title: UV-B irradiated mbd101 vs B73 control

source_name: UV-B irradiated mbd101 plants

tag: mbd101 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm.


title: UV-B irradiated chc101 vs UV-B irradiated B73

status: Public on Dec 31 2008

type: RNA

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: Hybridization was highly correlated as assessed from correlations between median signal intensities (r2 = 0.97 for both dyes; data not shown) and between log2 ratios of the signals (r2 = 0.94; data not shown).

hyb_protocol: Array hybridizations were carried out according to the manufacturer's instructions. For the experiments, Agilent Technologies microarrays were used, they contained 43,451 maize 60-mer probes and each slide had the same pattern of probes in quadruplicate (4x44 version), that were used to hybridize independent biological samples. Specifically, each array was hybridized with two samples, each of 0.825 μg labeled target cRNA, for 17 hours at 60°C. The samples were hybridized in a double loop design arrangement, as described by Kerr and Churchill et (2001).

scan_protocol: Data were acquired with an Agilent G2565BA scanner.

data_processing:
The slide images were processed with Feature Extraction (Agilent), including normalization of the data. After filtering out saturated spots flagged by Feature Extraction, and for each slide, we first calculated thresholds for background hybridizations with the internal negative controls.
All statistical analyses were performed using either the R package (http://www.r-project.org/) or Microsoft EXCEL (http://www.microsoft.com)

molecule: total RNA

organism: Zea mays

source_name: UV-B irradiated chc101 plants

label_protocol: Target cRNA was prepared and labeled with either Cy-3 or Cy-5 dye (PerkinElmer, Boston, MA, USA) from 3 μg of total RNA using an Agilent Low RNA Input Fluorescent Linear Amplification Kit. Array hybridizations were carried out according to the manufacturer's instructions.

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen, Carlsbad CA) and purified by ethanol precipitation.  The yield and RNA purity were determined spectrophotometrically with a SpectraMax 250 plate spectrophotometer (Molecular Devices, Sunnyvale, CA, USA) and verified by agarose gel analysis.

tag: chc101 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm.

source_name: UV-B irradiated B73 plants

tag: B73 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with CA filters to exclude wavelengths lower than 280 nm.


title: UV-B irradiated mbd101 vs mbd101 control

source_name: mbd101 control plants

tag: mbd101 plants were germinated under supplemental visible lighting to 10% of summer noon radiation without UV-B in greenhouse conditions. After that, plants were illuminated with UV-B lamps using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) for 8 h; leaf samples were collected immediately after the radiation treatment. The bulbs were covered with PE filters to exclude wavelengths lower than 320 nm.


title: 13690840 - 24_dor2_drought_3 vs 6_Col0_drought_3

status: Public on Sep 11 2008

city: Evry Cedex

first: Agnes

last: Yu

address: 2 rue Gaston Cremieux CP 5708

department: URGV

country: France

institute: INRA

description: Modification of the transcriptome by the eskimo mutation and response to stress.

hyb_protocol: 6_Col0_drought_3 Cy5 / 24_dor2_drought_3 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,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

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 indirect, amplification=yes, 1 ug total RNA used for amplification (Ambion kit) to produce aRNA. 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 : Fertiss clods watered w. nutritive solution pH=5,8 ; conductivity=1,6 ; <K+>2,6mEq ; <Ca2+>3,1mEq ; <Mg2+>0,8mEq ; <NH4+>0,9mEq ; <H+>1,8mEq ; <NO3->5,1mEq ; <PO4H2->0,9mEq ; <SO42->0,9mEq hygrometry : 70% temperature : 22°C light : 2:00am-3:00am=70microE ; 3:00am-5:00pm=130microE ; 5:00pm-6:00pm=70microE ; 6:00pm-2:00am=0microE

extract_protocol: Qiagen RNeasy Plant Mini Kit

treatment_protocol: Name:drought - environmental treatment - hydrometry,water:time 3day .

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

tag: Arabidopsis thaliana (columbia)  mutant (salk_089531) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: H187-63AR 1 (565)

status: Public on Dec 19 2008

city: Baltimore

first: Christine

last: Hann

state: MD

address: 1550 Orleans St., CRB2, Rm 562

department: Oncology

country: USA

institute: Johns Hopkins University School of Medicine

hyb_protocol: Hybridized to an Illumina Sentrix Human Ref-8 Expression Beadchip

scan_protocol: The hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using an Illumina BeadStation 500GX Genetic Analysis Systems scanner.

data_processing: Two biological samples from each tumor (H187 and H187-63AR) were hybridized to an Illumina BeadChip. Image level analysis and preprocessing was performed using BeadStudio software (Bead StudioGene Expression Module Users Guide May 2006) according to manufacturers recommendations. The preprocessing algorithm includes outlier detection and produces an average expression value for each oligonucleotide probe sequence.  Data analysis and plotting of the expression profiles was done using the R statistical platform and the Bioconductor bioinformatics software project. Pre-processed expression values were transformed to a log scale and averaged over replicates for each of the experimental conditions.  Genes having log2 fold changes greater than 1 were used to cluster samples for comparison and presentation.

