs were fragmented and labeled using the DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Embryos were isolated from wild type and mutant gravid adults by bleach treatment and shaken gently with good aeration in sterile buffer to hatch and collected 48 hours later.

extract_protocol:
C. elegans larvae were disrupted and fixed by brief sonication in 1% formaldehyde followed by incubation for 20 min. at room temperature. After washing, lysates were sonicated again to shear the DNA to an average length of 300-500 bp.  Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.

Genomic DNA regions of interest were isolated using an antibody against one of the following epitopes: the unmodified and Ser-5-P-modified heptad repeat (YSPTSPS) and of the C-terminal domain (CTD) of RNA PolII (8WG16 MMS-126R, Covance); the Ser-2-phosphorylated and non-modified heptad repeat of the CTD domain (ab5095, Abcam); O-linked N-acetylglucosamine modified peptides (RL2; ab2739, Abcam), HGAC85-derived O-linked N-acetylglucosamine {Turner et al., 1990, #40278} (MA1-076, Thermo Scientific), and Ser/Thr-O-linked N-acetylglucosamine (CTD 110.6; MMS-248R, Covance).

treatment_protocol: Starved L1 animals were wild type or one of two mutant strains: loss of the O-GlcNAc transferase ogt-1(ok430) and loss of the O-GlcNAcase oga-1(ok1207).

value: wild type

value: L1 larvae

tag: condition

value: starved

tag: antibody

value: CTD110.6:O-GlcNAcylated RNA Pol II CTD (MMS-248R, Covance)

source_name: Wild type input chromatin


title: CIN720832G

description: Hybridization OK

value: Male

value: distal small intestine


title: CIN632230C

description: Hybridization OK

value: IUGR


title: CIN720833C

description: Hybridization OK


title: CIN632210C

description: Hybridization OK


title: CIN720832C

description: Hybridization OK


title: CIN632214C

description: Hybridization OK


title: CIN622170G

description: Hybridization OK


title: CIN622637C

description: Hybridization OK


title: CIN622631C

description: Hybridization OK


title: CIN632237G

description: Hybridization OK


title: CIN632230G

description: Hybridization OK


title: CIN622005G

description: Hybridization OK


title: CIN632214G

description: Hybridization OK


title: CIN622637G

description: Hybridization OK


title: CIN632210G

description: Hybridization OK


title: CIN622169G

description: Hybridization OK


title: CIN622631G

description: Hybridization OK


title: CIN730762C

description: Hybridization OK


title: OGA S L1 5095

description:
OGA S L1 5095 ChIP
N2 S L1 Input Chromatin

data_processing:
The resulting CEL files were analyzed using Affymetrix TAS software.
Thresholds were selected, and the resulting BED files were analyzed using Genpathway proprietary software that provides comprehensive information on genomic annotation, peak metrics and sample comparisons for all peaks (intervals). To determine genes most strongly linked to O-GlcNAc associated (RL-2 reactive) chromatin regions, the input-normalized ChIP signal intensity for each probe from mutants unable to O-GlcNAcylate protein substrates (ogt-1(ok430)) was subtracted from that of mutants that are unable to remove GlcNAc from substrates (oga-1(ok1207)).  A value at, or above, 2.2 was used to threshold resulting data in order to determine O-GlcNAc peaks.  Bioinformatic analysis (GenPathway) was used to identify genes associated with RL2 peaks above threshold and located within 2 kb of the transcriptional start site (genome version, WS195).  Application of these criteria resulted in the identification of 828 genes associated with O-GlcNAc-positive chromatin.

The .bar files are two-column text files that list the chromosomal location and signal intensity for each probe on the array. The .bed files are a three-column file that lists the chromosomal number, start, and stop points for all peaks above threshold.

source_name: oga-1(ok1207) mutant ChIP

value: oga-1(ok1207) mutant

value: Pol II:RNA PolII CTD Ser-2-P (ab5095, Abcam)


title: CIN622023G

description: Hybridization OK


title: N2 S L1 5095

description:
N2 S L1 5095 ChIP
N2 S L1 Input Chromatin


title: OGA S L1 8WG16

description:
OGA S L1 8WG16 ChIP
N2 S L1 Input Chromatin

value: 8WG16:RNA PolII CTD (MMS-126R, Covance)


title: OGA S L1 HCAC85

description:
OGA S L1 HCAC85 ChIP
N2 S L1 Input Chromatin

value: HCAC85:O-GlcNAc (MA1-076, Thermo Scientific (prev Affinity BioReagents))


title: OGT S L1 RL1

description:
OGT S L1 RL1 ChIP
N2 S L1 Input Chromatin

source_name: ogt-1(ok430) mutant ChIP

value: ogt-1(ok430) mutant

value: RL1:Nuclear Pores (MA1-071, Affinity Bioreagents)


title: OGT S L1 5095

description:
OGT S L1 5095 ChIP
N2 S L1 Input Chromatin


title: N2 S L1 8WG16

description:
N2 S L1 8WG16 ChIP
N2 S L1 Input Chromatin


title: N2 S L1 HCAC85

description:
N2 S L1 HCAC85 ChIP
N2 S L1 Input Chromatin


title: OGT S L1 HCAC8

description:
OGT S L1 HCAC85 ChIP
N2 S L1 Input Chromatin


title: N2 S L1 RL2

description:
N2 S L1 RL2 ChIP
N2 S L1 Input Chromatin

value: RL2:O-GlcNAc (ab2739, Abcam)


title: OGT S L1 RL2

description:
OGT S L1 RL2 ChIP
N2 S L1 Input Chromatin


title: Colon Mucosa_RBB+C_3

type: other

city: St Lucia

first: Daniel

last: Aguirre de Carcer

state: QLD

address: 306 Carmody Rd

department: Livestock Industries

country: Australia

institute: CSIRO

description: No further description

hyb_protocol: As described in the CombiMatrix manual

scan_protocol: The hybridised microarray slides were scanned using an Axon Genepix 4000A microarray scanner, at 5micrometers resolution (Axon Instruments, Union City CA, USA).

