title: mouse657-lungs-C57BL/6J Control-rep-1

status: Public on Nov 30 2010

type: RNA

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

country: USA

institute: NIH

description: RMA expression value derived from Partek Genomics Suite software; core-exon analysis

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cDNAs were hybridized to The Affymetrix GeneChip® Mouse Exon 1.0 ST Array. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Affymetrix Expression Console software and the Cel files generated.

data_processing: Raw data were processed and analyzed using Partek Genomics Suite Software. Core-exon analysis was used and then gene-level estimates of expression were calculated.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: C57BL/6J Control

label_protocol: RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively. Per RNA labeling, 1 microgram of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip® WT Sense Target Labeling.  The total RNA was first subjected to a ribosomal RNA reduction using the Invitorgen RiboMinus Transcriptome Isolation Kit (catalog# K1550-01). The remaining rRNA striped RNA is reverse transcribed in the presence of T7(N6) primers and a double stranded cDNA is generated. An In Vitro Transcription is performed and the resulting cRNA is purified. A first strand cDNA is generated form the cRNA in the presence of dUTPs. After RNA hydrolysis, the single stranded cDNA is fragmented and end labeled with Biotin.

growth_protocol: The right lower lobe was inflated with OCT and then flash frozen in liquid nitrogen.

extract_protocol: Lung lobes were homogenized and then RNA was isolated using RNeasy Mini Kits (Qiagen), according to the manufacturer’s instructions. RNAs were DNAseI treated, then rRNAs were removed using Invitrogen RiboMinus kits.

treatment_protocol: Control mice were i.p. sensitized with 10 ug Der p 1 on days 1 and 8, then challenged with PBS on day 15. Treated mice were  i.p. sensitized with 10 ug Der p 1 days 1 and 8 and then challenged with 50 ug Der p 1 on day 15.  All mice were harvested on day 18 (72 hours after challenge).