organism: Homo sapiens

source_name: lung cancer cell line xenograft

label_protocol: Single stranded RNA was generated and labeled by incorporating biotin-16-UTP.

growth_protocol: 5 million of H187 or H187-63AR cells were injected subcutaneously into nude mice

extract_protocol: Total RNA was extracted from snap frozen tissues using Trizol and purified with RNAeasy columns. RNA quality was assessed using an Agilent 2100 Bioanalyzer. RNA samples were labeled according to the chip manufacturer’s recommended protocols. In brief, 0.5 μg of total RNA from each sample was labeled using the Illumina TotalPrep RNA Amplification Kit in a process of cDNA synthesis and in vitro transcription

treatment_protocol: Once the tumors reached >200mm3 the mice were treated with ABT-737 or vehicle control.  All the samples shown here were from mice treated with vehicle control.

tag: H187 derivative xenograft


title: H187-63AR 1 (513)


title: WT control

status: Public on Jul 04 2008

city: La Jolla

first: Biao

last: Wang

state: CA

address: 10010 North Torrey Pines Road

institute: Salk Institute

description: WT control

hyb_protocol: Affymetrix Hybridization control kit

scan_protocol: GeneChip Scanner 3000

data_processing: Affymetrix MAS5

organism: Drosophila melanogaster

source_name: Male fly heads, WT control

label_protocol: biotin

extract_protocol: RNA extracted from fly heads after 24hour fasting using RNAeasy kit

tag: WT control, male ~5 day old


title: TORC mutant

description: TORC mutant

source_name: Male fly heads, TORC mutant

tag: TORC mutant, male ~5 day old


title: 13697321 - sqe1 1 vs ler 1

status: Public on Jan 24 2009

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

description: Arabidopsis transcriptome microarray from wild type and mutant plants.

hyb_protocol: ler 1 Cy5 / sqe1 1 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%

source_name: ler 1

label_protocol: labeling

growth_protocol: leaf - Media=Pots	 hygrometry=60% RH	 Temperature=23ºC	 Light=130 uM/m2seg Long Day

treatment_protocol: no treatment

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

source_name: sqe1 1

tag: Arabidopsis thaliana (landsberg erecta) yes - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: TORC Neuronal resuce

description: TORC Neuronal resuce

source_name: Male fly heads, TORC neuronal resuce

tag: TORC Neuronal resuce, male ~5 day old


title: Spleen of 15-week garlic-fed mouse, biological rep2

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

description: Gene expression data from spleen of mice fed on raw garlic powder for 15 weekds

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with EukGE_2v5-450 protocol.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

organism: Mus musculus

source_name: 8-week old male C57BL/6J mouse fed on garlic diet for 15 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: 8-week old mice were divided into two groups and maintained in the SPF facility of Institute of Biomedical Sciences, Taipei, Taiwan, ROC.

extract_protocol: Total RNA was isolated from the frozen spleen tissues using Qiagen RNeasy Midi Kit according to the manufacturer's instructions.

treatment_protocol: Garlic bulbs (husk free) were homogenized with a food processor, lyophilized, ground into dry powder in a mortar with pestle and stored at -20 C until use. Mice were fed (ad libitum) a diet containing 20/ vitamin free casein, 10% sucrose, 53.95% cornstarch, 7% soybean oil, 3.5% AIN93 regular mineal mix, 1% AIN93G vitamin mix, 0.25% choline bitartrate (41.1% choline), 0.3% L-cysteine with the adition of 4% cellulose (Control diet) or 4% lyophilized raw garlic powder (Garlic diet). At the end of the 15-week treatment period, mice were sacrifificed by cervical dislocation to collect spleens, which were snap-frozen in liquid nitrogen for storage at -80C until use.

tag: Starting age

value: 8-week old; Gender male; Strain:C57BL/6J; Organ:Spleen

tag: Diet

value: 4% lyophilized raw garlic powder in a special diet (Yeh and Yeh, 1994)


title: 13690836 - 2_Col0_control_2 vs 20_dor2_control_2

hyb_protocol: 20_dor2_control_2 Cy5 / 2_Col0_control_2 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.

treatment_protocol: Name:control - genetic treatment - o nacl,nacl 200 mm:time 0 . NaCl was added to MS liquid (final concentration 200mM) for 30 min or 1 h. For control, no salt was added. Treatment was stopped by freezing in liquid nitrogen.


title: 13690842 - 21_dor2_control_3 vs 3_Col0_control_3

hyb_protocol: 3_Col0_control_3 Cy5 / 21_dor2_control_3 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.


