title: E17.5 Mouse testis_M19_2

status: Public on Dec 31 2009

city: Houston

first: Rui

last: Zhu

address: 1515 Holcombe Blvd.

department: Genetics

institute: UT MD Anderson Cancer Center

description: E17.5 Mouse testis_M19_2

hyb_protocol: Hybridization 1.Thaw 1 vial of the 20X eukaryotic hybridization controls and the vial of oligo B2 (included in the GeneChip Eukaryotic hybridization control kit) by heating the vials at 65C for 5 minutes. 2.Vortex the vials to ensure complete mixing and then briefly spin down the samples. 3.Prepare the hybridization cocktail as follows: Reagents                              Mini Array    Midi Array    Standard Array  Fragmented cRNA                  5mg           10mg          15 mg  Control oligo B2                     1.7ml         3.3ml          5ml  20X eukaryotic hybridization controls 5ml    10ml           15ml  Herring sperm DNA                 1ml             2ml            3ml  Acetylated BSA                     1ml             2ml            3ml  2X Hybridization buffer            50ml           100ml         150mul  Water                                  to 100ml      to 200ml     to 300ml  4.Equilibrate probe array to room temperature. 5.Heat the hybridization cocktail to 99C for 5 minutes, spin briefly and transfer to 45C for 5 minutes. 6.Spin hybridization/cocktail at maximum speed for 5 minutes to remove any insoluble material. 7.Wet the probe array by filling it through one of the septa with 1X hybridization buffer and incubate at 45C for 10 minutes with rotation. 8.Remove the buffer solution from the probe array and fill the probe array with the appropriate amount of the clarified hybridization cocktail. Hybridize overnight at 45C with rotation. Washing and Staining Probe Arrays Follow instructions for operation and usage of fluidics station as given in the Expression Analysis technical manual from Affymetrix.

scan_protocol: The arrays were stained with phycoerythrin-coupled avidin and scanned using a GeneArray Scanner 3000. The resultant output was analyzed using Affymetrix Microarray Suite software and examined for excessive background or evidence of RNA degradation. All microarray processing was performed in the Murine Microarray and Affymetrix Facility at the University of Texas M. D. Anderson Cancer Center.

data_processing: dChip (version 1.3) with log2 scaled.  Normalized.

label: Biotin

organism: Mus musculus

source_name: E17.5 male genital ridges, 129.MOLF-Chr 19

label_protocol:
Synthesis of Double Stranded cDNA from Total RNA (Using the Supercript Choice System by Gibco)
Use a starting amount of 5.0 – 40.0 mg total RNA.
First Strand cDNA Synthesis (using 5.0 mg of total RNA)
1.In a 1.5 mL microcentrifuge tube, combine the following: x mL of total RNA, 12- x mL of RNase/DNase free water and 1 mL of T7- (dT)24 primer.
2.Incubate at 70° C for 10 minutes. Centrifuge to collect contents at the bottom of the tube. Put on ice.
3.Add the following to the tube: 4 mL of 5X First strand cDNA buffer, 2 mL of 0.1 M DTT, and 1 mL of 10 mM dNTP mix.
4.Incubate at 42° C for 2 minutes.
5.Add to the tube 1 mL of Superscript II reverse transcriptase.
6.Incubate at 42° C for 1 hour. Centrifuge to collect contents at the bottom of the tube. Put on ice.
Second Strand cDNA Synthesis (using 5.0 mg of total RNA)
1.Add the following to the First Strand Synthesis tube: 91 mL of RNase/DNase free water, 30 mL of 5X Second strand reaction buffer, 3 mL of 10 mM dNTP mix, 1 mL of 10 U/mL DNA Ligase (E. coli), 4 mL of 10 U/mL DNA Polymerase I (E. coli), and 1 mL of 2 U/mL RNase H (E. coli).
2.Tap tube to mix. Centrifuge to collect contents at the bottom of the tube. Incubate at 16°C for 2 hours.
3.Add 2 mL [10 U] T4 DNA Polymerase.
4.Incubate at 16° C for 5 minutes.
5.Add 10 mL 0.5 M EDTA.
Cleanup of Double-Stranded cDNA
Phenol/Chloroform Extraction
1.Add 162 mL of (25:24:1) Phenol:chloroform:isoamyl alcohol. Vortex.
2.Centrifuge sample at maximum speed for 2 minutes.Transfer aqueous phase to fresh 1.5 mL microcentrifuge tube.
Ethanol Precipitation
1.Add 10 mg/mL of glycogen, 0.5 volumes of 7.5 M ammonium acetate, and 2.5 volumes of absolute ethanol to sample. Vortex.
2.Immediately spin at maximum speed for 20 minutes at room temperature.
3.Remove supernatant. Wash pellet with 500 mL of 80% ethanol. Spin at maximum speed for 5 minutes at room temperature.
4.Remove 80% ethanol. Wash again with 500 mL of 80% ethanol. Spin at maximum speed for 5 minutes at room temperature.
5.Air dry pellet.
6.Resuspend in 12 mL of RNase/Dnase free water. (You can store at -20°C. Save 1-2 mL aliquot to run on gel later.
Synthesis of Biotin-Labeled cRNA (Using In Vitro Transcription Reaction)
IVT Reaction (Using the ENZO BioArray High Yield RNA Transcript Labeling Kit)
1.Add the following to a fresh 1.5 mL microcentrifuge tube: x mL to give 1 mg double-stranded cDNA, 22 – x mL of RNase/Dnase free water, 4 mL of 10 X HY reaction buffer, 4 mL of 10 X Biotin labeled ribonucleotides, 4 mL of 10 X DTT, 4 mL of 10 X RNase inhibitor mix, and 2 mL of T7 RNA polymerase.
2.Incubate at 37°C for 4 – 5 hours, mixing tube every 30 – 45 minutes. (You can store at -20°C until ready to purify.
IVT Cleanup
-The preferred method for cRNA cleanup is by using RNeasy spin columns from Qiagen.
-The RNA elution step is performed twice to increase recovery.
-Ethanol precipitation (performed as described above) is performed following RNA elution and the RNA pellet is resuspended in 18 ml of water.
Quantifying the cRNA
1.Prepare 1:50 dilution of the RNA to a total of 100 ml.
2.Check OD at 260nm and 280 nm to determine sample concentration and purity. A 260/A280 ratio between 1.9 and 2.1 is acceptable.
3.The following formula is used to determine the cRNA yield.
Adjusted cRNA yield=RNA* - (total RNA#)($)
RNA* = amount of cRNA measured after IVT (mg)
total RNA# = sterting amount of total RNA (mg)
$ = fraction of cRNA reaction used in IVT
cRNA Fragmentation
1.To 20 mg of unadjusted cRNA 2 ml of 5X fragmentation buffer is added for every 8 ml of RNA and the total volume is adjusted to 40ml with water.
2.The fragmentation reaction is performed at 94C for 35 minutes and kept on ice post incubation.
3.An aliquot of cRNA is saved for gel analysis and the rest is stored at –20C until ready to perform hybridization.
Gel Electrophoresis
1.Run aliquots of purified cDNA (after ethanol precipitation), purified cRNA and fragmented cRNA on 1% agarose gel.
2.Mix RNA with loading dye and heat to 65C for 5 minutes before loading on the gel.

extract_protocol: 40 pairs of testes were pooled for two affymetrix arrays. RNA was isolated using Qiagen RNeasy mini kits. RNA was eluted in RNase free water and frozen at -80 degrees Celsius until sample quality could be assessed with the Agilent Bioanalyzer system.

tag: Background Srain

value: 129.MOLF-Chr 19

tag: Gender

value: male

tag: Tissue

value: testis

tag: Age


title: E15.5 Mouse testis_M19_2

type: RNA

state: TX

country: USA

description: E15.5 Mouse testis_M19_2

molecule: total RNA

source_name: E15.5 male genital ridges, 129.MOLF-Chr 19


title: pIC+PEI 4h

status: Public on Jan 01 2010

city: Madrid

first: Maria

middle: S

last: Soengas

address: Melchor Fernandez Almagro, 3

department: Molecular Pathology

country: Spain

institute: Spanish National Cancer Research Institute

description: SK-Mel-103 treated 4 hours with 1ug/ml of polyinosine-polycytidylic acid with polyethyleneimine

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

scan_protocol: Images were quantified using Agilent Feature Extraction Software

data_processing: Background substraction were carried out using normexp. Lowess method for within array normalization and quantiles method  for between array normalization were performed. Differentially expressed genes were obtained by using R limma package (Smyth et al., 2005) from Bioconductor project (http://www.bioconductor.org).    Smyth GK, Michaud J and Scott HS. (2005). Use of within-array replicate spots for assessing differential expression in microarray experiments.   Bioinformatics 21: 2067-2075.

organism: Homo sapiens

source_name: SK-Mel-103 Control 4h

label_protocol: Cy3 NT Cy5 treated (pIC/PEI-pIC)

growth_protocol: Dulbecco’s modified Eagle’s medium (Life Technologies, Rockville, MD, USA) supplemented with 10% fetal bovine serum (Nova-Tech Inc., Grand Island, NY, USA) penicillin (100 U/ml), streptomycin (100 U/ml)

extract_protocol: Total RNA extracted using Qiagen Rneasy mini kit following manufacturer's instructions

treatment_protocol: 1ug/ml of pIC or 1ug/ml pIC coupled with PEI

tag: SK-Mel-103 Time

source_name: pIC+PEI treated SK-Mel-103 4h

tag: SK-Mel-103 treated with 1ug/ml of polyinosine-polycytidylic acid with polyethyleneimine Age

value: 4 hours


title: pIC 4h

description: SK-Mel-103 treated 4 hours with 1ug/ml of polyinosine-polycytidylic acid

source_name: pIC treated SK-Mel-103 4h

tag: SK-Mel-103 treated with 1ug/ml of polyinosine-polycytidylic acid Age


title: E13.5 Mouse testis_M19_1

description: E13.5 Mouse testis_M19_1

source_name: E13.5 male genital ridges, 129.MOLF-Chr 19


title: E15.5 Mouse testis_129/Sv_2

description: E15.5 Mouse testis_129/Sv_2

source_name: E15.5 male genital ridges, 129/Sv


title: ZNF191 siRNA cells vs Control

city: ShangHai

first: Jianzhong

last: Li

address: GuoHe Road 325#

department: Department of Biochemical Pharmacy

country: China

institute: Second Military Medical University

description: Poor quality spots were flagged according to default FE criteria and corresponding values were removed.

hyb_protocol: 1.65microg of Cy3-labeled RNA and Cy5-labeled RNA were hybridized to each array in a 110microl total volume of hybridization buffer (Agilent Technologies) for 17 hours at 65°C. Washing was performed according to the Agilent protocol.

scan_protocol: Arrays were analyzed using the dynamic autofocus Agilent G2565BA microarray scanner and the Agilent Feature Extraction software (FE v9.4.1, GE1-v5_91_0806 protocol).