data_processing:
The images obtained were analysed using GenePix Pro 6.0 software (Axon Instruments), and probe signals were recorded as 635nm foreground – 635nm background intensities.
The raw signal data was first processed using the Genespring GX10 software (Agilent Technologies, Santa Clara, CA). Intensity values were transformed to log 2, and then normalized with the quantile normalization method. Probes with signal values lower than the highest negative control signals were removed from further analysis.

molecule: other

organism: human gut metagenome

source_name: Colon Mucosa

label_protocol: Aliquots (500ng) of the cRNA samples were spiked with 7ng of the control mitochondrial cRNA, then labelled and fragmented using the Label IT Array Cy5 labelling Kit (Mirus, Madison WI, USA).

extract_protocol: Colonic mucosal tissue was obtained from a surgical resection specimen of a 73 year old male subject with colorectal cancer. The specimen was immediately examined post-operatively and an area of normal mucosa was subsequently cut into sections to approximate the tissue mass attained by colonoscopic biopsy sampling. The duplicate DNA preparations were pooled and used as a template for prokaryote rrs gene amplification by PCR, performed in triplicate per extraction method using primers 4Fa (Hershberger et al 1996), 27F (Lane 1990) and 1492R-T7, modified from Lane (1990) to include a T7 promoter, in a single reaction. All PCR reactions were performed in triplicate for each sample, then pooled and purified using the Minielute PCR purification kit (Qiagen Inc., Valencia CA, USA). Single stranded cRNA was then produced from 500 ng aliquots of the pooled PCR products, using the MEGAScript T7 In Vitro transcription kit (Ambion, Austin TX, USA) as specified by the manufacturer. The resulting cRNA samples were purified using the MEGAclear Kit (Ambion), and the size and purity of the products obtained at each step was assessed by agarose gel electrophoresis and with a ND-1000 spectrophotometer (NanoDrop Technologies).

treatment_protocol: RBB+C Method

tag: tissue

value: Colon mucosa


title: Colon Mucosa_SaltingOut_3

description: No further description

treatment_protocol: Salting Out Method


title: Colon Mucosa_HMW_3

description: No further description

treatment_protocol: HMW Method


title: Colon Mucosa_HMW_2

description: No further description


title: modified plants, biological rep1

city: Nanjing

first: Hansong

last: Dong

address: Weigang NO.1

department: Plant Pathology

country: China

institute: Nanjing Agricultural University

description: Transgenic plant with background of Arabidopsis thaliana (L.) ecotype Col-0 grown under normal condition.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 ℃ on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene array Scanner3000 7G.

data_processing: The data were analyzed with GeneChip® Operating Software using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

source_name: total RNA from 200 modified plants

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

growth_protocol: For 35 d before use, wild type and transgenic plants grow in controlled environment chambers with 75% humidity and a 14-h-day (200 μE m−2 s−1 at 24°C) and 10-h-night (20°C) cycle.

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

treatment_protocol: Without treatment before RNA extraction.

value: green part of the whole plant

tag: ecotype

tag: line


title: WT plants, biological rep1

description: Gene expression data come from wild type plants which grow under normal condition.

source_name: total RNA from 200 WT plants

value: WT


title: WT plants, biological rep2


title: Colon Mucosa_RBB+C_2

description: No further description


title: Colon Mucosa_Qiagen ALLPrep_3

description: No further description

treatment_protocol: Qiagen ALLPrep Method


title: Colon Mucosa_Qiagen ALLPrep_2

description: No further description


title: Colon Mucosa_SaltingOut_2

description: No further description


title: Colon Mucosa_RBB+C_1

description: No further description


title: CIN622014G

description: Hybridization OK

tag: deathweight

value: suckling

value: CONTROL


title: Colon Mucosa_HMW_1

description: No further description


title: modified plants, biological rep2


title: Colon Mucosa_SaltingOut_1

description: No further description

source_name: Colon mucosa

extract_protocol: Colonic mucosal tissue was obtained from a surgical resection specimen of a 73 year old male subject with colorectal cancer.  The specimen was immediately examined post-operatively and an area of normal mucosa was subsequently cut into sections to approximate the tissue mass attained by colonoscopic biopsy sampling. Duplicate DNA preparations were pooled and used as a template for prokaryote rrs gene amplification by PCR, performed in triplicate per extraction method using primers 4Fa (Hershberger et al 1996), 27F (Lane 1990) and 1492R-T7, modified from Lane (1990) to include a T7 promoter, in a single reaction. All PCR reactions were performed in triplicate for each sample, then pooled and purified using the Minielute PCR purification kit (Qiagen Inc., Valencia CA, USA). Single stranded cRNA was then produced from 500 ng aliquots of the pooled PCR products, using the MEGAScript T7 In Vitro transcription kit (Ambion, Austin TX, USA) as specified by the manufacturer. The resulting cRNA samples were purified using the MEGAclear Kit (Ambion), and the size and purity of the products obtained at each step was assessed by agarose gel electrophoresis and with a ND-1000 spectrophotometer (NanoDrop Technologies).


title: mock transfected, biological replicate 3

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

hyb_protocol: Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).

data_processing: Data were normalized using the GCRMA algorithm

source_name: Dgcr8 -/- ES cells harvested 12 hours after mock transfection

growth_protocol: cells were grown in transfected and grown in the absence of LIF for 12 hours

extract_protocol: RNA was prepared using Trizol (Invitrogen)

treatment_protocol: cells were transfected with miRIDIAN miRNA mimics at 50nM (Dharmacon, ThermoFisher) using Dharmafect 1 transfection reagent

tag: cell type

value: embryonic stem cell

tag: genotype

value: Dgcr8 -/-


title: miR-294 transfected, biological replicate 2

scan_protocol: Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).