title: Rescue control

description: Rescue control

source_name: Male fly heads, rescue control

tag: Rescue control, male ~5 day old


title: 13690874 - 25_dor2_salt_1 vs 7_Col0_salt_1

hyb_protocol: 7_Col0_salt_1 Cy5 / 25_dor2_salt_1 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.

treatment_protocol: Name:salt_150mM - environmental treatment - abiotic stress,salt:quantity 150mM time 4day . 60% of clods saturation with 150mM NaCl; NaCl added at day 3, stressed from day 3 to day 7; Experiment started with plants which were bolting. At T0 clods were saturated with nutritive solution (100% of saturation), then clods were weighted twice a day and saturation were adjusted at the maximum observed targeted saturation for a group of plants: 60% for the control plants, 20% for the water stressed plants (as examples plants were 40% saturated at day3 and 25% at day 5), 60% with mM NaCl for the salt treated plants (starting when % of saturation of drought treated plants were<to the control plants, at day 3)


title: 13690875 - 7_Col0_salt_1 vs 25_dor2_salt_1

hyb_protocol: 25_dor2_salt_1 Cy5 / 7_Col0_salt_1 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.


title: 13690841 - 3_Col0_control_3 vs 21_dor2_control_3

hyb_protocol: 21_dor2_control_3 Cy5 / 3_Col0_control_3 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.


title: 13690835 - 20_dor2_control_2 vs 2_Col0_control_2

hyb_protocol: 2_Col0_control_2 Cy5 / 20_dor2_control_2 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.


title: 13690839 - 6_Col0_drought_3 vs 24_dor2_drought_3

hyb_protocol: 24_dor2_drought_3 Cy5 / 6_Col0_drought_3 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.


title: UV-B irradiated mbd101 vs UV-B irradiated chc101


title: UV-B irradiated mbd101 vs UV-B irradiated B73


title: H187 Control 1 (57)

tag: H187 xenograft


title: Rat right heart, 18 hour High Dose, Rep 5

status: Public on Jul 01 2008

city: Charlotte

first: Nina

last: Sanapareddy

state: NC

address: 1542 Garden Terrace

institute: Carolinas Healthcare system

description: Gene expression data from Rat right ventricle, 18 hour high dose microsphere bead induced PE sample.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on RAT 230-2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner G2500A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Rattus norvegicus

source_name: Rat right heart

label_protocol: Sample was labelled by Affymetrix standard protocol

extract_protocol: Trizol RNA extraction followed  by Qiagen Clean up.

treatment_protocol: Rat hearts were dissected out, briefly profused, right ventricle was dissected, snapfrozen in Liquid nitrogen. Frozen tissue was powdered in liquid nitrogen and tissue powder used for RNA extraction.

tag: Heart tissue


title: Rat right heart, 18 hour High Dose, Rep 4


title: Rat right heart, 18 hour High Dose, Rep 2


title: Rat right heart, 18 hour Low Dose, Rep 3

description: Gene expression data from Rat right ventricle, 18 hour Low dose microsphere bead induced PE sample.


title: 13690833 - 23_dor2_drought_2 vs 5_Col0_drought_2

hyb_protocol: 5_Col0_drought_2 Cy5 / 23_dor2_drought_2 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.


title: H187 Control 2 (58)


title: 13690834 - 5_Col0_drought_2 vs 23_dor2_drought_2

hyb_protocol: 23_dor2_drought_2 Cy5 / 5_Col0_drought_2 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.


title: Rat right heart, 18 hour Low Dose, Rep 2


title: Rat right heart, 18 hour Vehicle, Rep 5

description: Gene expression data from Rat right ventricle, 18 hour vehicle sample.


title: Rat right heart, 18 hour High Dose, Rep 3


title: Rat right heart, 18 hour High Dose, Rep 1


title: Rat right heart, 18 hour Vehicle, Rep 2


title: Rat right heart, 18 hour Vehicle, Rep 1


title: 13690830 - 8_Col0_salt_2 vs 26_dor2_salt_2

hyb_protocol: 26_dor2_salt_2 Cy5 / 8_Col0_salt_2 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.


title: Rat right heart, 18 hour Low Dose, Rep 4


title: Rat right heart, 18 hour Low Dose, Rep 1


title: Rat right heart, 6 hour High Dose, Rep 4

description: Gene expression data from Rat right ventricle, 6 hour high dose microsphere bead induced PE sample.


title: Rat right heart, 18 hour Vehicle, Rep 4


title: Rat right heart, 18 hour Low Dose, Rep 5


title: Rat right heart, 18 hour Vehicle, Rep 3


title: Rat right heart, 6 hour High Dose, Rep 5


title: Rat right heart, 6 hour High Dose, Rep 3


title: 13690832 - 26_dor2_salt_2 vs 8_Col0_salt_2

hyb_protocol: 8_Col0_salt_2 Cy5 / 26_dor2_salt_2 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.