data_processing: GeneSpring 10.0 quantile normalization

source_name: human embryo kidney cells transfected with ZNF191 siRNA vectors

label_protocol: Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: ZNF191 siRNA

source_name: human embryo kidney cells transfected with empty vectors

label_protocol: Agilent’s recommended procedures for microarray-based one-color gene expression analysis were followed. Briefly, 350ng of total RNA with control RNA Spike In were amplified and labeled with Cy5-CTP using the T7-based Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies, Santa Clara, CA). After purification (RNeasy Mini Kit, QIAGEN), labeled cRNAs were quantified for yield and dye incorporation using a Nanodrop spectrophotometer.

tag: HEK293 cell line


title: E17.5 Mouse testis_129/Sv_2

description: E17.5 Mouse testis_129/Sv_2

source_name: E17.5 male genital ridges, 129/Sv


title: E15.5 Mouse testis_129/Sv_1

description: E15.5 Mouse testis_129/Sv_1


title: 2377.s2-2

city: Mississauga

first: Clement

last: Kent

state: ON

address: 3359 Mississauga Rd N

department: Biology

country: Canada

institute: Univ. of Toronto Mississauga

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: Mas 5.0

label: biotin

organism: Drosophila melanogaster

source_name: Heads M+F mutant sitters Fed Rep2

label_protocol: Standard Affymetrix

growth_protocol: Flies were tested 6-7 days post eclosion in groups with equal numbers of males and females at 25C at 60% RH as described (Shaw et al 2002, Nature 417:287-291)

extract_protocol: Trizol; RNA was extracted as described (Dierick & Greenspan 2006, Nat. Genet. 38:1023-1031) and prepared accoding to the Affymetrix protocols.

treatment_protocol: Flies were either kept on normal food overnight (Fed) or kept in vials with moistened filter paper overnight (Food deprived)

tag: Strain

value: s2; Gender:males+females; Age:6-7 days; Tissue:head; Treatment:Fed


title: E13.5 Mouse testis_129/Sv_1

description: E13.5 Mouse testis_129/Sv_1

source_name: E13.5 male genital ridges 129/Sv


title: E17.5 Mouse testis_129/Sv_1

description: E17.5 Mouse testis_129/Sv_1


title: E13.5 Mouse testis_M19_2

description: E13.5 Mouse testis_M19_2


title: 2373.Ss2-1

source_name: Heads M+F mutant sitters Food deprived Rep1

value: s2; Gender:males+females; Age:6-7 days; Tissue:head; Treatment:Food deprived


title: E13.5 Mouse testis_129/Sv_2

description: E13.5 Mouse testis_129/Sv_2


title: E15.5 Mouse testis_M19_1

description: E15.5 Mouse testis_M19_1


title: 2374.Ss2-2

source_name: Heads M+F mutant sitters Food deprived Rep2


title: 2375.Ss2-3

source_name: Heads M+F mutant sitters Food deprived Rep3


title: ZNF191-overexpressed cells vs Control

source_name: human embryo kidney cells transfected with pcDNA3-ZNF191

label_protocol: Agilent’s recommended procedures for microarray-based one-color gene expression analysis were followed. Briefly, 350ng of total RNA with control RNA Spike In were amplified and labeled with Cy3-CTP using the T7-based Low RNA Input Linear Amplification Kit, PLUS, One-Color (Agilent Technologies, Santa Clara, CA). After purification (RNeasy Mini Kit, QIAGEN), labeled cRNAs were quantified for yield and dye incorporation using a Nanodrop spectrophotometer.

extract_protocol: Total RNA was isolated using the NucleoSpin RNAII Kit (Macherey-Nagel, Düren, DE) and quantified via spectrophotometry (Nanodrop, Labtech). RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: ZNF191-overexpressed cells


title: 2372.See-3

source_name: Heads M+F sitters Food deprived Rep3

value: ee; Gender:males+females; Age:6-7 days; Tissue:head; Treatment:Food deprived


title: 2378.s2-3

source_name: Heads M+F mutant sitters Fed Rep3


title: 2370.See-1

source_name: Heads M+F sitters Food deprived Rep1


title: E17.5 Mouse testis_M19_1

description: E17.5 Mouse testis_M19_1

source_name: E17.5 male genital ridges, 129.MOLF-Chr 19


title: 2376.s2-1

source_name: Heads M+F mutant sitters Fed Rep1


title: 2371.See-2

source_name: Heads M+F sitters Food deprived Rep2


title: 2369.ee-3

source_name: Heads M+F sitters Fed Rep3

value: ee; Gender:males+females; Age:6-7 days; Tissue:head; Treatment:Fed


title: 2368.ee-2

source_name: Heads M+F sitters Fed Rep2


title: 2364.SBB-1

source_name: Heads M+F Rovers Food deprived Rep1

value: BB; Gender:males+females; Age:6-7 days; Tissue:head; Treatment:Food deprived


title: 13697189 - gdh123_b-root vs WT_b-root

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: Identification of the function and regulation of the GDH enzyme in plants

hyb_protocol: WT_b-root Cy5 / gdh123_b-root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: root - Media Hydropony NO3 6mM hygrometry 75% Temperature 21°C Light 120mE

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (col-0)  mutant (gdh1-2-3-) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: 2367.ee-1

source_name: Heads M+F sitters Fed Rep1


title: 2366.SBB-3

source_name: Heads M+F Rovers Food deprived Rep3


title: 2362.BB-2

source_name: Heads M+F Rovers Fed Rep2

value: BB; Gender:males+females; Age:6-7 days; Tissue:head; Treatment:Fed


title: 2363.BB-3

source_name: Heads M+F Rovers Fed Rep3


title: 2365.SBB-2

source_name: Heads M+F Rovers Food deprived Rep2


title: IFNg+Ado_treated4hr_mouse_macrophage_pooled_data

city: Davis

first: Kimberly

middle: E

last: Barnholt

state: CA

address: 451 E. Health Sciences Drive

department: Internal Medicine

institute: University of California, Davis

description: gene expression data from macrophages after IFNg-induced activation plus adenosine treatment

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software (GCOS) Version 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: RAW 264.7 mouse macrophage cell line treated with IFNg + adenosine for 4 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were seeded in T75 flasks and grown to 80-90% confluency in a humidified environment at 37 degrees C and 5% CO2. Cells were grown in DMEM supplemented with 10% FBS and antibiotics.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit according to the manufacturer's instructions

treatment_protocol: Growth medium was removed and new DMEM was added 1 hour before treatment. Cells treated were treated with IFNg (1000U/ml) or IFNg (1000U/ml) and adenosine (300 uM) for 4 hours.

tag: adherent cell line


title: IFNg_treated4hr_mouse_macrophage_pooled_data

description: gene expression data from macrophages after IFNg-induced activation

source_name: RAW 264.7 mouse macrophage cell line treated with IFNg for 4 hours


title: 2361.BB-1

source_name: Heads M+F Rovers Fed Rep1


title: PBMC_Fasted_Caf_11

city: Wageningen

first: Jaap

last: Keijer

state: gld

address: Marijkeweg 40

department: Human and Animal Physiology

country: Netherlands

institute: Wageningen University

description: The data table contains normalized sample (Cy5) signal intensity, and not normalized log ratio (test/reference) data

hyb_protocol: Hybridization was performed by preparing a 2x cRNA target solution containing 825 ng Cy5-labeled cRNA, 825 ng Cy3-labeled pool cRNA and 11 µL 10x blocking agent in a total volume of 52.8 µL. Then 2.2 µL fragmentation buffer was added and incubated at 60°C for 30 min. Fragmentation was stopped by adding 55 µL 2x GEx hybridization buffer HI-RPM and hybridized on 4x 44K G4131F whole genome Agilent arrays (Agilent Technologies, Inc. Santa Clara, CA) for 17 h at 65°C in Agilent hybridization chambers in an Agilent hybridization oven rotating at 10 rpm. After hybridization the arrays were subsequently washed with ‘GE wash buffer 1’ for 1 min at room temperature, ‘GE wash buffer 2’ for 1 min at approximately 37°C, acetonitrile for 1 min at room temperature and 30 s at room temperature with ‘stabilization and drying solution’ according to manufacturers protocol (Agilent Technologies).

scan_protocol: Arrays were scanned with an Agilent Microarray Scanner (Agilent Technologies). Spot intensities were quantified using Feature extraction 8.5 (Agilent Technologies).

data_processing: Median density values and background values of each spot were extracted for both the experimental samples (Cy5) and the reference samples (Cy3). Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average Cy5 signal intensity, over all arrays, lower than 2-fold average Cy5 local background were discarded. Subsequently, the remaining Cy5 signal intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

organism: Rattus norvegicus

source_name: PBMC, Fasted, Cafetaria,  11

label_protocol: 0.5 μg RNA of each sample was reverse transcribed using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent), according to the manufacturer’s protocol (all materials and reagents are from Agilent Technologies, Palo Alto, CA, USA unless stated otherwise). Half of the cDNA sample (10 µL) was used for linear RNA amplification and labelling with Cy5 or Cy3. All reactions were performed using half of the amounts indicated by the manufacturer. Briefly, a transcription master mix was prepared (7.65 µL nuclease-free water; 10 µL 4x transcription buffer; 3 µL 0.1 M DTT; 4 µL NTP mix, 3.2 µL 50% PEG; 0.25 µL RNaseOUT; 0.3 µL inorganic pyrophosphatase; 0.4 µl T7 RNA Polymerase; 1.2 µL cyanine 3-CTP or cyanine 5-CTP, total volume 30 µL). 30 µL of transcription mastermix was added to10 µL cDNA. In vitro transcription and labelling were carried out at 40°C for 2 h. The labelled cRNA samples were purified using Qiagen Rneasy mini-spin columns (Qiagen, Venlo, The Netherlands). Dye incorporation and cRNA concentration was measured using the ‘micro-array measurement mode’ of the Nanodrop spectrophotometer (NanoDrop Technologies Wilmintog, Delaware, USA). Yield of each individual sample was >825 ng and specific activity >8.0 pmol Cy3 or Cy5 per µg cRNA. All Cy3 cRNAs were pooled to serve as a standard reference pool.

growth_protocol: Blood samples (1.5-2.5 mL) were collected from rats in feeding conditions from the safena vein, using heparine in NaCl (0.9%) as anticoagulant.

extract_protocol: Total RNA from PBMC samples was extracted using Tripure Reagent (Roche Diagnostic Barcelona, Spain) and purified with a Quiagen RNesay Mini Kit spin columns (Izasa SA, Barcelona, Spain).

treatment_protocol: Immediately after blood collection, PBMC were isolated by Ficoll gradient separation.

tag: Wistar, Gender

value: Male, Age:6 months, Tissue:PBMC

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.