source_name: Dgcr8 -/- ES cells harvested 12 hours after transfection with miR-294


title: reactor 5 (aer) vs reactor 6 (aer)_2514964100128b

description: reactor 5 (aer) vs reactor 6 (aer)

data_processing: 1.Used script to split 2-array imagene file of Cy3 intensity into eight separate Cy3 files.  2.Used script to split 2-array imagene file of Cy5 intensity into eight separate Cy5 files.  3.For each indidivual array, a merge file was produced consisting of merging the Cy3 and Cy5 intensity files created in step 1 and 2. The merged file is provided as supplementary file for each array.  4.Background correction (Mean values). Values below 0 (higher background than foreground) were disregarded 5. LOWESS normalization was performed using the BASE plugin 6. Normalised data was further processed using an R package (limma) to get to sample to sample comparisons with p-values (false discovery rate)

source_name: L. plantarum Reactor 5 aerobic

growth_protocol: non-pH controlled Batch cultivation MRS-broth

source_name: L. plantarum Reactor 6 aerobic


title: mock transfected, biological replicate 2

label_protocol: Gladstone Genomic Core facility standard protocols were used (http://www.gladstone.ucsf.edu/gladstone/site/genomicscore/section/1914).


title: mock transfected, biological replicate 1


title: OGA S L1 RL2

description:
OGA S L1 RL2 ChIP
N2 S L1 Input Chromatin

tag: developmental stage

value: L1 larvae

value: starved

value: wild type


title: let-7c transfected, biological replicate 2

source_name: Dgcr8 -/- ES cells harvested 12 hours after transfection with let-7c


title: miR-294 transfected, biological replicate 3


title: reactor 5 (aer) vs reactor 4 (aer)_2514964100128a

description: reactor 5 (aer) vs reactor 4 (aer)

source_name: L. plantarum Reactor 4 aerobic


title: miR-294 transfected, biological replicate 1


title: let-7c transfected, biological replicate 3


title: Colon Mucosa_Qiagen ALLPrep_1

description: No further description

extract_protocol: Colonic mucosal tissue was obtained from a surgical resection specimen of a 73 year old male subject with colorectal cancer.  The specimen was immediately examined post-operatively and an area of normal mucosa was subsequently cut into sections to approximate the tissue mass attained by colonoscopic biopsy sampling.  Duplicate subsamples of the tissue were subjected to the Qiagen Allprep DNA/RNA extraction kit.  The duplicate DNA preparations were pooled and used as a template for prokaryote rrs gene amplification by PCR, performed in triplicate per extraction method using primers 4Fa (Hershberger et al 1996), 27F (Lane 1990) and 1492R-T7, modified from Lane (1990) to include a T7 promoter, in a single reaction. All PCR reactions were performed in triplicate for each sample, then pooled and purified using the Minielute PCR purification kit (Qiagen Inc., Valencia CA, USA). Single stranded cRNA was then produced from 500 ng aliquots of the pooled PCR products, using the MEGAScript T7 In Vitro transcription kit (Ambion, Austin TX, USA) as specified by the manufacturer. The resulting cRNA samples were purified using the MEGAclear Kit (Ambion), and the size and purity of the products obtained at each step was assessed by agarose gel electrophoresis and with a ND-1000 spectrophotometer (NanoDrop Technologies).


title: let-7c transfected, biological replicate 1


title: reactor 6 (aer) vs reactor 5 (aer)_2514964100136b

description: reactor 6 (aer) vs reactor 5 (aer)


title: reactor 2 (resp) vs reactor 3 (resp)_2514964100135a

description: reactor 2 (resp) vs reactor 3 (resp)

source_name: L. plantarum Reactor 2 resp

treatment_protocol: heme +K2

source_name: L. plantarum Reactor 3 resp


title: reactor 3 (resp) vs reactor 6 (aer)_2514964100135b

description: reactor 3 (resp) vs reactor 6 (aer)


title: reactor 6 (aer) vs reactor 1 (resp)_2514964100136a

description: reactor 6 (aer) vs reactor 1 (resp)

source_name: L. plantarum Reactor 1 resp


title: reactor 1 (resp) vs reactor 2 (resp)_2514964100131a

description: reactor 1 (resp) vs reactor 2 (resp)


title: reactor 5 (aer) vs reactor 4 (aer)_2514964100134a

description: reactor 5 (aer) vs reactor 4 (aer)


title: reactor 4 (aer) vs reactor 1 (resp)_2514964100134b

description: reactor 4 (aer) vs reactor 1 (resp)


title: reactor 2 (resp) vs reactor 5 (aer)_2514964100131b

description: reactor 2 (resp) vs reactor 5 (aer)


title: WMARS clay fraction rep #1

city: Auburn

first: Mark

middle: R

last: Liles

state: AL

address: Rm 316, Rouse Life Sciences Building

department: Biological Sciences

institute: Auburn University

description: This sample is of the 16S rRNA gene PCR amplified using primer sets 31F (division Acidobacteria-specific) and 1492R (universal)

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

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

data_processing: mean signal intensity of triplicate probes

organism: uncultured Acidobacteriota bacterium

source_name: WMARS clay fraction # 1

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

growth_protocol: For E. coli cultures containing the cloned 16S rRNA gene, 2 ml cultures were grown overnight at 37oC.  Plasmid DNA was extracted using a Promega SV96 kit and the cloned Acidobacteria rDNA template was PCR amplified in the presence of Cy3-labeled dCTPs and unincorporated label was removed by Centricon spin columns

extract_protocol: For soil samples, total soil DNA was extracted by MoBio soil kit extraction.  The soil Acidobacteria rDNA template was PCR amplified in the presence of Cy3-labeled dCTPs and unincorporated label was removed by Centricon spin columns

value: 16S rRNA gene amplicon

tag: source

value: WMARS clay fraction


title: 85E8 16S rRNA gene clone

source_name: 85E8 16S rRNA gene clone

value: accession AY214905


title: 17F9 16S rRNA gene clone

source_name: 17F9 16S rRNA gene clone

value: accession AF245036


title: Control_vs_H2O2_Recovery after 3hours_Nipponbare_R1_A

status: Public on Dec 31 2009

city: Orono

first: Benildo

middle: G

last: de los Reyes

state: ME

address: 5735 Hitchner Hall

department: School of Biology and Ecology

institute: University of Maine

description: This experiment was performed with two independent biological replicates (R1 and R2). The whole genome microarray consisting of a total of ~45,000 oligonucleotides was printed on two separate slides (Slides A and B).