title: Rat right heart, 6 hour High Dose, Rep 2


title: Rat right heart, 6 hour Low Dose, Rep 4

description: Gene expression data from Rat right ventricle, 6 hour Low dose microsphere bead induced PE sample.


title: Rat right heart, 6 hour High Dose, Rep 1


title: Rat right heart, 6 hour Low Dose, Rep 1


title: Rat right heart, 6 hour Low Dose, Rep 3


title: Rat right heart, 6 hour Low Dose, Rep 5


title: Rat right heart, 6 hour Vehicle, Rep 4

description: Gene expression data from Rat right ventricle, 6 hour vehicle sample.


title: Rat right heart, 2 hour High Dose, Rep 3

description: Gene expression data from Rat right ventricle, 2 hour high dose microsphere bead induced PE sample.


title: UV-B irradiated chc101 vs. mbd101 control

hyb_protocol: Array hybridizations were carried out according to the manufacturer's instructions. For the experiments, Agilent Technologies microarrays were used, they contained 43,451 maize 60-mer probes and each slide had the same pattern of probes in quadruplicate (4x44 version), that were used to hybridize independent biological samples. Specifically, each array was hybridized with two samples, each of 0.825 μg labeled target cRNA, for 17 hours at 60°C. The samples were hybridized in a double loop design arrangement, as described by Kerr and Churchill et (2001).


title: Rat right heart, 6 hour Low Dose, Rep 2


title: Rat right heart, 2 hour High Dose, Rep 5


title: Rat right heart, 2 hour High Dose, Rep 2


title: Rat right heart, 2 hour Low Dose, Rep 4

description: Gene expression data from Rat right ventricle, 2 hour Low dose microsphere bead induced PE sample.


title: Rat right heart, 6 hour Vehicle, Rep 3


title: Rat right heart, 2 hour Low Dose, Rep 3


title: Rat right heart, 2 hour Vehicle, Rep 5

description: Gene expression data from Rat right ventricle, 2 hour vehicle sample.


title: Rat right heart, 2 hour Low Dose, Rep 2


title: Rat right heart, 2 hour Vehicle, Rep 2


title: Rat right heart, 2 hour High Dose, Rep 1


title: Rat right heart, 6 hour Vehicle, Rep 5


title: Rat right heart, 6 hour Vehicle, Rep 1


title: Brain RMLC MOE430A

city: Zurich

first: Gino

last: Miele

address: Schmelzbergstrasse 12

department: Institute for Neuropathology

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: Affymetrix Hybridisation, wash and stain procedures

scan_protocol: Affymetrix 3000 scanner

label: Biotin

source_name: Brain, 145 days post-inoculation

label_protocol: Affymetrix 1-cycle kit

extract_protocol: Trizol

tag: Strain


title: Rat right heart, 2 hour Vehicle, Rep 4


title: Brain MockC MOE430A


title: Rat right heart, 6 hour Vehicle, Rep 2


title: Rat right heart, 2 hour Low Dose, Rep 1


title: Brain RMLB MOE430A


title: Brain MockB MOE430A


title: Rat right heart, 2 hour Low Dose, Rep 5


title: Brain RMLA MOE430A


title: Brain RMLC MOE430B


title: Brain RMLA MOE430B


title: Nitrosomonas europaea_exposure to 1 uM NaCN_60min_biological rep2

status: Public on Jun 21 2008

city: Corvallis

first: Sunhwa

last: Park

state: OR

address: 116 Gilmore

department: Biological & Ecological Eng.

institute: Oregon State University

description: the activity of nitrosomonas europaea was inhibited about more than 50% by 1 uM NaCN.

hyb_protocol: 0.16 ug/ul of six cDNA samples (three controls and three treatments) were hybridized at 60 rpm for 16 h to zebrafish genome array.

scan_protocol: The arrays were scanned using Affymetrix GeneChip Scanner 3000 at 570 nm.

data_processing: The data was analyzed with single array analysis in GeneChip Operating Software (GCOS)

organism: Nitrosomonas europaea

source_name: N. europaea cultured in Batch reactor with growth medium containing 5 mM total ammonia source,exposure to 1 uM NaCN, 60 min.

label_protocol: The 3’termini of the cDNA fragmentation were labeled with 7.5 mM GeneChip DNA labeling reagent (Affymetrix).

growth_protocol: (NH4)2SO4 (5 mM) in growth medium, 700rpm, in gas-tight 2 L glass Kimax media bottle, injection of 1 uM NaCN

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.