tag: gender

value: male

tag: tissue

value: whole lung

tag: strain


title: mouse661-lungs-C57BL/6J Treated-rep-1

source_name: C57BL/6J Treated


title: mouse643-lungs-C57BL/6J Control-rep-1


title: mouse659-lungs-C57BL/6J Treated-rep-1


title: mouse645-lungs-C57BL/6J Control-rep-1


title: mouse646-lungs-C57BL/6J Treated-rep-1


title: mouse637-lungs-BALB/cJ Treated-rep-1

source_name: BALB/cJ Treated

value: BALB/cJ


title: mouse649-lungs-C57BL/6J Treated-rep-1


title: mouse658-lungs-C57BL/6J Treated-rep-1


title: mouse631-lungs-BALB/cJ Control-rep-3

source_name: BALB/cJ Control


title: mouse631-lungs-BALB/cJ Control-rep-2


title: mouse647-lungs-C57BL/6J Treated-rep-1


title: mouse644-lungs-C57BL/6J Control-rep-1


title: mouse655-lungs-C57BL/6J Control-rep-1


title: mouse656-lungs-C57BL/6J Control-rep-1


title: mouse660-lungs-C57BL/6J Treated-rep-1


title: mouse633-lungs-BALB/cJ Control-rep-1


title: mouse632-lungs-BALB/cJ Control-rep-1


title: mouse634-lungs-BALB/cJ Treated-rep-1


title: mouse636-lungs-BALB/cJ Treated-rep-1


title: mouse648-lungs-C57BL/6J Treated-rep-1


title: mouse635-lungs-BALB/cJ Treated-rep-1


title: mouse631-lungs-BALB/cJ Control-rep-1


title: mouse625-lungs-BALB/cJ Treated-rep-1


title: mouse624-lungs-BALB/cJ Treated-rep-1


title: mouse623-lungs-BALB/cJ Treated-rep-1


title: mouse622-lungs-BALB/cJ Treated-rep-1


title: mouse620-lungs-BALB/cJ Control-rep-1


title: mouse621-lungs-BALB/cJ Control-rep-1


title: mouse538-lungs-C57BL/6J Treated-rep-3


title: mouse619-lungs-BALB/cJ Control-rep-1


title: mouse538-lungs-C57BL/6J Treated-rep-1


title: mouse538-lungs-C57BL/6J Treated-rep-2


title: mouse540-lungs-C57BL/6J Treated-rep-3


title: mouse540-lungs-C57BL/6J Treated-rep-2


title: mouse540-lungs-C57BL/6J Treated-rep-1


title: mouse537-lungs-C57BL/6J Control-rep-1


title: mouse536-lungs-C57BL/6J Control-rep-1


title: mouse534-lungs-C57BL/6J Treated-rep-1


title: mouse520-lungs-BALB/cJ Treated-rep-2


title: mouse518-lungs-BALB/cJ Treated-rep-3


title: mouse528-lungs-BALB/cJ Treated-rep-1


title: mouse531-lungs-C57BL/6J Control-rep-1


title: mouse526-lungs-BALB/cJ Treated-rep-3


title: mouse529-lungs-C57BL/6J Control-rep-1


title: mouse524-lungs-BALB/cJ Control-rep-1


title: mouse522-lungs-BALB/cJ Control-rep-1


title: mouse526-lungs-BALB/cJ Treated-rep-1


title: mouse530-lungs-C57BL/6J Control-rep-1


title: mouse520-lungs-BALB/cJ Treated-rep-3


title: mouse532-lungs-C57BL/6J Treated-rep-1


title: mouse520-lungs-BALB/cJ Treated-rep-1


title: mouse526-lungs-BALB/cJ Treated-rep-2


title: mouse521-lungs-BALB/cJ Control-rep-1


title: mouse525-lungs-BALB/cJ Treated-rep-1


title: mouse518-lungs-BALB/cJ Treated-rep-1


title: mouse518-lungs-BALB/cJ Treated-rep-2


title: mouse517-lungs-BALB/cJ Treated-rep-1


title: mouse513-lungs-BALB/cJ Control-rep-1


title: mouse513-lungs-BALB/cJ Control-rep-2


title: mouse513-lungs-BALB/cJ Control-rep-3


title: mouse514-lungs-BALB/cJ Control-rep-1


title: PCA_donorvsacceptor_potentiostat_BR2B

status: Public on Nov 23 2010

city: Washington

first: Sarah

last: Strycharz

state: DC

address: 4555 Overlook Ave.

department: CBMSE

institute: Naval Research Laboratory

description: total RNA was directly labeled with the Micromax ASAP labeling kit, using 10 ug total RNA for each sample.

hyb_protocol: Combimatrix 100 ul volume cap.

scan_protocol: Slide was scanned using GenePix software and a GenePix 4000b scanner

data_processing:
The raw total intensities were treated as follows to generate the M Log2 ratios for this work. Background signal was calculated from a set of negative control spots incorporated into the array. As the negative control sequences are not design specific (ie. are found in all of the ESOAs independent of the organism being sampled) some will inevitably demonstrate strong cross hybridization with the sample of interest. To avoid this issue the negative control spots were ranked according to their total intensity. The average of the lowest 30% was calculated. Background signal was calculated as this mean + 2 standard deviations. The background signal was then subtracted from the total intensity for each spot. Probes whose signal was not greater than zero after background subtraction were omitted from further analysis. For the remaining data, the logged ratios [M=log2 (Ex/Ct)] are then calculated and Lowess global normalization is performed. During the data preprocessing, M vs. A plots before and after normalization, and side-by-side box plots for all arrays are used to assess array quality.(3) LIMMA mixed model analysis (R-package LIMMA(2))is applied to the normalized logged ratios to identify differentially expressed genes. Specifically, biological replicates are treated as a randomized block to allow for modeling correlations within them. LIMMA calculates a moderated t statistic for each probe, which is the ratio of the estimated mean logged intensity ratio and the Empirical Bayes estimate of its standard error. The P-value of each oligo is then corrected for multiple comparisons according to Benjamini and Hockberg's procedure(1) to control the false discovery rate. Oligos are ranked according to the adjusted P-values and were called differentially expressed if the adjusted P-values are < 0.001. Note that multiple oligonucleotide probes from the same gene are analyzed separately and a gene is called differentially expressed if at least half of its probes are called differentially expressed.
1. Benjamini, Y., and Y. Hochberg. 1995. Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 57:289-300.
2. Smyth, G. K. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:Article3.
3. Smyth, G. K., and T. Speed. 2003. Normalization of cDNA microarray data. Methods 31:265-73.

organism: Geobacter sulfurreducens

source_name: Geobacter sulfurreducens current-consuming biofilm

label_protocol: Micromax ASAP direct RNA labeling protocol

extract_protocol: TE-sucrose hot-phenol extraction method, subsequent DNAse treatment with Ambion DNA-free protocol.