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer composed of 50% formamide, 5X SSC, 0.1% SDS, and 10 mM DTT. Hybridization was performed by applying the labeled mixture of control and H2O2-treated samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Lifterslip by Erie/Fisher Scientific). The hybridization assembly was mounted in sealed and humidified thermal hybridization blocks (SciGene Hybex Microarray Incubation System). Hybridization was performed at 42C from 18 to 20 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions: Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 0.1% SDS; Buffer 2, 0.1x SSC plus 0.1% SDS; Buffer 3, 0.1x SSC. Washing with buffers 1 and 2 was performed at 42C, and with buffer 3 at room temperature. All washing were carried out for 10 minutes each step.

scan_protocol: Microarrays were scanned at 635nm and 532nm using the Axon 4000A scanner. Scan image was acquired and processed by the GenePix Pro 5.1.

data_processing: Quality flagging was performed on the microarray scans using GenePix Pro 5.1. A complex quality control query was used to identify and select high quality spots (features) from the entire microarray matrix. This query was formulated to exclude features that belong to any of the following filter criteria: 1) The feature intensity is near background level; 2) The feature is irregular or not uniform (spotting irregularity); and 3) The background around the feature is not uniform (hybridization irregularity). Only the features that passed these stringent filter criteria were included in subsequent bioinformatics analysis of the gene expression data. Gene expression data in each image was normalized globally prior to high level analysis. VALUES represent the log of the ratio between the background subtracted intensity values at Cy5 (635 nm) and Cy3 (532 nm) (635/532). Data sorting was performed by MS Access. All high level (T-tests and hierarchical clustering) analyses were performed with the MeV Bioinformatics tools (TIGR).

organism: Oryza sativa

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 9 hour

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP, The resulting aRNA molecules were chemically labeled with Cy3 fluorescent dye.

growth_protocol: Seedlings were germinated in ample water and allowed to develop to V3-stage at ambient temperature (29C) in a growth room.

extract_protocol: Total RNA was isolated from control seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 9 hrs

tag: Rice (cv. Nipponbare) leaves V3-stage.

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hours and then transferred to water for 3 hours

growth_protocol: Seedlings were germinated in ample water and allowed to develop to V3-stage under ambient temperature. Seedlings were subjected to H2O2 condition in a growth chamber for the designated duration.

extract_protocol: Total RNA was isolated from H2O2-treated seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hrs and transferred to water for 3 hours.


title: WMARS soil rep #1

source_name: WMARS soil #1

value: WMARS  soil


title: WMARS soil rep #2

source_name: WMARS soil #2

value: WMARS soil


title: Control_vs_H2O2_Recovery after 6 hours_Nipponbare_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 12 hour

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 12 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hours and then transferred to water for 6 hours

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hrs and transferred to water for 6 hours.


title: WMARS clay fraction rep #2

source_name: WMARS clay fraction # 2


title: 220H 16S rRNA gene clone No betaine added

value: accession AY214900


title: 220H 16S rRNA gene clone

source_name: 220H 16S rRNA gene clone


title: Control_vs_H2O2_Nipponbare_01H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 1 hour

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 1 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 1 hour

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 1hr.


title: Control_vs_H2O2_Nipponbare_06H_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 6 hours

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 6 hrs

tag: Rice (cv. Nipponbare) leaves V3-stage

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hours

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hrs.


title: Control_vs_H2O2_Recovery after 6 hours_Nipponbare_R2_A

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hr and then transferred to water for 6hrs.


title: FRIGIDA rep3

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

hyb_protocol: For each sample, 10ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Arabidopsis microarray for 16 hours at 45ºC.Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000.  Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter.

data_processing: The microarrays were analysed using the statistical analysis language R; utilising the limma and CNA libraries under the BioConductor frame work. Analysis of high-density tiling microarrays is deemed particularly difficult as the restrictions in probe design does not allow for discrimination in favour of  probes exhibiting high predicted target binding and subsequent fluorescence under a chosen hybridisation temperature. In custom tiling microarrays, the difficulties are further exacerbated as typically only a small region of the genome is tiles; at very high density. This makes normalisation of the data particularly difficult: almost all published normalisation algorithms are based on the assumption that a significant majority of transcript probes on the microarray remain unchanged under any given experimental condition. Custom tiling microarrays do not only invalidate this assumption, but with it almost all normalisation algorithms.  We used an algorithm which computes a global rank-invariant set of transcripts; which is then in turn employed to normalize all microarrays across experimental conditions. Following normalisation, linear models were fit to the data according to; and t-scores for all contrasts of interest were obtained. The t-scores were used as more reliable estimates of CGH-type data than averaged expression ratios as we let variation affect the quality of the scores. Segments of scores were obtained using the method of Olshen, A.B. et al 2004 where p-values were obtained though permutations of t-scores contained in segments.

source_name: FRIGIDA

label_protocol: Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences).  After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences).  The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).

extract_protocol: RNA was extracted by TRIreagent (SIGMA) and purified by using Invitrogen Ribominus

value: seedling

value: FRIGIDA


title: Control_vs_H2O2_Nipponbare_01H_R2_A

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 1 hr.