treatment_protocol: Injection of 1uM NaCN, 60min

tag: N. europaea cells cultured in 25 mM (NH4)2SO4 (50 mM of total NH4+) were harvested in mid to late exponential phase. The cells (OD600=0.07) were washed twice with 40 mM NaHPO4 (pH 7.8) to remove residual ammonia and were resuspended in 2 L of fresh growth medium containing 5 mM total ammonia. The cells (1 L) were then placed in 2 L glass Kimax media bottle, one for control and another one for treatment condition. Once the cell reached pseudo-steady state in Batch-reactor, the 1 uM NaCN was injected into just treatment reactor.


title: Brain RMLB MOE430B


title: Brain MockA MOE430B


title: Nitrosomonas europaea_exposure to 1 uM NaCN_60min_biological rep1


title: Rat right heart, 2 hour Vehicle, Rep 3


title: Nitrosomonas europaea_exposure to 1 uM NaCN_60min_biological rep3


title: Nitrosomonas europaea_control condition_60min_biological rep2

description: showed 100 % activity of nitrosomonas europaea, control condition(no inhibition), Quasi-steady state

source_name: N. europaea cultured in Batch reactor with growth medium containing 5 mM total ammonia source, 60 min

growth_protocol: (NH4)2SO4 (5 mM) in growth medium, 700rpm, in gas-tight 2 L glass Kimax media bottle, no injection of cyanide

treatment_protocol: No injection of cyanide, 60min


title: Rat right heart, 2 hour Vehicle, Rep 1


title: Nitrosomonas europaea_control condition_60min_biological rep1

extract_protocol: Total cellular RNA was extracted using 1 ml of Trizol (Ambion Inc., Austin, TX) following the manufacturer’s instructions. The extracted RNA was then purified with RNeasy Mini kit (Qiagen Inc., Valencia, CA.) and treated with RNase-free DNase ? (Qiagen) to digest residual chromosomal DNA.


title: Rat right heart, 2 hour High Dose, Rep 4


title: Nitrosomonas europaea_control condition_60min_biological rep3


title: Brain MockA MOE430A


title: 13281162 - fls2KO flg22 30min vs fls2KO flg22 20min

status: Public on Jun 02 2008

description: Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants?

hyb_protocol: fls2KO flg22 20min Cy5 / fls2KO flg22 30min 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

source_name: fls2KO flg22 20min

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 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: plantlet - Media : 1x MS medium (Duchefa), 1% sucrose and 1% agar. 12-day old seedlings were then transferred to liquid MS medium for 2 days before flg22 treatment (two seedlings per 500 ul of medium in wells of 24-well-plates). Temperature : 22°C Light : continuous light conditions of 60 uE m-2 sec-1 (Biolux lamps)

extract_protocol: Pool of extract, fls2KO flg22 20min set1:0.5ug, fls2KO flg22 20min set2:0.5ug.

treatment_protocol: Name:flg22 - compound based treatment - biotic stress,flg22:quantity 0.01mM . flg22 = flagellin derived elicitor Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg22 peptide to a final concentration of 10 uM.; Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.

tag: Arabidopsis thaliana (columbia)  mutant (fls2 KO) - age:14daydev.stage (Boyes et al. Plant Cell 2001):seedling

source_name: fls2KO flg22 30min

extract_protocol: Pool of extract, fls2KO flg22 30min set1:0.5ug, fls2KO flg22 30min set2:0.5ug.


title: Brain MockC MOE430B


title: 13281165 - Col-0 flg22 20min vs Col-0 flg22 10min

hyb_protocol: Col-0 flg22 10min Cy5 / Col-0 flg22 20min 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.

source_name: Col-0 flg22 10min

extract_protocol: Pool of extract, Col-0 flg22 10min set1:0.5ug, Col-0 flg22 10min set2:0.5ug.

tag: Arabidopsis thaliana (columbia)  - age:14daydev.stage (Boyes et al. Plant Cell 2001):seedling

source_name: Col-0 flg22 20min

extract_protocol: Pool of extract, Col-0 flg22 20min set1:0.5ug, Col-0 flg22 20min set2:0.5ug.


title: 13281177 - fls2KO flg22 60min vs fls2KO flg22 30min

hyb_protocol: fls2KO flg22 30min Cy5 / fls2KO flg22 60min 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.

source_name: fls2KO flg22 60min

extract_protocol: Pool of extract, fls2KO flg22 60min set1:0.5ug, fls2KO flg22 60min set2:0.5ug.


title: 13281063 - fls2KO flg22 30min vs fls2KO flg22 60min

hyb_protocol: fls2KO flg22 60min Cy5 / fls2KO flg22 30min 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.


title: 13281164 - Col-0 flg22 10min vs Col-0 flg22 20min

hyb_protocol: Col-0 flg22 20min Cy5 / Col-0 flg22 10min 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.


title: 13281161 - fls2KO flg22 20min vs fls2KO flg22 30min

hyb_protocol: fls2KO flg22 30min Cy5 / fls2KO flg22 20min 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.