label_protocol: 0.5 μg RNA of each sample was reverse transcribed using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent), according to the manufacturer’s protocol_ch2 (all materials and reagents are from Agilent Technologies, Palo Alto, CA, USA unless stated otherwise). Half of the cDNA sample (10 µL) was used for linear RNA amplification and labelling with Cy5 or Cy3. All reactions were performed using half of the amounts indicated by the manufacturer. Briefly, a transcription master mix was prepared (7.65 µL nuclease-free water; 10 µL 4x transcription buffer; 3 µL 0.1 M DTT; 4 µL NTP mix, 3.2 µL 50% PEG; 0.25 µL RNaseOUT; 0.3 µL inorganic pyrophosphatase; 0.4 µl T7 RNA Polymerase; 1.2 µL cyanine 3-CTP or cyanine 5-CTP, total volume 30 µL). 30 µL of transcription mastermix was added to10 µL cDNA. In vitro transcription and labelling were carried out at 40°C for 2 h. The labelled cRNA samples were purified using Qiagen Rneasy mini-spin columns (Qiagen, Venlo, The Netherlands). Dye incorporation and cRNA concentration was measured using the ‘micro-array measurement mode’ of the Nanodrop spectrophotometer (NanoDrop Technologies Wilmintog, Delaware, USA). Yield of each individual sample was >825 ng and specific activity >8.0 pmol Cy3 or Cy5 per µg cRNA. All Cy3 cRNAs were pooled to serve as a standard reference pool.


title: PBMC_Re-feeded_Caf_15

source_name: PBMC, Re-feeded, Cafetaria,  15


title: PBMC_Fed_Caf_7

source_name: PBMC, Fed, Cafetaria, 7


title: PBMC_Re-feeded_Caf_6

source_name: PBMC, Re-feeded, Cafetaria,  6


title: PBMC_Re-feeded_Caf_12

source_name: PBMC, Re-feeded, Cafetaria,  12


title: PBMC_Re-feeded_Caf_3

source_name: PBMC, Re-feeded, Cafetaria,  3


title: PBMC_Fasted_Caf_8

source_name: PBMC, Fasted, Cafetaria,  8


title: PBMC_Fasted_Caf_14

source_name: PBMC, Fasted, Cafetaria,  14


title: PBMC_Re-feeded_Caf_9

source_name: PBMC, Re-feeded, Cafetaria,  9


title: PBMC_Fasted_Caf_2

source_name: PBMC, Fasted, Cafetaria,  2


title: PBMC_Fasted_Caf_5

source_name: PBMC, Fasted, Cafetaria,  5


title: PBMC_Fed_Caf_10

source_name: PBMC, Fed, Cafetaria, 10


title: PBMC_Re-feeded_Con_15

source_name: PBMC, Re-feeded, Control,  15


title: PBMC_Re-feeded_Con_12

source_name: PBMC, Re-feeded, Control,  12


title: PBMC_Fed_Caf_4

source_name: PBMC, Fed, Cafetaria, 4


title: PBMC_Re-feeded_Con_3

source_name: PBMC, Re-feeded, Control,  3


title: PBMC_Fed_Caf_13

source_name: PBMC, Fed, Cafetaria, 13


title: PBMC_Fasted_Con_11

source_name: PBMC, Fasted, Control,  11

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.


title: PBMC_Re-feeded_Con_9

source_name: PBMC, Re-feeded, Control,  9


title: PBMC_Re-feeded_Con_6

source_name: PBMC, Re-feeded, Control,  6


title: PBMC_Fed_Caf_1

source_name: PBMC, Fed, Cafetaria, 1


title: PBMC_Fasted_Con_14

source_name: PBMC, Fasted, Control,  14


title: PBMC_Fasted_Con_8

source_name: PBMC, Fasted, Control,  8


title: PBMC_Fasted_Con_2

source_name: PBMC, Fasted, Control,  2


title: PBMC_Fed_Con_7

source_name: PBMC, Fed, Control,  7


title: PBMC_Fed_Con_13

source_name: PBMC, Fed, Control,  13


title: PBMC_Fasted_Con_5

source_name: PBMC, Fasted, Control,  5


title: PBMC_Fed_Con_4

source_name: PBMC, Fed, Control,  4


title: Ovine GW9662 5

status: Public on Dec 28 2009

city: Augusta

first: Jing

last: Tian

state: GA

address: 1459 Laney Walker BLVD

department: Vascular Biology Center

institute: Medical College of Georgia

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45°C to the array chips (Affymetrix). Genechips were washed ans stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Microarray data were processed and normalized using RMA.

organism: Ovis aries

source_name: PAEC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 10% FBS-DMEM

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini kit.

treatment_protocol: Ovine PAECs were treated with vehicle (DMSO)  or 5μM GW9662 for 24 hours

tag: GW9662 treated


title: Ovine GW9662 2


title: Ovine GW9662 1


title: Ovine GW9662 4


title: Ovine Control 4

tag: Control


title: Ovine GW9662 3


title: Ovine Control 2


title: Bovine Control 5

organism: Bos taurus

source_name: BAEC


title: Ovine Control 1


title: Bovine Control 4


title: PBMC_Fed_Con_1

source_name: PBMC, Fed, Control,  1


title: Bovine Control 3


title: Ovine Control 5


title: Bovine Control 2


title: Bovine Control 1


title: Ovine Control 3


title: Adult_brain-5

status: Public on Dec 22 2009

city: Toronto

first: David

middle: J. H.

last: Shih

address: 686 Bay St

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

hyb_protocol: Hybridization is carried out in Illumina Intellihyb chambers at 58 °C (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina)

scan_protocol: Following hybridization, washing, and staining with streptavidin-Cy3, the chips were scanned using an Illumina BeadArray reader.

data_processing:
Data analyses were performed with Illumina BeadStudio (v3.1.7) and Bioconductor packages (v2.3) in the R programming environment (v 2.7.1). The image data were analyzed using the BeadStudio, the output files of which were imported into the R using the lumi package (v1.8.3). Probe set signal intensities were averaged. Expression profiles were then log2 transformed and quantile normalized for downstream analyses.

The Illumina Human6 V2 Expression BeadChip platform runs each sample in  duplicates, but BeadStudio has collapsed the duplicates prior to our  normalization in R. Therefore, each sample is associated with two raw TXT  files, one for each technical replicate on the chip.

Raw data files column header definitions are as follows:
Code: Array address id (corresponds to the Array_Address_Id field of GPL6102; Illumina refers to it as ProbeID in the BeadStudio summary output as well as their array annotation file)
Grn: Bead signal intensity
GrnX: X-coordinate of the bead
GrnY: Y-coordinate of the bead

label: biotinylated-UTP

source_name: Normal adult whole brain

label_protocol: Following manufacturer's instructions, 250 ng total RNA was used for cRNA in vitro transcritpion and labeling with the Illumina TotalPrep RNA Amplication Kit using biotinylated-UTP (Ambion, Austin, TX)

extract_protocol: Standard Trizol extraction

tag: Histology

tag: Age (months)


status: Public on Dec 27 2009

city: Yokohama

first: Miyako

last: Kusano

state: Kanagawa

address: 1-7-22, Suehiro, Tsurumi

country: Japan

institute: RIKEN CSRS

description: Gene expression data from leaf blades of the empty vector control for the rice Os-LBD37-overexpressor.

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

organism: Oryza sativa

source_name: The 5th and 6th leaf blades of the rice Os-LBD37-overexpressor line RK16331-13, replicate 3

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

extract_protocol: Total RNA was extracted applying ISOGEN (Nippon Gene) before using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: The rice Os-LBD37-overexpressor line RK16331-13, The 5th and 6th leaf blades, T1 generation, Hygromycin- resistant rice seedlings were hydroponically grown (Makino et al., 1983).

tag: Makino, A., Mae, T., and Ohira, K. (1983). Photosynthesis and Ribulose 1,5-Bisphosphate Carboxylase in Rice Leaves

value: Changes in Photosynthesis and Enzymes Involved in Carbon Assimilation from Leaf Development through Senescence. Plant Physiol 73, 1002-1007.


title: Adult_brain-6

tag: Gender


title: Adult_brain-3


title: Adult_brain-2


source_name: The 5th and 6th leaf blades of the rice Os-LBD37-overexpressor line RK16331-13, replicate 1


title: Adult_brain-4


title: empty vector control for rice Os-LBD37-overexpressor, replicate 3

source_name: The 5th and 6th leaf blades of the empty vector control, replicate 3

tag: The empty vector control (FOX3), The 5th and 6th leaf blades, T1 generation, Hygromycin- resistant rice seedlings were hydroponically grown (Makino et al., 1983).


source_name: The 5th and 6th leaf blades of the rice Os-LBD37-overexpressor line RK16331-13, replicate 2


title: Adult_brain-7


title: Adult_brain-1


title: empty vector control for rice Os-LBD37-overexpressor, replicate 2

source_name: The 5th and 6th leaf blades of the empty vector control, replicate 2


title: empty vector control for rice Os-LBD37-overexpressor, replicate 1

source_name: The 5th and 6th leaf blades of the empty vector control, replicate 1


title: Fetal_brain-7

source_name: Normal fetal whole brain


title: Fetal_brain-5


title: Fetal_brain-6


title: Fetal_brain-4


title: PNET45

source_name: Primary primitive neuroectodermal tumour

value: PNET


title: PNET48


title: Fetal_brain-3


title: PNET42

value: female


title: PNET41


title: PNET47


title: PNET39

value: PNET with ependymoblastic differentation


title: PNET44


title: PNET40


title: PNET37


title: Fetal_brain-2


title: PNET36


title: PNET43


title: Fetal_brain-1


title: PNET46


title: PNET35


title: PNET31


title: PNET20


title: PNET34


title: PNET22


title: PNET30


title: PNET19


title: PNET25


title: PNET17


title: PNET32


title: PNET18


title: PNET6

value: PNET with ependymal differentation


title: PNET7


title: PNET15

value: PNET/medulloepithelioma


title: PNET4


title: PNET9


title: PNET5

value: PNET/ependymoblastoma


title: PNET3


title: NORMAL - 5

status: Public on Nov 30 2009

city: Chennai

first: Rajkumar

last: T

state: Tamilnadu

address: Adyar

department: Molecular Oncology

country: India

institute: Cancer Institute (WIA)

description: hov245 Nor

hyb_protocol: The Cy3 and Cy5 labeled aRNA was used for hybridization onto the microarray chips from Stanford Functional Genomics Facility (SFGF) containing 44,544 spots, for 16 hrs in Lucidea SlidePro hybridization chamber (GE Health care) at 420C . After hybridization, slides were washed in 0.1X SSC,1X SSC  followed by 0.1X SSC and dried.