title: FRIGIDA + 2 weeks cold rep2

source_name: FRIGIDA + 2 weeks cold


title: FRIGIDA + 2 weeks cold rep3


title: Control_vs_H2O2_Nipponbare_06H_R1_A


title: FRIGIDA rep2


title: Control_vs_H2O2_Nipponbare_03H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient tempserature (29C); Treatment = water (control) for 3 hours

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 3 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 3 hours

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 3 hrs.


title: WT rep6

source_name: WT


title: FRIGIDA rep4


title: Control_vs_H2O2_Nipponbare_03H_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient tempserature (29C); Treatment = water (control) for 3 hour


title: 16H1 16S rRNA gene clone

source_name: 16H1 16S rRNA gene clone

value: accession AF245035


title: FRIGIDA + 2 weeks cold + 7 days warm rep1

source_name: FRIGIDA + 2 weeks cold + 7 days warm


title: WT rep5


title: WT rep4


title: WT rep1


title: FRIGIDA + 2 weeks cold rep1


title: FRIGIDA + 2 weeks cold + 7 days warm rep2


title: 35s::FCA rep4


title: WT rep2


title: Control_vs_H2O2_Recovery after 3hours_Nipponbare_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 9 hour

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hours and then transferred to water for 3 hours

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hr and then transferred to water for 3hrs.


title: 35s::FCA rep3


title: FRIGIDA rep 1


title: 35s::FCA rep2


title: WT rep3


title: Patient_6

city: London

first: Hagen

last: Kulbe

address: Charterhouse Square

department: Centre for Cancer and Inflammation

country: United Kingdom

institute: Institute of Cancer and the CR-UK Clinical Centre, Barts and The London School of Medicine and Dentistry

description: ascites cell sample from patient no. 6 treated with therapeutic anti-human TNFα antibody infliximab

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridised for 16 hr at 45C on GeneChip human U133plus2.0 expression array. Genechips were washed and stained in the Affymetrix Fludics Station 450.

scan_protocol: Genechips were scanned using the Affymetrix Genechip Scanner 3000G

data_processing: Data was analysed using Biocondutor 1.95 running on R2.6.0. Probe set expression measures were calcualted using the Affy package Robust Multichip Average default method.

organism: Homo sapiens

source_name: ascites cell sample from non-responsive patient to infliximab

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

growth_protocol: Cell pellets from primary ovarian cancer were obtained from fresh ascites samples.

extract_protocol: Trizol extraction of total RNA was performed and purified further with the Rneasy kit (Qiagen) according to the manufacturers instructions

treatment_protocol: no treatment

value: cells from primary ovarian cancer were obtained from fresh ascites samples


title: 35s::FCA rep1


title: SP3

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: CAL-51 breast cancer side population (SP) cells

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

extract_protocol: Rneasy

treatment_protocol: Med3, 80 % confluency

value: breast cancer


title: SP2


title: Patient_4

description: ascites cell sample from patient no. 4 treated with therapeutic anti-human TNFα antibody infliximab

source_name: ascites cell sample from responsive patient to infliximab


title: Patient_5

description: ascites cell sample from patient no. 5 treated with therapeutic anti-human TNFα antibody infliximab


title: NSP2

source_name: CAL-51 breast cancer non-side population (NSP) cells


title: NSP3


title: Patient_3

description: ascites cell sample from patient no. 3 treated with therapeutic anti-human TNFα antibody infliximab


title: SP1


title: NSP1


title: Patient_2

description: ascites cell sample from patient no. 2 treated with therapeutic anti-human TNFα antibody infliximab


title: Patient_1

description: ascites cell sample from patient no. 1 treated with therapeutic anti-human TNFα antibody infliximab


title: Patient_7

description: ascites cell sample from patient no. 7 treated with therapeutic anti-human TNFα antibody infliximab


title: TOV21G_rep3

description: parental ovarian cancer cell line

source_name: parental TOV21G cell line

growth_protocol: The human ovarian cancer cell lines TOV21G, TOV112D and IGROV-1 (from ATCC, Rockville, MD, USA) were cultured in endotoxin-free RPMI 1640 medium supplemented with 3.7 g.l NaHCO3 and 10% FCS. SKOV-3 cellls were cultured in endotoxin-free DMEM medium and 10% FCS.

tag: tissue type

value: ovarian cancer

tag: cell line

value: parental TOV21G


title: T112D_rep1

description: parental ovarian cancer cell line

source_name: parental T112D cell line

value: parental T112D


title: Patient_9

description: ascites cell sample from patient no. 9 treated with therapeutic anti-human TNFα antibody infliximab


title: TOV21G_rep2

description: parental ovarian cancer cell line


title: SKOV3_rep1

description: parental ovarian cancer cell line

source_name: parental SKOV cell line

value: parental SKOV


title: IGROV1_rep3

description: parental ovarian cancer cell line

source_name: parental IGROV cell line

value: parental IGROV


title: SKOV3_rep3

description: parental ovarian cancer cell line


title: T112D_rep2

description: parental ovarian cancer cell line


title: IGROV1_rep2

description: parental ovarian cancer cell line


title: T112D_rep3

description: parental ovarian cancer cell line


title: TOV21G_rep1

description: parental ovarian cancer cell line


title: Control_vs_H2O2_Recovery_after_6_hours_Nipponbare_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 12 hours

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hours and then transferred to water for 6 hours

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hr and then transferred to water for 6 hrs.


title: IGROV1_rep1

description: parental ovarian cancer cell line


title: SKOV3_rep2

description: parental ovarian cancer cell line


title: Patient_8

description: ascites cell sample from patient no. 8 treated with therapeutic anti-human TNFα antibody infliximab


title: Control_vs_H2O2_Recovery after 3 hours_Nipponbare_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 9 hours