title: 13281059 - fls2KO flg22 20min vs fls2KO flg22 10min

hyb_protocol: fls2KO flg22 10min Cy5 / fls2KO flg22 20min 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.

source_name: fls2KO flg22 10min

extract_protocol: Pool of extract, fls2KO flg22 10min set1:0.5ug, fls2KO flg22 10min set2:0.5ug.


title: 13281056 - fls2KO flg22 10min vs fls2KO 0min

hyb_protocol: fls2KO 0min Cy5 / fls2KO flg22 10min 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.

source_name: fls2KO 0min

extract_protocol: Pool of extract, fls2KO 0min set1:0.5ug, fls2KO 0min set2:0.5ug.


title: 13281057 - fls2KO flg22 10min vs fls2KO flg22 20min

hyb_protocol: fls2KO flg22 20min Cy5 / fls2KO flg22 10min 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.


title: 13281169 - Col-0 flg22 60min vs Col-0 flg22 30min

hyb_protocol: Col-0 flg22 30min Cy5 / Col-0 flg22 60min 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.

source_name: Col-0 flg22 30min

extract_protocol: Pool of extract, Col-0 flg22 30min set1:0.5ug, Col-0 flg22 30min set2:0.5ug.

source_name: Col-0 flg22 60min

extract_protocol: Pool of extract, Col-0 flg22 60min set1:0.5ug, Col-0 flg22 60min set2:0.5ug.


title: 13279351 - Col-0 flg22 10min vs Col-0 0min

hyb_protocol: Col-0 0min Cy5 / Col-0 flg22 10min 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.

source_name: Col-0 0min

extract_protocol: Pool of extract, Col-0 0min set1:0.5ug, Col-0 0min set2:0.5ug.


title: 13281049 - Col-0 0min vs Col-0 flg22 10min

hyb_protocol: Col-0 flg22 10min Cy5 / Col-0 0min 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.


title: Brain MockB MOE430B


title: 13281050 - fls2KO 0min vs fls2KO flg22 10min

hyb_protocol: fls2KO flg22 10min Cy5 / fls2KO 0min 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.


title: 13281062 - Col-0 flg22 30min vs Col-0 flg15 30min

hyb_protocol: Col-0 flg15 30min Cy5 / Col-0 flg22 30min 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.

source_name: Col-0 flg15 30min

extract_protocol: Pool of extract, Col-0 flg15 30min (1):0.5ug, Col-0 flg15 30min (2):0.5ug.

treatment_protocol: Name:flg15 30min - compound based treatment - biotic stress,flg15:quantity 10000mM time 30min . Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg15 peptide to a final concentration of 10 uM. Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.

tag: Arabidopsis thaliana (columbia)  - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

extract_protocol: Pool of extract, Col-0 flg22 30min (1):0.5ug, Col-0 flg22 30min (2):0.5ug.

treatment_protocol: Name:flg22 30min - compound based treatment - biotic stress,flg22:quantity 10000mM time 30min . Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg22 peptide to a final concentration of 10 uM. Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.


title: 13279310 - dcl4-1 flg22 30min vs dcl4-1 flg15 30min

hyb_protocol: dcl4-1 flg15 30min Cy5 / dcl4-1 flg22 30min 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.

source_name: dcl4-1 flg15 30min

extract_protocol: Pool of extract, dcl4-1 flg15 30min (1):0.5ug, dcl4-1 flg15 30min (2):0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (dcl4-1) - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: dcl4-1 flg22 30min

extract_protocol: Pool of extract, dcl4-1 flg22 30min (1):0.5ug, dcl4-1 flg22 30min (2):0.5ug.


title: 13279313 - ler flg22 30min vs ler flg15 30min

hyb_protocol: ler flg15 30min Cy5 / ler flg22 30min 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.

source_name: ler flg15 30min

extract_protocol: Pool of extract, ler flg15 30min (1):0.5ug, ler flg15 30min (2):0.5ug.

tag: Arabidopsis thaliana (landsberg erecta)  - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: ler flg22 30min

extract_protocol: Pool of extract, ler flg22 30min (1):0.5ug, ler flg22 30min (2):0.5ug.


title: 13278974 - Col-0 flg22 30min vs Col-0 flg22 60min

hyb_protocol: Col-0 flg22 60min Cy5 / Col-0 flg22 30min 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.


title: 13281060 - Col-0 flg15 30min vs Col-0 flg22 30min

hyb_protocol: Col-0 flg22 30min Cy5 / Col-0 flg15 30min 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.


title: 13279309 - dcl4-1 flg15 30min vs dcl4-1 flg22 30min

hyb_protocol: dcl4-1 flg22 30min Cy5 / dcl4-1 flg15 30min 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.


title: 13278968 - ler flg15 60min vs ler flg22 60min

hyb_protocol: ler flg22 60min Cy5 / ler flg15 60min 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.