scan_protocol: The slides were scanned in ProScanArray (Perklin Elmer) . Gridding was done using Scan array Express software package (version -3). The integrated or mean intensity of signal within the spot was calculated. The files were saved as GPR files

data_processing: The Foreground Median intensity for Cy3 and Cy5, Background Median intensity for Cy3 and Cy5, spot size data were imported into BRB-ArrayTools software using the Import wizard function. Background correction was not done. Global normalization was used to median center the log-ratios on each array in order to adjust for differences in labeling intensitites of the Cy3 and Cy5 dyes

source_name: Normal cervix

label_protocol: 1µg of total RNA from tumor sample and universal RNA (Stratagene Cat No: – 740000-41) was reverse transcribed using array script  at 420C for 2 hrs to obtain cDNA using the Amino Allyl MessageAmp II aRNA amplification kit (Ambion,AM1797). The cDNA was amplified by invitro transcription in the presence of T7 RNA polymerase; aRNA thus obtained was purified and quantitated in NanoDrop. 20 µg of tumor aRNA was labeled using NHS ester of Cy5 dye and control universal aRNA was labeled using NHS ester of Cy3 dye.

extract_protocol: RNA isolation was done from all the samples using the RNeasy RNA extraction kit  (Qiagen) as per manufacturer’s instructions. RNA obtained was quantitated using Nanodrop and quality checked using Agilent Bioanalyser.

tag: NORMAL

source_name: Universal Reference RNA

tag: Stratagene's universal RNA obtained from multiple cell lines


title: NORMAL - 4

description: hov244 Nor


title: PNET24


title: CANCER - 26

source_name: Cervical cancer

tag: CANCER

value: IIB

value: Poorly differentiated carcinoma

value: High

value: RT

value: FAILED


title: CANCER - 28

value: SCC


title: CANCER - 25

value: NED


title: CANCER - 19

value: IB

value: RT+ CT


title: CANCER - 27

value: IIIB

value: Intermediate


title: CANCER - 24

value: IIA


title: CANCER - 23


title: NORMAL - 2

description: hov231 Nor


title: Stroma genes in the PDAC CAM model on day 6 (T6)

status: Public on Dec 01 2009

city: Talence

first: Martin

last: Hagedorn

address: Av des Facultes

institute: University Bordeaux 1

description: Human pancreatic adenocarcinoma cells (BxPC3) one day after grafting (T1) on the chick-chorio-allantoic membrane were compared to tumors after 6 days on the CAM (T6) to identify gene associated with tumor invasion and angiogenesis.

hyb_protocol: Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.

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

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

organism:
Gallus gallus
Homo sapiens

source_name: CAM isolated at E16 six day after grafting of BxPC3 tumor cells (same RNA as GSM362337)

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'standard protocol'

growth_protocol: Chick embryos were incubated at 37.8ºC and 75% humidity.

extract_protocol: CAMs were immediately snap-frozen in liquid nitrogen after excision. Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.

treatment_protocol: 3-5 million BxPC3 cells were deposited on the surface of the intact CAM. CAMs were excised and snap-frozen in liquid nitrogen prior to mRNA isolation

tag: CAM was isolated from a chick embryo at developmental day 16


title: Stroma genes in the PDAC CAM model on day 1 (T1)

source_name: CAM isolated at E11 one day after grafting of BxPC3 tumor cells (same RNA as GSM362328)

tag: CAM was isolated from a chick embryo at developmental day 11


title: CANCER - 17


title: CANCER - 20


title: CANCER - 18


title: CANCER - 21


title: CANCER - 22


title: NORMAL - 1

description: hov203 Nor


title: PNET2

value: male


title: CANCER - 14


title: CANCER - 12

value: RT+CT


title: CANCER - 16


title: CANCER - 15


title: CANCER - 7


title: CANCER - 6


title: CIN3 - 3


title: CANCER - 11


title: CANCER - 9


title: PNET16

value: PNET


title: CANCER - 8


title: CIN3 - 2


title: CANCER - 13


title: CANCER - 10


title: CANCER - 5


title: CIN1 - 2


title: CIN1 - 3


title: CIN1 - 4


title: CANCER - 3


title: CANCER - 4


title: CIN1 - 1


title: CIN3 - 1


title: CANCER - 2


title: CANCER - 1


title: MCF10A-MYC-serumdeprived-rep4

status: Public on Nov 24 2009

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

hyb_protocol: Hybridization was performed according to the manufacturer's recommended protocols by the UHN Microarray Centre (Toronto, Canada).

scan_protocol: Scanning was performed according to the manufacturer's recommended protocols by the UHN Microarray Centre (Toronto, Canada).

data_processing: Array data were loaded into the R statistical environment (v2.8.1) using the affy package (v1.20.0) of the BioConductor open-source project. Pre-processing employed the GCRMA algorithm as implemented in BioConductor (v2.14.1). A custom CDF mapping all probes to unique Entrez Gene IDs (hgu133plus2hsentrezg, v11.0.1) was used.

source_name: MCF10A, ectopic MYC expression, serum-deprived

label_protocol: Labeling was performed according to the manufacturer's recommended protocols by the UHN Microarray Centre (Toronto, Canada).

extract_protocol: RNA was harvested from exponentially growing MCF10A cells using TRIZOL® Reagent  (Invitrogen), as per manufacturer’s protocols.

tag: Cell-Line

value: MCF10A, Culturing Conditions:Serum-Deprived, Ectopic Gene:MYC


title: MCF10A-MYC-serumdeprived-rep3


title: MCF10A-GFP-serumdeprived-rep4

source_name: MCF10A, ectopic GFP expression, serum-deprived

value: MCF10A, Culturing Conditions:Serum-Deprived, Ectopic Gene:GFP


title: MCF10A-MYC-growing-rep3

source_name: MCF10A, ectopic MYC expression, growth conditions

value: MCF10A, Culturing Conditions:Growth, Ectopic Gene:MYC


title: MCF10A-GFP-serumdeprived-rep1


title: MCF10A-GFP-serumdeprived-rep3


title: MCF10A-GFP-growing-rep4

source_name: MCF10A, ectopic GFP expression, growth conditions

value: MCF10A, Culturing Conditions:Growth, Ectopic Gene:GFP


title: MCF10A-MYC-serumdeprived-rep2


title: MCF10A-MYC-serumdeprived-rep1


title: MCF10A-MYC-growing-rep1


title: MCF10A-GFP-growing-rep3


title: MCF10A-MYC-growing-rep2


title: MCF10A-GFP-growing-rep1


title: MCF10A-GFP-serumdeprived-rep2


title: MCF10A-GFP-growing-rep2


title: NORMAL - 3

description: HOV243 Nor


title: LAME 95

status: Public on Nov 01 2009

city: Jouy-en-Josas

first: Olivier

last: Sandra

address: Domaine de Vilvert

department: UMR BDR

hyb_protocol: Samples were then combined according to their fluorescent intensity(picomoles), denatured 2 min at 95°C, and co hybridized on the 13 257 oligoarray at 42°C for 16 to 18 hr using the Corning Pronto!TM Universal Microarray Kits according to the manufacturer~s recommendations (Fischer Scientific Bioblock, Illkirsch, France). After stringent washes to remove unbound cDNA, slides were scanned using a GenePix 4000B scanner (Axon instrument, France) and features were analysed with GenePix Pro Version 4.0 software (Axon Instrument).

scan_protocol: Feature extraction software : Genepix Pro - Scanner : Genepix 4000B

data_processing: Varmixt normalization Data were normalized by a global loess regression

label_protocol: Twenty microg of each RNA sample was converted into aminoallyl-labelled cDNA with oligo-dT primers, amino-allyl-dUTP (Sigma, Saint-Quentin-Fallavier, France) and superscript II Reverse Transcriptase (Invitrogen, Cergy-Pontoise, France). The cDNA was purified on a Microcon PCR column according to the manufacturer's protocol (Millipore, St-Quentin-en-Yvelines, France) and added to an aliquot of fluorescent dye (Cy3 or Cy5: GE HealthCare, Vélizy, France). Unused reactive sites were blocked by hydroxylamine 4M, and fluorescent probes were purified on QiaQuick columns according to the manufacturer's recommendations (Qiagen, Courtaboeuf, France). Every probe was quantified using Nanodrop spectrophotometer and quality was assessed on an agarose gel electrophoresis 1% TAE 1X. The mean lengths of the fluorescent probes were analyzed by the Typhoon Imaging system scanner (GE HealthCare, Vélizy, France).

extract_protocol: Total RNA from frozen tissue was isolated by homogenization using Trizol Reagent (Invitrogen, Cergy-Pontoise, France) according to the manufacturer's recommendations. All RNA samples were purified on Qiagen columns according to the manufacturer's protocol (RNeasy Mini kit, Qiagen, Courtaboeuf, France). Quality and integrity of total extracted and purified RNA were determined by Agilent 2100 bio analyser (Massy, France). The RIN of each RNA sample was between 7.5 to 9.5 (84).

tag: Area

value: Caruncular

source_name: FIV B99111 (IVF-ET)


title: LAME 98

source_name: FIV B9073 (IVF-ET)

source_name: IAT B9109 (AI)


title: LAME 96

source_name: FIV B99058 (IVF-ET)


title: MCF10A-MYC-growing-rep4


title: LAME 97


title: LAME 94

value: Intercaruncular


title: LAME 93

source_name: FIV B00054 (IVF-ET)


title: LAME 88


title: LAME 92

source_name: IAT B9098 (AI)


title: LAME 99


title: LAME 89


title: LAME 90

source_name: FIV B00049 (IVF-ET)


title: LAME 87


title: LAME 91


title: LAME 86


title: LAME 127

description: For the AI versus SCNT comparison, it is made by an indirect comparison for the intercaruncular zones: - with first a comparison between CJ (cycle) versus NT (SCNT) - then CJ (cycle)  versus IAJ (AI)

source_name: B857 CJ

source_name: B4 IAJ (AI)


title: LAME 126

source_name: B8 CJ


title: LAME 85


title: LAME 128

source_name: B3 IAJ (AI)


title: LAME 119

source_name: B7 CJ


title: LAME 123

source_name: B808 CJ

source_name: B6 IAJ (AI)


title: LAME 124


title: LAME 118

source_name: B873 NT (SCNT)


title: LAME 116

source_name: B888 NT (SCNT)


title: LAME 111

source_name: B904 NT (SCNT)


title: LAME 107

source_name: POOL2 NT (SCNT)

source_name: POOL1 IAJ (AI)


title: LAME 121

source_name: B5 CJ

source_name: B2 IAJ (AI)


title: LAME 112


title: LAME 108

source_name: POOL1 NT (SCNT)

source_name: POOL2 IAJ (AI)


title: LAME 109

source_name: B811 NT (SCNT)


title: LAME 113

source_name: B902 NT (SCNT)

source_name: B857 CJ


title: LAME 110


title: LAME 115


title: LAME 106


title: LAME 103

source_name: FIV B00054 (IVF-ET)


title: LAME 104

source_name: FIV B99111 (IVF-ET)


title: LAME 105


title: LAME 122


title: LAME 125

source_name: B8 CJ

source_name: B4 IAJ (AI)


title: LAME 120

source_name: B7 CJ


title: LAME 102


title: LAME 114


title: LAME 117

source_name: B873 NT (SCNT)