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hrs and then transferred to water for 3 hours.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hrs and then transferred to water for 3 hours.


title: Control_vs_H2O2_Nipponbare_03H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 3 hours

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 3 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 3 hr.


title: Control_vs_H2O2_Recovery after 6 hours_Nipponbare_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 12 hour

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 12 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hrs and then transferred to water for 6 hours.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 6 hrs and then transferred to water for 6 hours.


title: Control_vs_H2O2_Nipponbare_06H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 6 hours

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hrs


title: Control_vs_H2O2_Recovery after 3 hours_Nipponbare_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 9 hour

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 9 hr


title: Control_vs_H2O2_Nipponbare_06H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C) Treatment = water (control) for 6 hours

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 6 hours


title: Control_vs_H2O2_Nipponbare_03H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C) Treatment = water (control) for 3 hours

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 3 hours


title: Control_vs_Cold_Nipponbare_18H_R2_B

hyb_protocol: Equal amounts of Cy5- and Cy3-labeled samples were combined, dried by speed-vac centrifugation and then dissolved in 1x hybridization buffer composed of 50% formamide, 5X SSC, 0.1% SDS, and 10 mM DTT. Hybridization was performed by applying the labeled mixture of control and cold stress samples onto the area of the microarray slide corresponding to the spot matrix and then covered with cover slip (Lifterslip by Erie/Fisher Scientific). The hybridization assembly was mounted in sealed and humidified thermal hybridization blocks (SciGene Hybex Microarray Incubation System). Hybridization was performed at 42C from 18 to 20 hours. Following hybridization, the cover slips were gently peeled-off and the slides were washed in three stringency buffer solutions: Buffer 1, 2x SSC (3M sodium chloride, 0.3M sodium citrate) plus 0.1% SDS; Buffer 2, 0.1x SSC plus 0.1% SDS; Buffer 3, 0.1x SSC. Washing with buffers 1 and 2 was performed at 42C, and with buffer 3 at room temperature. All washing were carried out for 10 minutes each step.

data_processing: Quality flagging was performed on the microarray scans using GenePix Pro 5.1. A complex quality control query was used to identify and select high quality spots (features) from the entire microarray matrix. This query was formulated to exclude features that belong to any of the following filter criteria: 1) The feature intensity is near background level; 2) The feature is irregular or not uniform (spotting irregularity); and 3) The background around the feature is not uniform (hybridization irregularity). Only the features that passed these stringent filter criteria were included in subsequent bioinformatics analysis of the gene expression data. Gene expression data in each image was normalized globally prior to high level analysis. VALUES represent the log of the ratio between the background subtracted intensity values at Cy5 (635 nm) and Cy3 (532 nm) (635/532). Data sorting was performed by MS Access. All high level  (T-tests and hierarchical clustering) analysis was performed by the MeV Bioinformatics tools (TIGR).

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 18 hours at control temperature (29C)

label_protocol: The target RNA sample was processed in a multi-step procedure using the MessageAmp II aRNA amplification method (Ambion). The cDNA synthesis reaction was primed with oligo-dT catalyzed by ArrayScript reverse transcriptase (Ambion). The resulting cDNA was used as template for in vitro transcription using T7 enzyme cocktail (Ambion) producing up to 20 ug of aRNA per reaction labeled with aminoallyl-dUTP, The resulting aRNA molecules were chemically labeled with Cy5 fluorescent dye.

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 18 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 18 hours at cold stress (10C)

growth_protocol: Seedlings were germinated in ample water and allowed to develop to V3-stage under ambient temperature. Seedlings were subjected to cold stress condition (10C) in a growth chamber for the designated duration.

extract_protocol: Total RNA was isolated from cold-treated seedlings using the TriZol extraction method according to manufacturer's (Invitrogen) protocol.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 18 hrs.


title: Control_vs_H2O2_Nipponbare_01H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 1 hour

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 1 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 1 hr


title: Control_vs_Cold_Nipponbare_96H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 96 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hrs.


title: Zebrafish QKD  embryo_TB_biological rep2

city: Suita

first: Yusuke

last: Kamachi

state: Osaka

address: 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences

country: Japan

institute: Osaka University

description: Gene expression data from embryos injected with MOs for sox2/3/19a/19b quadruple knockdown at tailbud stage.

hyb_protocol: 10 micrograms of fragmented cRNA probes were hybridized to the GeneChip array and posthybridization staining and washing were performed according to the manufacture’s instruction (Affymetrix).

scan_protocol: GeneChip arrays were scanned with GS3000 scanner.

data_processing: Data were processed using the RMA program.

organism: Danio rerio

source_name: Zebrafish sox2/3/19a/19b knockdown embryo at tailbud stage

label_protocol: cRNA probes were prepared using 4 microgram total RNA with a one-cycle cDNA synthesis kit (Affymetrix).

growth_protocol: Embryos were grown in in 0.03% Red Sea salt solution.

extract_protocol: Total RNA was prepared from 100 embryos using Ribo Pure kit (Ambion).

value: whole embryo

value: TL


title: Control_vs_Cold_Nipponbare_36 H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 36 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 36 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 36 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 36 hrs


title: Control_vs_Cold_Nipponbare_24 H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 24 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 24 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 24 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 24 hrs


title: Zebrafish QKD  embryo_TB_biological rep1


title: Zebrafish QKD  embryo_ 30%E_biological rep2

description: Gene expression data from embryos injected with MOs for sox2/3/19a/19b quadruple knockdown at 30% epiboly stage.

source_name: Zebrafish sox2/3/19a/19b knockdown embryo at 30% epiboly stage


title: Prp17 delta replicate 2

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Raw Intensity

organism: Saccharomyces cerevisiae

source_name: Haploid yeast cell

label_protocol: Affymetrix protocol

extract_protocol: Hot phenol protocol

value: Prp17 delta

value: From Open Biosystems


title: Control_vs_Cold_Nipponbare_04 H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 04 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 04 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 04 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 04 hrs


title: Zebrafish QKD  embryo_ 75%E_biological rep1

description: Gene expression data from embryos injected with MOs for sox2/3/19a/19b quadruple knockdown at 75% epiboly stage.