source_name: ler flg22 60min

extract_protocol: Pool of extract, ler flg22 60min (1):0.5ug, ler flg22 60min (2):0.5ug.

treatment_protocol: Name:flg22 60min - compound based treatment - biotic stress,flg22:quantity 10000mM time 60min . Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg22 peptide to a final concentration of 10 uM. Plantlets were collected 60min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.

source_name: ler flg15 60min

extract_protocol: Pool of extract, ler flg15 60min (1):0.5ug, ler flg15 60min (2):0.5ug.

treatment_protocol: Name:flg15 60min - compound based treatment - biotic stress,flg15:quantity 10000mM time 60min . Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg15 peptide to a final concentration of 10 uM. Plantlets were collected 60min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.


title: 13279312 - ler flg15 30min vs ler flg22 30min

hyb_protocol: ler flg22 30min Cy5 / ler flg15 30min 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.


title: 13281163 - rdr6-1 flg15 30min vs rdr6-1 flg22 30min

hyb_protocol: rdr6-1 flg22 30min Cy5 / rdr6-1 flg15 30min 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.

source_name: rdr6-1 flg22 30min

extract_protocol: Pool of extract, rdr6-1 flg22 30min (1):0.5ug, rdr6-1 flg22 30min (2):0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (rdr6-1) - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: rdr6-1 flg15 30min

extract_protocol: Pool of extract, rdr6-1 flg15 30min (1):0.5ug, rdr6-1 flg15 30min (2):0.5ug.


title: 13279315 - dcl1-9 flg22 60min vs dcl1-9 flg15 60min

hyb_protocol: dcl1-9 flg15 60min Cy5 / dcl1-9 flg22 60min 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.

source_name: dcl1-9 flg15 60min

extract_protocol: Pool of extract, dcl1-9 flg15 60min (1):0.5ug, dcl1-9 flg15 60min (2):0.5ug.

tag: Arabidopsis thaliana (landsberg erecta)  mutant (dcl1-9) - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: dcl1-9 flg22 60min

extract_protocol: Pool of extract, dcl1-9 flg22 60min (1):0.5ug, dcl1-9 flg22 60min (2):0.5ug.


title: 13281175 - ler flg22 60min vs ler flg15 60min

hyb_protocol: ler flg15 60min Cy5 / ler flg22 60min 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.


title: 13278966 - rdr6-1 flg22 30min vs rdr6-1 flg15 30min

hyb_protocol: rdr6-1 flg15 30min Cy5 / rdr6-1 flg22 30min 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.


title: 13279314 - dcl1-9 flg15 30min vs dcl1-9 flg22 30min

hyb_protocol: dcl1-9 flg22 30min Cy5 / dcl1-9 flg15 30min 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.

source_name: dcl1-9 flg22 30min

extract_protocol: Pool of extract, dcl1-9 flg22 30min (1):0.5ug, dcl1-9 flg22 30min (2):0.5ug.

source_name: dcl1-9 flg15 30min

extract_protocol: Pool of extract, dcl1-9 flg15 30min (1):0.5ug, dcl1-9 flg15 30min (2):0.5ug.


title: 13366448 - dcl4-1 flg15 30min vs dcl4-1 flg22 30min

growth_protocol: whole plant - Media: 1x MS medium (Duchefa), 1% sucrose and 1% agar. 12-day old seedlings were then transferred to liquid MS medium for 2 days (two seedlings per 500 ul of medium in wells of 24-well-plates) and then treated. Temperature: 22°C Light: continuous light conditions of 60 uE m-2 sec-1 (Biolux lamps).

extract_protocol: Pool of extract, dcl4-1 flg22 30min set1:0.5ug, dcl4-1 flg22 30min set2:0.5ug.

treatment_protocol: Name:flg22 10(u)M - compound based treatment - compound addition,flg22:quantity 10000mM time 30min . Add 10uM flagellin in liquid MS medium and harvest samples at 30 minutes.

extract_protocol: Pool of extract, dcl4-1 flg15 30min set1:0.5ug, dcl4-1 flg15 30min set2:0.5ug.

treatment_protocol: Name:flg15 10(u)M - compound based treatment - compound addition,flg15:quantity 10000mM time 30min . Add 10uM flagellin in liquid MS medium and harvest samples at 30 minutes.


title: 13275765 - dcl1-9 flg15 60min vs dcl1-9 flg22 60min

hyb_protocol: dcl1-9 flg22 60min Cy5 / dcl1-9 flg15 60min 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.


title: 13366156 - Col0 flg22 30min vs Col0 flg15 30min

hyb_protocol: Col0 flg15 30min Cy5 / Col0 flg22 30min 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.

source_name: Col0 flg15 30min

extract_protocol: Pool of extract, Col0 flg15 30min set1:0.5ug, Col0 flg15 30min set2:0.5ug.

source_name: Col0 flg22 30min

extract_protocol: Pool of extract, Col0 flg22 30min set1:0.5ug, Col0 flg22 30min set2:0.5ug.