title: LAME 101

source_name: FIV B00049 (IVF-ET)


title: LAME 100


title: LAME 47 #2

source_name: intercaruncle B904

tag: Biotechnology

value: SCNT

source_name: caruncle B904


title: LAME 42 #2

source_name: intercaruncle B902

source_name: caruncle B902


title: LAME 46 #2

source_name: caruncle B811

source_name: intercaruncle B811


title: LAME 44 #2


title: LAME 45 #2


title: LAME 43 #2

source_name: caruncle B873

source_name: intercaruncle B873


title: LAME 48 #2


title: LAME 40 #2

source_name: caruncle B888

source_name: intercaruncle B888


title: LAME 41 #2


title: LAME 39 #2


title: LAME 36 #2

source_name: caruncle B9073

value: IVF-ET

source_name: intercaruncle B9073


title: LAME 37 #2

source_name: intercaruncle B00049

source_name: caruncle B00049


title: LAME 38 #2


title: LAME 33 #2

source_name: intercaruncle B98052

source_name: caruncle B98052


title: LAME 29 #2

source_name: intercaruncle B99111

source_name: caruncle B99111


title: LAME 28 #2

source_name: intercaruncle B2

value: AI

source_name: caruncle B2


title: LAME 30 #2


title: LAME 34 #2


title: B cells_Postmenopausal_Smoking_low BMD_rep3

status: Public on Sep 30 2009

city: Omaha

first: Peng

last: Xiao

state: NE

address: 601 N 30th ST Suite 6730

department: Biomedical Sciences & Osteoporosis Research Center

institute: Creighton University Medical Center

description: Gene expression data from low BMD postmenopausal female smoker

hyb_protocol: The microarray was washed with Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) and RMA.

source_name: B cells in blood

label_protocol: Standard Affymetrix protocol.

extract_protocol: Total RNA from B cells was extracted using Qiagen Rneasy Mini Kit (Qiagen Inc.,CA).

treatment_protocol: B cells isolated from 70mL of whole blood using a B cells positive method Dynabeads CD19 (Pan B)Kit (Invitrogen Life Technologies Dynal Biotech Inc.,CA) following manufacturer's instructions

tag: Postmenopause, smoking

tag: Low BMD


title: LAME 21 #2

source_name: caruncle B98114

source_name: intercaruncle B98114


title: LAME 31 #2

source_name: intercaruncle B99045

source_name: caruncle B99045


title: LAME 25 #2

source_name: caruncle B1

source_name: intercaruncle B1


title: LAME 22 #2


title: LAME 24 #2

source_name: caruncle B98095

source_name: intercaruncle B98095


title: LAME 20 #2

source_name: intercaruncle B99035

source_name: caruncle B99035


title: LAME 27 #2


title: LAME 26 #2


title: B cells_Postmenopausal_Smoking_low BMD_rep7


title: B cells_Postmenopausal_Smoking_low BMD_rep10


title: B cells_Postmenopausal_Smoking_low BMD_rep8


title: B cells_Postmenopausal_Smoking_low BMD_rep4


title: LAME 23 #2


title: LAME 32 #2


title: LAME 19 #2


title: B cells_Postmenopausal_Smoking_low BMD_rep9


title: B cells_Postmenopausal_Smoking_low BMD_rep1


title: B cells_Postmenopausal_Smoking_low BMD_rep6


title: LAME 35 #2

source_name: intercaruncle B9073

source_name: caruncle B9073


title: B cells_Postmenopausal_Smoking_high BMD_rep8

description: Gene expression data from high BMD postmenopausal female smoker

tag: High BMD


title: B cells_Postmenopausal_Smoking_high BMD_rep7


title: B cells_Postmenopausal_Smoking_high BMD_rep5


title: B cells_Postmenopausal_Smoking_high BMD_rep9


title: B cells_Postmenopausal_Smoking_high BMD_rep3


title: B cells_Postmenopausal_Smoking_high BMD_rep4


title: B cells_Postmenopausal_Smoking_high BMD_rep2


title: B cells_Postmenopausal_Smoking_high BMD_rep6


title: B cells_Postmenopausal_Smoking_high BMD_rep1


title: LIVER_CONTROL REP3

city: Beijing

first: yun

last: cheng

address: 100 Xi-Si-Huan-Zhong-Lu

department: Department of immunology

institute: Beijing 302 Hospital

description: 36 Rats were randomly divided into three group:control group(12), model group(12) and drug group(12). At last, randomly choosing 3 Rat from each group to do genechip analysis.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: GCOS 1.2 software

source_name: LIVER_CONTROL REP3

label_protocol: Affymetrix standard protocol

extract_protocol: Affymetrix standard protocol

tag: Strain

value: Wistar

tag: Weigh

tag: Tissue

value: liver

tag: Group

value: control


title: LIVER_ Model REP3

source_name: LIVER_ Model REP3

tag: Gender

value: model


title: ileal intestinal epithelial cells - wild type mice

status: Public on Sep 04 2009

city: Lund

first: Knut

last: Kotarsky

state: Skane

address: Tornavägen 10

department: Experimental Medical Siences

country: Sweden

institute: Lund University

description: Ileum of 4 C57/Bl6 mice were collected. Tissue sectioned and laser capture microscopy was performed using a Zeiss/Palm laser capture system.

hyb_protocol: Standard Affymetrix protocols by core facility

data_processing: Array data analysis was performed using dCHIP2004 software by user

source_name: small intestinal epithelial cell of wild type mice

extract_protocol:
Appr. 16 000 epithelial cells were collected by laser capture microscopy (Zeiss system).
Total RNA was extracted from the catapulted samples using RNA microprep kit (Stratagene). Fourty ng total RNA was expanded by two rounds of in vitro cRNA amplification

tag: strain C57Bl/6, 7-9 weeks old; ileal sample


title: LIVER_ Drug REP1

source_name: LIVER_ Drug REP1

value: Drug


title: LIVER_ Model REP2

source_name: LIVER_ Model REP2

value: male


title: LIVER_CONTROL REP1

source_name: LIVER_CONTROL REP1


title: LIVER_CONTROL REP2

source_name: LIVER_CONTROL REP2


title: LIVER_ Drug REP2

source_name: LIVER_ Drug REP2


title: colonic epithelial cells - wild type mice

description: Proximal colon of 4 C57/Bl6 mice were collected. Tissue sectioned and laser capture microscopy was performed using a Zeiss/Palm laser capture system.

scan_protocol: Standard Affymetrix protocols by core facility

source_name: colonic epithelial cells of wild type mice

tag: strain C57Bl/6, 7-9 weeks old, colon


title: B cells_Postmenopausal_Smoking_low BMD_rep5

source_name: B cells in blood


title: LIVER_ Model REP1

source_name: LIVER_ Model REP1


title: DGDG_T=2

status: Public on Sep 01 2009

first: Leo

middle: H

last: De Graaff

address: Dreijenplein 10

department: Microbiology

institute: Wageningen University and Research Centre

description:
T=2_DGDG.CEL
scanned on day 1

hyb_protocol: Washing, staining, and hybridization was done according to the Hybridization, Wash, and Stain kit (Affymetrix) according to the manufacturers' recommendations

scan_protocol: Arrays were scanned on an Agilent G2500A Gene Array scanner. Pixel value was 3 um, wavelength 570 nm. Arrays were scanned on two days (see Sample description).

data_processing: RMA values were calculated using GeneSpring 7.3.1 (Agilent Technologies), where the RMA preprocessor was used to import the .CEL files.

organism: Aspergillus niger

source_name: induced 1 mM DGDG, T=2 hours

label_protocol: Extracted totalRNA was processed following the Affymetrix user manual (Eukaryotic Target) using the One-cycle target labeling and control reagents kit (Affymetrix). 15 ug of cRNA was used for labeling.

growth_protocol: Fermentor vessels containing 2.2 liters of minimal medium, supplements, and 100 mM sorbitol were inoculated with 1.1e6 spores per mL and maintained at 30 C. Aeration was done over headspace (50 L/h) while stirring at 300 rpm until dissolved oxygen concentration dropped below 60%. Then, stirrer speed was adjusted to 750 rpm and aeration switched to sparger inlet. The culture was allowed to grow for 14 hours.

extract_protocol: Frozen mycelium was ground using a dismembrator, followed by a trizol-chloroform extraction using the Qiagen Rneasy mini columns according to the “yeast protocol”.

treatment_protocol: 14 hours after the aeration switch to sparger, 20 mL sample was removed from the fermentor. Either complex wheat gluten oil, or olive oil, or pure DGDG (digalactosyldiglycerides) dissolved in MM with 0.2% Triton X-100 as emulsifier (final concentration in fermentor 1 mM oil, 0.002% Triton X-100) was added to a fermentor. To one fermentor, only MM with 0.2% Triton X-100 (final concentration in fermentor: 0.002%) was added as negative control fermentation. At 30 minutes, 1 hour or 2 hours after induction, a 20 mL-sample was removed from the fermentor and the mycelium was snap-frozen in liquid N2 until further use.

tag: Strain 872.11


title: olive_oil_T=1

description:
T=1_olive_oil.CEL
scanned on day 2

source_name: induced 1 mM olive oil, T=1 hour


title: colonic epithelial cells - germ-free mice

description: Proximal colon of 4 C57/Bl6 germ-free mice were collected. Tissue sectioned (10 mikrom), stained with hematoxilin and laser capture microscopy was performed using a Zeiss/Palm laser capture system.

source_name: colonic epithelial cells of germ-free mice

label_protocol: Standard Affymetrix protocols by core facility

tag: strain C57/BL6, female, 7-9 weeks old,


title: olive_oil_T=2

description:
T=2_olive_oil.CEL
scanned on day 2

source_name: induced 1 mM olive oil, T=2 hours


title: DGDG_T=0

description:
T=0_DGDG.CEL
scanned on day 1

source_name: not induced, fermentor DGDG


title: olive_oil_T=0

description:
T=0_olive_oil.CEL
scanned on day 2

source_name: not induced, fermentor olive oil


title: triton_T=2

description:
T=2_triton.CEL
scanned on day 2

source_name: induced 0.002% Triton X-100, T= 2 hours


title: wheat_oil_T=2

description:
T=2_wheat_oil.CEL
scanned on day 2

source_name: induced 1 mM wheat oil, T= 2 hours


title: DGDG_T=0_5

description:
T=0_5_DGDG.CEL
scanned on day 1

source_name: induced 1 mM DGDG, T=30 min


title: triton_T=0

description:
T=0_triton.CEL
scanned on day 1

source_name: not induced, fermentor triton


title: triton_T=1

description:
T=1_triton.CEL
scanned on day 1

source_name: induced 0.002% triton X-100, T= 1 hour


title: ileal intestinal epithelial cells - germ-free mice

description: Ileum of 4 C57/Bl6 germ-free mice were collected. Tissue sectioned, stained with hematoxilin and laser capture microscopy was performed using a Zeiss/Palm laser capture system.