source_name: Zebrafish sox2/3/19a/19b knockdown embryo at 75% epiboly stage


title: Control_vs_Cold_Nipponbare_12 H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 12 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 12 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 12 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 12 hrs


title: Control_vs_Cold_Nipponbare_02 H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 02 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 02 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 02 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 02 hrs


title: Prp18 delta replicate 3

data_processing: Normalized value: probe match minus mismatch, quantile normalized across all our samples

value: Prp18 delta

value: From Open Biosystems; mat A; clone ID 4636


title: Prp17 delta Upf1 delta replicate 1

value: Prp17 delta Upf1 delta

value: Derived from Open Biosystems; mat A; clone ID 4201 in which the UPF1 gene was deleted with HIS


title: Zebrafish QKD embryo_ 30%E_biological rep1


title: Prp17 delta Upf1 delta replicate 2


title: Prp18 delta replicate 2


title: Control_vs_Cold_Nipponbare_0.5H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hour at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 0.5 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hour at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 0.5 hr


title: Zebrafish wt embryo_ TB_biological rep2

description: Gene expression data from control uninjected embryos at tailbud stage.

source_name: Zebrafish wild-type embryo at tailbud stage


title: Control_vs_Cold_Nipponbare_R24H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 120 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 120 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at cold stress (10C) and then transfer to ambient temperature (29C) in a growth room for 24 hrs.

growth_protocol:
Seedlings were germinated in ample water and allowed to develop to V3-stage under ambient temperature. Seedlings were subjected to cold stress condition (10C) in a growth chamber for the designated duration.
To recovery, seedlings were transfered to ambient temperature for 24 hours.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hrs and then transfer to ambient temperature (29C) in a growth room for 24 hrs.


title: Prp18 delta replicate 1


title: Control_vs_Cold_Nipponbare_48H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 48 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 48 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 48 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 48 hrs.


title: Control_vs_Cold_Nipponbare_96H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 96 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hr


title: Prp18 delta Upf1 delta replicate 1

source_name: Haploid yeast cell

value: Prp18 delta Upf1 delta

value: Derived from Open Biosystems; mat A; clone ID 4636 in which the UPF1 gene was deleted with HIS


title: Zebrafish QKD  embryo_ 75%E_biological rep2


title: Prp17 delta replicate 3

value: From Open Biosystems; mat A; clone ID 4201


title: Prp18 delta Upf1 delta replicate 2


title: Zebrafish wt embryo_ 75%E_biological rep1

description: Gene expression data from control uninjected embryos at 75% epiboly stage.

source_name: Zebrafish wild-type embryo at 75% epiboly stage


title: Zebrafish wt embryo_ TB_biological rep1


title: Control_vs_Cold_Nipponbare_06 H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 06 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 06 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 06 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 06 hrs


title: Zebrafish wt embryo_ 75%E_biological rep2


title: Control_vs_H2O2_Nipponbare_01H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at ambient temperature (29C); Treatment = water (control) for 1 hour

treatment_protocol: Control samples (seedlings at V3 stage) were in water for 1 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings  ambient temperature (29C); Treatment = 4mM H2O2  (oxidative stress) for 1 hour

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated in 4mM H2O2 treatment for 1 hr.


title: Control_vs_Cold_Nipponbare_36H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 36 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 36 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 36 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 36 hr


title: Control_vs_Cold_Nipponbare_24H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 24 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 24 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 24 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 24 hr


title: Zebrafish wt embryo_ 30%E_biological rep2

description: Gene expression data from control uninjected embryos at 30% epiboly stage.

source_name: Zebrafish wild-type embryo at 30% epiboly stage


title: Prp17 delta replicate 1

growth_protocol: Synthetic complete medium at 30° C


title: Control_vs_Cold_Nipponbare_48H_R1_B

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 48 hr

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 48 hr


title: Prp18 delta Upf1 delta replicate 3


title: Control_vs_Cold_Nipponbare_0.5H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 0.5 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 0.5 hr


title: Zebrafish wt embryo_ 30%E_biological rep1


title: Control_vs_Cold_Nipponbare_06H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 6 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 6 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 6 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 6 hr


title: Control_vs_Cold_Nipponbare_04H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 4 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 4 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 4 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 4 hr


title: Control_vs_Cold_Nipponbare_18H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 18 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 18 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 18 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 18 hr


title: Control_vs_Cold_Nipponbare_12H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 12 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 12 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 12 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 12 hr


title: Control_vs_Cold_Nipponbare_02H_R1_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 2 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 2 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 2 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 2 hrs


title: Control_vs_Cold_Nipponbare_12H_R2_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 12 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 12 hrs


title: Control_vs_Cold_Nipponbare_06H_R2_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 6 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 6 hrs


title: Control_vs_Cold_Nipponbare_24 H_R2_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 24 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 24 hrs.


title: Control_vs_Cold_Nipponbare_R24H_R2_B

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 120 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 120 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at cold stress (10C) and then transfer to ambient temperature (29C) in a growth room for 24 hours.

growth_protocol: Seedlings were germinated in ample water and allowed to develop to V3-stage under ambient temperature. Seedlings were subjected to cold stress condition (10C) in a growth chamber for the designated duration. To recovery, seedlings were transfered to ambient temperature for 24 hours.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hrs and then transfer to ambient temperature in a growth room for 24 hours.


title: Control_vs_Cold_Nipponbare_18 H_R2_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 18 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 18 hrs.


title: Control_vs_Cold_Nipponbare_48 H_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 48 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 48 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 48 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 48 hrs.