title: 13690380 - dcl2-dcl3-dcl4 flag22 set2 vs Col flag22 set2

hyb_protocol: Col flag22 set2 Cy5 / dcl2-dcl3-dcl4 flag22 set2 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 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

source_name: Col flag22 set2

extract_protocol: Col flag22 set2:2.43ug.

treatment_protocol: Name:flag 22 dcl234 - biotic stress - compound addition,flg22:time 30min . 14-day old were transferred into MS liquid medium and then supplied with flg22 peptide to a final concentration 100nM.; Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.

tag: Arabidopsis thaliana (columbia)  - age:14daydev.stage (Boyes et al. Plant Cell 2001):1-5 rosette leaf,10-15 rosette leaf

source_name: dcl2-dcl3-dcl4 flag22 set2

extract_protocol: dcl2-dcl3-dcl4 flag22 set2:5.2ug.

tag: Arabidopsis thaliana (columbia)  mutant (dcl2-1 dcl3-1 dcl4-2) - age:14daydev.stage (Boyes et al. Plant Cell 2001):1-5 rosette leaf,10-15 rosette leaf


title: 13690379 - Col flag22 set2 vs dcl2-dcl3-dcl4 flag22 set2

hyb_protocol: dcl2-dcl3-dcl4 flag22 set2 Cy5 / Col flag22 set2 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.


title: 13366155 - Col0 flg15 30min vs Col0 flg22 30min

hyb_protocol: Col0 flg22 30min Cy5 / Col0 flg15 30min 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.


title: 13690744 - dcl2-dcl3-dcl4 ctrl set1 vs Col ctrl set1

hyb_protocol: Col ctrl set1 Cy5 / dcl2-dcl3-dcl4 ctrl set1 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.

source_name: Col ctrl set1

extract_protocol: Col ctrl set1:4.63ug.

source_name: dcl2-dcl3-dcl4 ctrl set1

extract_protocol: dcl2-dcl3-dcl4 ctrl set1:3.87ug.


title: 13690746 - dcl2-dcl3-dcl4 flag22 set1 vs Col flag22 set1

hyb_protocol: Col flag22 set1 Cy5 / dcl2-dcl3-dcl4 flag22 set1 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.

source_name: Col flag22 set1

extract_protocol: Col flag22 set1:4.99ug.

source_name: dcl2-dcl3-dcl4 flag22 set1

extract_protocol: dcl2-dcl3-dcl4 flag22 set1:5.74ug.


title: 13690745 - Col flag22 set1 vs dcl2-dcl3-dcl4 flag22 set1

hyb_protocol: dcl2-dcl3-dcl4 flag22 set1 Cy5 / Col flag22 set1 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.


title: 13366464 - dcl4-1 flg22 30min vs dcl4-1 flg15 30min

hyb_protocol: dcl4-1 flg15 30min Cy5 / dcl4-1 flg22 30min 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.

source_name: dcl4-1 flg15 30min

source_name: dcl4-1 flg22 30min


title: 13690747 - dcl2-dcl3-dcl4 flag15 set1 vs dcl2-dcl3-dcl4 flag22 set1

hyb_protocol: dcl2-dcl3-dcl4 flag22 set1 Cy5 / dcl2-dcl3-dcl4 flag15 set1 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.

source_name: dcl2-dcl3-dcl4 flag15 set1

extract_protocol: dcl2-dcl3-dcl4 flag15 set1:4.08ug.

treatment_protocol: Name:flag 15 dcl234 - biotic stress - compound addition,flg15:time 30min . 14-day old were transferred into MS liquid medium and then supplied with flg15 peptide to a final concentration 100nM.; Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.


title: 13690387 - Col flag22 set1 vs Col flag15 set1

hyb_protocol: Col flag15 set1 Cy5 / Col flag22 set1 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.

source_name: Col flag15 set1

extract_protocol: Col flag15 set1:5.02ug.


title: 13690375 - Col flag22 set2 vs Col flag15 set2

hyb_protocol: Col flag15 set2 Cy5 / Col flag22 set2 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.

source_name: Col flag15 set2

extract_protocol: Col flag15 set2:3.27ug.


title: 13690374 - Col flag15 set2 vs Col flag22 set2

hyb_protocol: Col flag22 set2 Cy5 / Col flag15 set2 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.


title: 13690372 - Col ctrl set2 vs dcl2-dcl3-dcl4 ctrl set2

hyb_protocol: dcl2-dcl3-dcl4 ctrl set2 Cy5 / Col ctrl set2 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.

source_name: dcl2-dcl3-dcl4 ctrl set2

extract_protocol: dcl2-dcl3-dcl4 ctrl set2:4.03ug.

source_name: Col ctrl set2

extract_protocol: Col ctrl set2:7.3ug.