source_name: ileal intestinal epithelial cells of germ-free mice

tag: strain C57/BL6, female, 7-9 weeks old, ileum, germ-free mice


title: olive_oil_T=0_5

description:
T=0_5_olive_oil.CEL
scanned on day 2

source_name: induced 1 mM olive oil, T=30 min


title: triton_T=0_5

description:
T=0_5_triton.CEL
scanned on day 2

source_name: induced 0.002% triton X-100, T= 30 min


title: DGDG_T=1

description:
T=1_DGDG.CEL
scanned on day 1

source_name: induced 1 mM DGDG, T=1 hour


title: B cells_Postmenopausal_Smoking_high BMD_rep10

source_name: B cells in blood


title: SJL_cornea_rep3

city: Iowa City

first: Markus

last: Kuehn

state: IA

address: 375 Newton Road

department: Ophthalmology and Visual Sciences

institute: University of Iowa

hyb_protocol: According to the standard Affymetrix protocol

data_processing: Data were processed and normalized using ArrayAssist software.

source_name: strain: SJL/J; thick cornea

growth_protocol: Mice were maintained on a 4% fat NIH 31 diet provided ad libitum, and were housed in cages containing Cellu-dri bedding. The environment was kept at 21°C with a 12-h light:12-h dark cycle

extract_protocol: RNA was extracted, treated with DNase I, and purified (Aurum Total RNA Mini Kit; Bio-Rad Laboratories).

tag: strain

value: SJL/J; adult; male, thick cornea


title: wheat_oil_T=0

description:
T=0_wheat_oil.CEL
scanned on day 2

source_name: not induced, fermentor wheat oil


title: LIVER_ Drug REP3

source_name: LIVER_ Drug REP3


title: B6_cornea_rep1

scan_protocol: According to the standard Affymetrix protocol

source_name: strain: C57Bl/6J

value: C57Bl/6J; adult; male


title: B6_cornea_rep3

label_protocol: According to the standard Affymetrix protocol


title: wheat_oil_T=1

description:
T=1_wheat_oil.CEL
scanned on day 2

source_name: induced 1 mM wheat oil, T= 1 hour


title: KS_cornea_rep1

source_name: strain: C57BLKS/J; thin cornea

value: C57BLKS/J; adult; male, thin cornea


title: SJL_cornea_rep2


title: Placental Control (c)

city: Seattle

first: Bradford

last: Stadler

state: WA

address: 815 Mercer Street; South Building, Room A581

department: Biochemistry

institute: University of Washington

description: Sample labeling, hybridization, scanning, data extraction and processing was performed at Agilent Technologies (Santa Clara, CA).

hyb_protocol: Follow manufacturer's protocol at the manufacturer's web site at http://www.agilent.com/; Briefly, samples were lyophilized with speed-vac, resuspended in sterile H2O; Hybridization buffer and blocking agent were added and the samples were heated to 100 degree C for 5, then placed on ice, then hybridized at 55 degree for 20 hours in an Agilent SureHyb chamber in a rotating hybridization oven

scan_protocol: Follow manufacturer's protocol at the manufacturer's web site at http://www.agilent.com/; Briefly, the slides were scanned at 5µM resolution

data_processing: Follow manufacturer's protocol at the manufacturer's web site at http://www.agilent.com/; additionally, data extraction and value definition are described in Wang et al., RNA. 2007 Jan;13(1):151-9. The normalization was internal for each array and consists of background subtraction and derivation of the gTotal Gene Signal from an average of multiple probe and probe replicates for each miRNA on the array. This is reflected in the gTotal Gene Signal for each miRNA Value for each array.

source_name: Human placental total RNA

label_protocol:
Follow manufacturer's protocol at the manufacturer's web site at http://www.agilent.com/
Briefly, 100 ng total RNA was dephosphorylated, labeled with Cy3 for 2 hrs at 16 degrees C, and desalted with a spin column

extract_protocol: Cells were harvested from tissue culture plates and total RNA was extracted using Trizol; samples were DNase treated and resuspended in sterile H2O

tag: Human placenta total RNA, purchased from Ambion. Catalog # AM7950. Lot #030301510J. Female donor, caucasian, age 35.


title: Placental Control (b)


title: wheat_oil_T=0_5

description:
T=0_5_wheat_oil.CEL
scanned on day 2

source_name: induced 1 mM wheat oil, T= 30 min


title: H7 Diff

description: Cells were grown, treated and harvested and total RNA was prepared at University of Washington. Sample labeling, hybridization, scanning, data extraction and processing was performed at Agilent Technologies (Santa Clara, CA).

source_name: hESC Cell Line (H7, WA07)

growth_protocol: 4 Days culture on matrigel-coated plates w/ DMEM + 20% FBS to induce undirected differentiation

tag: Human embryonic stem cell line


title: H14 Undiff

source_name: hESC Cell Line (H14, WA14)

growth_protocol: 4 Days culture on matrigel-coated plates w/ MEF-CM (mouse embryonic fibroblast-conditioned media) to maintain hESC growth


title: H7 Undiff

treatment_protocol: 4 Days culture on matrigel-coated plates w/ MEF-CM (mouse embryonic fibroblast-conditioned media) to maintain hESC growth


title: HSF6 Diff

source_name: hESC Cell Line (HSF6, UC06)

treatment_protocol: 4 Days culture on matrigel-coated plates w/ DMEM + 20% FBS to induce undirected differentiation


title: KS_cornea_rep3


title: BG01 Diff

source_name: hESC Cell Line (BG01, hESBGN-01)


title: H14 Diff


title: KS_cornea_rep2


title: NTera-2 Diff

source_name: NTera-2 (Human embryonal carcinoma cell line)

growth_protocol: 4 Days culture on matrigel-coated plates w/ DMEM + 20% FBS and 5 µM retinoic acid to induce differentiation (differentiation is directed towards ectodermal lineages)

tag: Transformed embryonal carcinoma cell line derived from human teratocarcinoma


title: HSF6 Undiff


title: BG01 Undiff


title: BG03 Diff

source_name: hESC Cell Line (BG03, hESBGN-03)


title: NTera-2 Undiff

growth_protocol: 4 Days culture on matrigel-coated plates w/ MEF-CM (mouse embryonic fibroblast-conditioned media) to maintain NTera-2 growth


title: SJL_cornea_rep1


title: B cells_Postmenopausal_Smoking_low BMD_rep2

tag: Postmenopause, smoking


title: B6_cornea_rep2


title: H9 Undiff

source_name: hESC Cell Line (H9, WA09)


title: H9 Diff


title: BG03 Undiff


title: H3Cter binding gcn5delta/clr3delta cells KCl 60 min

status: Public on Aug 01 2009

type: genomic

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

institute: Karolinska Institute

description: immunoprecipitated material using antibodies against Histone H3 (H3Cter)

hyb_protocol: Fragmented genomic DNA  was hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR according to  Affymetrix chromatin immunoprecipitation assay protocol. 2005-2006

scan_protocol: According to affymetrix chromatin immunoprecipitation assay protocol. 2005-2006

data_processing: Tiling analysis software (TAS) from Affymetrix

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S. pombe strain Hu1036 grown to mid log phase in YES at 25°C, then treated with KCl (final concentration 1M) 60 min

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol: affymetrix chromatin immunoprecipitation assay protocol. 2005-2006

growth_protocol: Yeast cells grow at 25°C in YES medium to log phase.

extract_protocol: Experimental procedure was essentially according to Robyr and Grunstein, Method 31 (2003) 83-89

treatment_protocol: Treatment for each sample is described in "source name"

tag: genotype

value: h90, gcn5delta::KanMX4, clr3delta::KanMX6, leu1-32, ura4-D18, ade6-M210


title: H1 Diff

description: Cells were grown, treated and harvested and total RNA was prepared at University of Washington.  Sample labeling, hybridization, scanning, data extraction and processing was performed at Agilent Technologies (Santa Clara, CA).

source_name: hESC Cell Line (H1, WA01)


title: H3Cter binding wild type cells KCl 60 min

source_name: S. pombe strain Fy368 grown to mid log phase in YES at 25°C, then treated with KCl (final concentration 1M) 60 min


title: H13 Diff

source_name: hESC Cell Line (H13, WA13)


title: Gcn5-myc binding

description: immunoprecipitated material using anti-myc antibodies

source_name: S. pombe strain Hu2020 grown to mid log phase in YES at 25°C

value: h-, gcn5-myc::KanMX6, leu1-32, ura4-D18, ade6-M210


title: H3Cter binding gcn5 delta cells KCl 60 min

source_name: S. pombe strain Hu0799 grown to mid log phase in YES at 25°C, then treated with KCl (final concentration 1M) 60 min

value: h-, gcn5delta::KanMX4, leu1-32, ura4-D18, ade6-M210


title: Input

description: whole cell lysate, used to correct for any hybridization bias, also refered to as input.

source_name: S. pombe strain Fy368 grown to mid log phase in YES at 25°C


title: H3K14Ac binding wild type cells KCl 60 min

description: immunoprecipitated material using antibodies against acetylated lysine 14 on Histone H3(H3K14Ac), antibodies from Upstate


title: H3K14Ac binding gcn5delta/clr3delta cells KCl 60 min

description: immunoprecipitated material using antibodies against acetylated lysine 14 on Histone H3(H3K14Ac)


title: Placental Control (a)


title: H13 Undiff


title: BG02 Diff

source_name: hESC Cell Line (BG02, hESBGN-02)


title: RTSV-infected TW16-69, rep 2

status: Public on Aug 31 2009

city: Metro Manila

first: IL-RYONG

last: CHOI

address: DAPO Box 7777

country: Philippines

institute: International Rice Research Institute

description: Biological replication 2 of 2, RTSV-infected TW16-69 at 7DAI

hyb_protocol: Hybridization kit: in situ hybridization plus Hybridization manufacturer: Agilent Technologies Hybridization manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray Scanner Manufacturer: Agilent Technologies Software: Scanner Control software Manual: Agilent Technologies

data_processing:
Software: Feature Extraction version 8.1.1.1
Manufacturer: Agilent Technologies
Manual: Agilent Technologies

organism: Oryza sativa Indica Group

source_name: Mock TW16-69, rep 2

label_protocol:
Kit: Low RNA Input Linear Amplification kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol:
Pre-treatment:
Growth environment: greenhouse
Growth: pot culture (D: 120mm x H: 150mm)
Growth media: Soil collected fielf of International Rice Research Institute, Philippines. Autoclaved prior to use.
No. of seedlings per pot: 5
Light condition: Natural conditions
Temperature: 28±3℃

Post-treatment:
Growth environment: greenhouse
Light condition: Natural conditions
Temperature: 28±3℃
Growth length: 7 DAI

extract_protocol:
Separation: trimming
Extraction source: frozen
Extraction source: leaves pooled from 5 individual plants
Kit: TRIzol
Manual: Invitrogen

treatment_protocol:
Growth stage: two leaves visible
Light condition: Natural conditions
Temperature: 28±3℃
Virus inoculation: mock inoculation (virus-free GLH)
Virus inoculation: 3 virus-free GLH (Nephotettix virescence) per 1 seedling
GLH inoculation: 24 hours

tag: Near isogenic line from Utri Merah and Taiching Native 1

value: two youngest leaves

source_name: RTSV TW16-69, rep 2

treatment_protocol:
Virus inoculation: 24 hours
Growth stage: two leaves visible
Light condition: Natural conditions
Temperature: 28±3℃
Virus inoculation: rice tungro spherical virus
Virus inoculation: 3 viruliferous GLH (Nephotettix virescence) per 1 seedling


title: untreated-none-2

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

description: Response of human bronchial epithelial cells to chronicly applied low doses of cigarette smoke condensate and subsequent demethylation agent

hyb_protocol: 10 μg of cRNA/sample were hybridized for 16 h at 45°C. Washing and staining with streptavidin-conjugated phycoerythrin were done using a GeneChip Fluidics Station 400 (Affymetrix).

scan_protocol: Standard Affymetrix procedures using an Affymetrix GeneChip Scanner 3000

data_processing: Raw gene expression data generated by the GeneChip Operating Software (Affymetrix) were normalized for all probe sets on the array using the gcrma method.