title: Control_vs_Cold_Nipponbare_04H_R2_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 4 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 4 hrs


title: Control_vs_Cold_Nipponbare_0.5H_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hour at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 0.5 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hour at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 0.5 hr


title: Control_vs_Cold_Nipponbare_R24 H_R2_A


title: Control_vs_Cold_Nipponbare_02H_R2_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 2 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 2 hrs


title: Control_vs_Cold_Nipponbare_36 H_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 36 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 36 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 36 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 36 hrs.


title: Control_vs_Cold_Nipponbare_96 H_R2_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 96 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hrs.


title: Prp17 delta Upf1 delta replicate 3

source_name: Haploid yeast cell


title: Control_vs_Cold_Nipponbare_12 H_R1_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 12 hrs

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 12 hrs


title: Control_vs_Cold_Nipponbare_48 H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hours at control temperature (29C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 48 hrs


title: Control_vs_Cold_Nipponbare_96 H_R1_A

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hrs


title: Control_vs_Cold_Nipponbare_36 H_R1_A

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 36 hrs


title: Control_vs_Cold_Nipponbare_24 H_R1_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 24 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 24 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 24 hrs


title: Control_vs_Cold_Nipponbare_04H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 04 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 04 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 04 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 04 hrs


title: Control_vs_Cold_Nipponbare_0.5H_R1_A

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 0.5 hr

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 0.5 hours at cold stress (10C)


title: 256µg/ml Novobiocin-treated campylobacter (0.5 hour) Cy5 slide 47

status: Public on Dec 28 2009

city: Ames

first: Yang

last: Wang

state: IA

address: 1113 Vet Med

department: VMPM

institute: Iowa State University

hyb_protocol: After purification, the fluorescent labeling of the DNA was quantitated, and equal amounts of labeled cDNA of the wild-type and the mutant were mixed and dried in a speed vacuum concentrator. After resuspension with hybridization buffer provided by the slide manufacturer, the mixture was denatured by heating at 95 ◦C for 10 min. The hybridization mixture was loaded onto a microarray slide and hybridized in a shaking incubator at 42 ºC for 24 h. Slides were washed as the manufacture’s recommendations and dried by centrifugation.

scan_protocol: Using a ScanArray Express laser scanner (Applied Biosystem Inc., Foster City, CA) each dye channel of each slide was scanned at a 10 μm resolution using three predetermined laser power and photomultiplier gain settings. Thus for each slide six scans were performed, three separate scans at different settings of each of the two dye channels.

data_processing: ImaGene software (BioDiscovery, El Segundo, CA) was used for spot finding and to measure the spot-specific mean signal strength of each spot. The fluorescentc intensities of all spots were log2 transformed. The median of the three log2-transformed spot signals was determined and this value was used as spot signal for all further calculations. As an additional measure against intensity dependent dye bias the data was then subjected to LOWESS normalization.

organism: Campylobacter jejuni

source_name: C. jejuni NCTC-11168

label_protocol: cDNA was synthesized using aminoallyl-dNTP according to the manufacturer’s instruction. After purification, aminoallyl labeled cDNA was fluorescently labeled with Cy-3/cy-5 mono-Reactive Dye Pack (Amersham Biosciences, Piscataway, NJ)

extract_protocol: Total RNA was isolated using RNAprotectTM bacteria reagent (Qiagen) and an RNeasy kit (Qiagen) according to the manufacturer’s protocol with an optional step of on-column DNase treatment with RNase-Free DNase (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: agent

value: 10X MIC Novobiocin for 0.5 hours


title: Control_vs_Cold_Nipponbare_06H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 06 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 06 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 06 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 06 hrs


title: 256µg/ml Novobiocin-treated campylobacter (0.5 hour) Cy3 slide 50


title: untreated campylobacter (0.5 hour) cy5 slide 49


title: Control_vs_Cold_Nipponbare_R24 H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at R24 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 120 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 96 hours at cold stress (10C) and then transfer to ambient temperature (29C) in a growth room for 24 hours.

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 96 hrs and then transfer to ambient temperature in a growth room for 24 hours.


title: 256µg/ml Novobiocin-treated campylobacter (0.5 hour) Cy5 slide 46


title: untreated campylobacter (0.5 hour) cy3 slide 46


title: untreated campylobacter (0.5 hour) cy5 slide 50


title: 256µg/ml Novobiocin-treated campylobacter (0.5 hour) Cy3 slide 49


title: Control_vs_Cold_Nipponbare_18 H_R1_A

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 18 hours at control temperature (29C)

treatment_protocol: Control samples (seedlings at V3 stage) were incubated at ambient temperature (29C) for 18 hrs

source_name: Rice (Oryza sativa, spp. japonica cv. Nipponbare) seedlings at 18 hours at cold stress (10C)

treatment_protocol: Treatment samples (seedlings at V3 stage) were incubated at low temperature (10C) for 18 hrs


title: UBR2-/- testes

city: Pittsburgh

first: Jee Young

last: An

state: PA

address: 3501 Terrace St. Salk 647D

institute: University of Pittsburgh

description: Expression data from 2 testes of different mice at 17 days old

hyb_protocol: Following fragmentation, 6.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Mouse Expression 430A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Genechip Operating System  using MAS5.0 algorithm with default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150

source_name: testes from 17 days old UBR2-/- mice

label_protocol: Biotinylated cRNA were produced from total RNA.

growth_protocol: Mice were maintaied in the animal facility at University of Pittsburgh.

extract_protocol: Total RNA were extracted using Trizol (Invitorgen) and RNeasy-mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Testes were collected from 17 days old mice, washed in PBS, and processed immediately for RNA extraction.

tag: strain

value: 129SV and C57BL mixed

value: testis

tag: age

value: 17 days old


title: Wild type testes

source_name: testes from 17 days old wild type mice

value: wild type