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: none

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA using Affymetrix GeneChip One-Cycle Target Labeling and Control Reagents according to the manufacturer’s protocol.

growth_protocol: BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.

extract_protocol: Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol. RNA was isolated from BEAS-2B cells treated chronically for one month with CSC or DMSO as well as untreated cells. The quality of RNA samples was tested using capillary electrophoresis (Agilent Bioanalyzer, Switzerland).

treatment_protocol: BEAS-2B cells were treated twice a week with 5µg/ml of CSC. Control cell line was treated with the same volume of DMSO.

tag: Treatment

value: untreated

tag: Demethylation

tag: Replicate


title: H1 Undiff


title: dmso-none-2

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: none

value: dmso


title: csc-none-3

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: none

value: csc


title: untreated-aza-2

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Demethylation: aza

value: aza


title: H3K14Ac binding gcn5 delta cells KCl 60 min


title: RTSV-infected TW16-4, rep 1

description: Biological replication 1 of 2, RTSV-infected TW16-4 at 7DAI

source_name: Mock TW16-4, rep 1

tag: Tissue

source_name: RTSV TW16-4, rep 1

treatment_protocol:
Growth stage: two leaves visible
Light condition: Natural conditions
Temperature: 28±3℃
Virus inoculation: rice tungro spherical virus
Virus inoculation: 3 viruliferous GLH (Nephotettix virescence) per 1 seedling
Virus inoculation: 24 hours


title: BG02 Undiff


title: dmso-aza-1

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: aza


title: RTSV-infected TW16-4, rep 2

description: Biological replication 2 of 2, RTSV-infected TW16-4 at 7DAI

source_name: RTSV TW16-4, rep 2

source_name: Mock TW16-4, rep 2


title: csc-none-1

tag: normal human bronchial epithelial cells (BEAS-2B)


title: untreated-none-1


title: csc-none-2


title: untreated-aza-1


title: RTSV-infected TW16-69, rep 1

description: Biological replication 1 of 2, RTSV-infected TW16-69 at 7DAI

source_name: Mock TW16-69, rep 1

source_name: RTSV TW16-69, rep 1


title: untreated-none-3


title: csc-aza-1

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Demethylation: aza


title: untreated-aza-3


title: csc-aza-2


title: dmso-aza-2


title: dmso-none-1


title: untreated: m4: i3: d06

description: Effects of chronic exposure of human bronchial epithelial cells to low doses of cigarette smoke condensate

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 4; Replicate: 3

growth_protocol: BEAS-2B cells were cultured in Bronchial Epithelial cell Growth Medium (BEGM), prepared by supplementing Bronchial Epithelial Basal Medium with SingleQuotesTM (Lonza, Switzerland) which contains retinoic acid, epidermal growth factor, epinephrine, transferrin, triiodothyronin, insulin, hydrocortisone, antimicrobial agents, and bovine pituitary extract. In addition, BEGM medium was supplemented with 10% FCS, penicillin/streptomycin and 2mM glutamate.Ten lung cancer cell lines were cultured in RPMI-1640 medium (Gibco, Invitrogen), supplemented with 10 % FCS and penicillin/streptomycin.

treatment_protocol: BEAS-2B cells were treated twice a week with 20µg/ml of CSC (~IC20 in MTT assay, data not shown). Control cell line was treated with the same volume of DMSO. After the addition of CSC or DMSO, cells were maintained in the same medium until the next passage.

tag: Month

tag: Batch


title: dmso-aza-3


title: untreated: m4: i2: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 4; Replicate: 2


title: untreated: m2: i2: d07

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 2; Replicate: 2


title: dmso: m3: i3: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 3; Replicate: 3


title: untreated: m4: i1: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 4; Replicate: 1


title: untreated: m1: i3: d08

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 1; Replicate: 3


title: untreated: m3: i3: d06

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 3; Replicate: 3


title: untreated: m3: i2: d04

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 3; Replicate: 2


title: untreated: m3: i1: d06

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 3; Replicate: 1


title: untreated: m2: i3: d03

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 2; Replicate: 3


title: untreated: m1: i2: d01

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 1; Replicate: 2


title: untreated: m2: i1: d07

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 2; Replicate: 1


title: dmso: m4: i3: d06

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 4; Replicate: 3


title: untreated: m1: i1: d02

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: untreated; Month: 1; Replicate: 1


title: dmso: m4: i1: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 4; Replicate: 1


title: dmso-none-3

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Demethylation: none


title: dmso: m4: i2: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 4; Replicate: 2


title: dmso: m1: i3: d08

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 1; Replicate: 3


title: dmso: m3: i1: d04

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 3; Replicate: 1


title: dmso: m3: i2: d04

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 3; Replicate: 2


title: csc: m4: i3: d06

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 4; Replicate: 3


title: dmso: m2: i2: d03

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 2; Replicate: 2


title: dmso: m1: i1: d02

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 1; Replicate: 1


title: dmso: m2: i1: d07

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 2; Replicate: 1


title: csc: m4: i1: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 4; Replicate: 1


title: csc: m4: i2: d06

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 4; Replicate: 2


title: csc: m3: i3: d05

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 3; Replicate: 3


title: dmso: m1: i2: d01

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 1; Replicate: 2


title: dmso: m2: i3: d03

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: dmso; Month: 2; Replicate: 3


title: csc: m3: i2: d04

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 3; Replicate: 2


title: csc: m2: i3: d03

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 2; Replicate: 3


title: csc: m1: i3: d08

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 1; Replicate: 3


title: csc: m1: i2: d01

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 1; Replicate: 2


title: SW2-un-5

scan_protocol: Standard Affymetrix procedures using a Hewlett-Packard scanner

source_name: SW2 Cell line

growth_protocol: Ten lung cancer cell lines (from squamous cell carcinomas: Calu 1, Hotz, U1752; from adenocarcinoma: Calu 6, ZL25, and Calu3; from small cell lung cancer: SW2; from adeno-squamous carcinoma: A549, H125; and from large cell carcinoma: H 460) were kindly provided by Dr. R. Stahel (University of Zurich, Switzerland). Cell lines were cultured in RPMI-1640 medium (Gibco, Invitrogen), supplemented with 10 % FCS and penicillin/streptomycin.

extract_protocol: Total RNA from cell lines was extracted using the RNeasy Mini kit (Qiagen, Switzerland) according to the manufacturer’s protocol.

treatment_protocol: Ten lung cancer cell lines were treated with both the demethylating agent 5AzaC (Fluka, Switzerland) and the inhibitor of histone deacetylases TSA, (Sigma, Country.) (5AzaC/TSA treatment). Cells were treated three times with 1µM 5AzaC for 24 hours (day 1, 3 and 5 with addition of fresh medium on day 2 and 4), whereas TSA (10 nM) was added only once on day 5 (along with the 3rd dose of 5AzaC). On day 1, cells were ~30% confluent to allow them to propagate and replicate their DNA in the presence of 5AzaC. After one day of recovery (day 7), cells were harvested and total RNA was extracted.

tag: Cell line

tag: RunID


title: Calu6-un-3

source_name: Calu6 Cell line


title: SW2-aza-2

value: Aza


title: SW2-un-3


title: csc: m2: i1: d07

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 2; Replicate: 1


title: Calu6-aza-3


title: SW2-aza-4


title: Calu6-un-2


title: SW2-aza-3


title: csc: m2: i2: d03

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 2; Replicate: 2


title: Calu6-aza-1


title: Calu1-aza-3

source_name: Calu1 Cell line


title: Calu1-un-3


title: csc: m1: i1: d01

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 1; Replicate: 1


title: Calu6-un-1


title: Calu6-aza-2


title: U1752-un-2

source_name: U1752 Cell line


title: U1752-un-1


title: SW2-un-4


title: Calu1-un-1


title: Calu1-aza-1


title: Calu1-aza-2


title: U1752-aza-1


title: Calu1-un-2


title: U1752-aza-3


title: U1752-aza-2


title: Hotz-un-2

source_name: Hotz Cell line

value: Hotz


title: Hotz-un-1


title: Calu3-aza-1

source_name: Calu3 Cell line


title: Hotz-aza-3


title: ZL25-un-3

source_name: ZL25 Cell line


title: Calu3-un-1


title: Calu3-aza-2


title: Hotz-aza-1


title: Calu3-aza-3


title: Hotz-aza-2


title: Calu3-un-2


title: ZL25-un-1


title: ZL25-aza-2


title: ZL25-aza-3


title: H460-un-2

source_name: H460 Cell line


title: H125-un-3

source_name: H125 Cell line


title: H125-un-2


title: U1752-un-3


title: csc: m3: i1: d04

source_name: normal human bronchial epithelial cells (BEAS-2B); Treatment: csc; Month: 3; Replicate: 1


title: H460-un-1


title: ZL25-aza-1


title: H460-un-3


title: H125-aza-2


title: H125-un-1


title: H125-aza-3


title: Hotz-un-3


title: H460-aza-3


title: epimastigotes

city: Athens

first: Todd

middle: A

last: Minning

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

description: axenic culture in LIT medium

hyb_protocol: Prehybridization  The T. cruzi microarrays were obtained from the Pathogen Functional Resources Facility.  The microarray description is available at http://pfgrc.tigr.org.  The microarrays were prehybridized immediately preceding hybridization as described on the PFGRC website.  Briefly, arrays are incubated in prehybridization solution (4X SSC, 40% formamide, 0.1% SDS, 0.5% BSA, and 25 mM Tris-HCl, pH 8.0) at 42oC for 1 h.  Slides are then washed at room temperature in 0.2% SDS, followed by 3 washes with water, and dried by centrifugation.    Microarray Hybridization  Six hybridizations were performed for each life-cycle stage.  The hybridizations consisted of three dye-swap experiments from three independent samples (biological replicates).  In each case, the experimental sample was from a single life-cycle stage and the control sample was an equal mixture of all four life-cycle stages.  Hybridizations were performed as previously described [3].  Briefly, equal volumes of control and experimental labeled cDNAs were combined with mouse CoT1-DNA (Life Technologies), poly(A)-DNA (Amersham Pharmacia Biotech), and hybridization buffer to yield final concentrations of 4X SSC, 40% formamide, 0.1% SDS, 0.5 µg/µl CoT1-DNA, 0.5 µg/µl poly(A)-DNA, and 25 mM Tris-Cl, pH 8.0).  Samples were heat denatured at 95oC for 3 m, centrifuged at 12,000 X g at room temperature for 1 m, applied to the prehybridized array in a MAUI mixer chamber (BioMicro Systems, Inc., Salt Lake City, Utah), placed in a MAUI hybridization apparatus and hybridized at 42oC for 16-20 h with constant mixing.  Following hybridization, the array, with attached mixer, was removed from the MAUI apparatus, the mixer was removed from the array, and the array was washed once for 2 m at room temperature in 300 ml PBS with 0.05% SDS, followed by 3 washes for 2 m each at room temperature in 300 ml PBS, and one wash for 1 m at room temperature in 300 ml 0.2X PBS.  The slide was then dried by centrifugation.

scan_protocol: Immediately following hybridization and washing, arrays were scanned on a ScanArray 4000 (GSI Lumonics, Wilmington, MA) at the Integrated Biotech Laboratories at the University of Georgia.  Microarrays were scanned at multiple laser and PMT settings in each channel to obtain TIFF images of matching sensitivity in the two channels.

data_processing: Microarray scans were quantified using the the TIGR SpotFinder module of TM4 (www.tm4.org).  The signal intensity files generated in SpotFinder were imported into the TIGR MIDAS module of TM4 (www.tm4.org) where they were filtered at an integrated intensity threshold of 10,000.  Within-slide replicate spots were checked for consistency.  Inconsistent within-slide replicate spots were assigned zero intensities and consistent within-slide replicate spots were averaged.  Normalization was performed by locally weighted least squares regression (LOWESS) within each sub-grid. The MeV files thus generated in MIDAS were paired by dye-swap and checked for dye-swap consistency.  Spots with greater than 2 standard deviations difference in log2 ratios between dye-swap replicates were removed from analysis.  Spots that were within threshold consistency were averaged.  These analyses generated 12 result files, one from each biological replicate for each of the four life-cycle stages.  Thus, each row in the final result files corresponded to eight independent measurements (2 channels X 2 replicate spots X 2 dye-swap hybridizations).  Using the TIGR MeV software the result files were filtered to remove genes with zero intensity in more than 3 result files, leaving 10,256 spots.  The genes and experiments were median centered and normalized.  To find spots with significant, repeatable, between-stage variation we analyzed the result files by Significance Analysis of Microarrays (SAM) [36] with a median false discovery rate (FDR) of 0.06071% and a 90th percentile FDR of 0.40582%.

label: Cy3, Cy5

organism: Trypanosoma cruzi

source_name: epimastigotes

label_protocol: Labeled first strand cDNA was synthesized from the total RNA samples using Superscript™ II reverse transcriptase (Life Technologies, Grand Island, NY) as previously described [3].  Briefly, 10 µg RNA were combined with 2 µg oligo-d(T) (Life Technologies), brought to 10 µl with water, denatured at 70oC for 10 m, and cooled on ice.  Final 30 ul reactions were assembled with final concentrations of 1X First Strand Buffer (Life Technologies), 10 mM DTT (Life Technologies), 0.5 mM dATP, dCTP, and dGTP (Amersham Pharmacia Biotech, Piscataway, NJ), 0.1 mM dTTP (Amersham Pharmacia Biotech), 0.1 mM Cy3- or Cy5-dUTP (Amersham Pharmacia Biotech), and 13.3 U/µl Superscript II reverse transcriptase (Life Technologies).  The reaction mixtures were incubated at 42oC for 2 h and stopped with the addition of 1.5 µL 20 mM EDTA.  To degrade the RNA template, 1.5 µL 500 mM NaOH were added and the reactions were heated at 70°C for 10 m.  The reactions were neutralized by adding 1.5 µL 500 mM HCl, and unincorporated fluorescent nucleotides were removed using GFX columns per the manufacturer’s instructions (Amersham Pharmacia Biotech).  The purified products were eluted using 50 µL TE, pH 8.0, and the labeled cDNA was completely dried in a SpeedVac (Savant Instruments, Holbrook, NY, USA) and resuspended in 10 µL water.

extract_protocol: Total RNA was isolated from parasites with the High Pure Total RNA Isolation Kit (Roche) per the manufacturer's instructions, including on-column DNase I digestion.

label: Cy5, Cy3

source_name: reference


title: H460-aza-1


title: A549-un-3

source_name: A549 Cell line


title: A549-aza-2


title: H460-aza-2


title: A549-un-1


title: A549-aza-3


title: A549-un-2


title: metacyclics

description: axenic culture in Grace's medium

source_name: metacyclics


title: trypomastigotes

description: in vitro cultured trypomastigotes from infected Vero cells

source_name: trypomastigotes


title: A549-aza-1


title: ZL25-un-2


title: amastigotes

description: in vitro cultured amastigotes from infected Vero cells

source_name: amastigotes


title: established NPC cell line_NPC-TW01

status: Public on Jul 30 2009

city: Miaoli County

first: Shu-Chen

last: Liu

address: 35 Keyan Road,Zhunan

country: Taiwan

institute: National Health Research Institutes

description: Test/Reference ratio data was derived from two experiments, including one dye-swap experiment.

hyb_protocol: Cy3- or Cy5-labeled cDNA was hybridized to Human 46K cDNA array at 42°C for 16 hrs in 25% formamide–5X SSC [1X SSC is 0.15 M NaCl plus 0.015 M sodium citrate]–0.1% sodium dodecyl sulfate [SDS]–0.1mg/ml salmon sperm DNA). For posthybridization processing, the array was washed twice (5 min each time, 42°C) in buffer I (2X  SSC, 0.1% SDS), followed by a wash (10 min, room temperature) in buffer II (0.1X  SSC, 0.1X  SDS). Finally, the array was washed four times (1 min each time) in buffer III (0.1X SSC).

scan_protocol: Scanned with a GenePix 4000B laser scanner (Axon), the array images were then processed with GenePix Pro software (Axon).

data_processing: Exogenous spike-in ScoreCard controls (Amersham Biosciences) were used to obtain a regression curve that relates the mean intensity to concentration of mRNA target in the sample. The normalization strategy has two steps. First, we used the above regression curve to select a set of constantly expressed genes. With these, hybridization signals were normalized using the robust scatter-plot smoothing regression (LOWESS) and median absolute deviation-based scale normalization. The constantly expressed gene set was also used to fit an intensity-dependent normalization curve for scale adjustment of each pin-group within each slide.

source_name: NPC-derived cell line

label_protocol: 40 μg total RNA from one NPC sample was needed for a dye-swap experiment. RNA was reverse transcribed to Cy3- or Cy5-labeled cDNA with the CyScribe First Strand labeling kit (Amersham Bioscience) in the presence of Cy3-dUTP or Cy5-dUTP (Amersham Bioscience). Oligo(dT)18-20 was used as the primer for reverse transcription.

growth_protocol: Primary nasopharyngeal epithelial cells were grown onto collagen-coated culture vessels and fed with Defined keratinocyte serum-free medium (GIBCO BRL). NPC cell lines were grown in Dulbecco's modified Eagle's medium (GIBCO BRL) supplemented with 10% FBS (Hyclone).

extract_protocol: Total RNA was extracted with the RNeasy purification kit (Qiagen)

tag: Nasopharyngeal carcinoma cells

tag: NPC-derived cell line

source_name: universal reference RNA

tag: pooled from 32 normal nasopharyngeal epithelial cell strains


title: established NPC cell line_HONE1


title: Primary nasopharyngeal carcinoma cell strain_025

source_name: primary NPC cell strain

tag: primary NPC cell strain


title: established NPC cell line_CNE1


title: 1 fmole of miRNAs

type: mixed

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

description: We hybridized different amounts of microRNAs from the mirVana miRNA Reference Panel v9.1 to microarrays.

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al) inside a MAUI mixer in a MAUI hybridization system (BioMicro® System Inc Salt Lake City UT USA).     Thomson J.M. Parker J. Perou C.M. and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer® Waltham MA USA).

data_processing: BlueFuse (BlueGenome Cambridge UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.

organism: synthetic construct

source_name: miRNAs from mirVana miRNA Reference Panel v9.1

label_protocol: Different amounts of miRNA standards in the panel  were ligated to a synthetic linker 5’-pCU-DY547-3’.   DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

extract_protocol: commercially available

tag: synthetic RNAs coresponding to human miRNAs

label: Alexa Fluor® 647

molecule: other

source_name: synthetic

tag: synthetic DNA oligos corrresponding to human miRNAs


title: 0.2 fmole of miRNAs


title: established NPC cell line_CNE2


title: Primary nasopharyngeal carcinoma cell strain_023


title: Primary nasopharyngeal carcinoma cell strain_015


title: Primary nasopharyngeal carcinoma cell strain_010


title: Primary nasopharyngeal carcinoma cell strain_008


title: Primary nasopharyngeal carcinoma cell strain_026


title: Primary nasopharyngeal carcinoma cell strain_009


title: Primary nasopharyngeal carcinoma cell strain_014


title: established NPC cell line_NPC-TW06


title: 13689486 - lpp2_ABA2 vs lpp2_C2

status: Public on Jul 01 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

description: Transcriptomic study of lpp2 KO mutant in response to abcsisic acid

hyb_protocol: lpp2_C2 Cy5 / lpp2_ABA2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: leaf - media : 2/3 soil 1/3 vermiculite Hygrometry : 60-80% temperature : 22°C light : 8h photoperiod

treatment_protocol: Name:Control - control buffer - control buffer,water+silwet:quantity 0.05percent time 2min . 2min and 1h of incubation, 2min and 2h of incubation

tag: Arabidopsis thaliana (col-0)  mutant (Atlpp2.2 -/-) - age:6week

treatment_protocol: Name:ABA - abiotic stress - hormone,abiotic stress,aba:quantity 0.01mM time 1min . Soaking 1 min then incubation 3 hours


title: 13688922 - Col0_C2 vs Col0_ABA2

hyb_protocol: Col0_ABA2 Cy5 / Col0_C2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  - age:6week


title: Primary nasopharyngeal carcinoma cell strain_003


title: 13688923 - Col0_ABA2 vs Col0_C2

hyb_protocol: Col0_C2 Cy5 / Col0_ABA2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.