tag: growth protocol

value: current-consuming biofilm

source_name: Geobacter sulfurreducens current-producing biofilm

value: current-producing biofilm


title: PCA_donorvsacceptor_potentiostat_BR3B


title: PCA_donorvsacceptor_potentiostat_BR1A


title: PCA_donorvsacceptor_potentiostat_BR2A


title: PCA_donorvscontrol_potentiostat_BR3B

source_name: Geobacter sulfurreducens current-consuming biofilm; experimental condition

source_name: Geobacter sulfurreducens no-current biofilm; control condition

value: no-current biofilm (control)


title: PCA_donorvscontrol_potentiostat_BR3A


title: PCA_donorvscontrol_potentiostat_BR1A


title: PCA_donorvscontrol_potentiostat_BR2B


title: PCA_donorvsacceptor_potentiostat_BR1B


title: PCA_donorvscontrol_potentiostat_BR2A


title: PCA_donorvscontrol_potentiostat_BR1B


title: PCA_donorvsacceptor_potentiostat_BR3A


title: S.anglica 5

status: Public on Nov 10 2010

city: RENNES

first: Chelaifa

last: Houda

address: Bat 14A campus de beaulieu

country: France

institute: Rennes1 university

description: gene expression in same growing conditions

hyb_protocol: A total of 1.65 µg of  Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2X GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and 100µl of the total volume prepared was hybridized to Agilent rice Oligo Microarrays (G2519F) for 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  using one color scan setting for 4x44k array.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

organism: Sporobolus anglicus

source_name: RNA leaves, allopolyploid

label_protocol: Total RNA (350 ng) was amplified and labeled using Agilent’s Low RNA Input Linear Ampliﬁcation Kit PLUS (One-color). The ampliﬁed cyanine 3–labeled cRNA samples were then puriﬁed using Qiagen’s RNeasy mini spin columns (Qiagen Inc., CA) and Cy3 incorporations were monitored using a Nanodrop ND-1000 Spectrophotometer.

growth_protocol: All plants were grown in the same conditions (30 cm3 daily watered pots containing 2:1 mixture of soil and sand respectively) under day temperature from 20 to 22°C and night temperature from 14 to 16°C.

extract_protocol: Total RNA was isolated from young leaves using Trizol reagent (Sigma, CA, USA) according to the manufacturer’s recommendations. Each RNA sample was quantified using a Nanodrop (Spectrophotometer, ND 1000) and the quality of RNA was checked on the Agilent 2100 Bioanalyzer.

value: leaves

tag: species status

value: Allopolyploid

tag: genome/variation

value: 12X ploidy


title: S.anglica 1


title: S.anglica 4


title: S.anglica 2


title: S.anglica 3


title: Mouse LV, WT 3

status: Public on Nov 19 2010

city: St. Louis

first: Anthony

middle: J

last: Muslin

state: MO

address: 660 s. Euclid ave

institute: Washington University

description: Gene expression data from mouse heart

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

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.

molecule: polyA RNA

source_name: Mouse Left Ventricle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

growth_protocol: Mice with targeted disruption of the akt2 gene were repeatedly backcrossed (more than 7 times) with WT C57Bl/6 mice obtained from the Jackson Laboratory prior to experimentation. Progeny were screened by tail-prep PCR. Only male mice were used.

extract_protocol: Qiagen RNeasy fibrous tissue mini-prep kit.

treatment_protocol: LV was harvest from 12-16 week-old mice

value: Mouse heart

tag: genotype

value: wild type


title: Young Control

status: Public on Nov 16 2010

city: Kyoto

first: Masaki

last: Fujishima

state: Kyoto

address: 369, Karasuma-dori, Gojo, Shimogyo-ku

department: Research and Development Department

country: Japan

institute: Sun Chlorella Corp.

description: Gene expression data from liver that 10-week-old was intake normal food.

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

scan_protocol: GeneChips were scanned using the GeneChip(R) Scanner 3000 7G System w/Workstation and AutoLoader

data_processing: GeneSpring GX v10.0 was used for normalization of data, with normalization carried out according to the “MAS5” algorithm. At this time, interchip correction was performed with the median value of the total sample. Values judged significant (Flag “P” (Present)) were used for analyses.

source_name: Liver, normal food, 10-week-old mouse

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

extract_protocol: RNALater treated liver, after which the total RNA was extracted by RNeasy Plus Mini Kit(QIAGEN)

tag: agent

value: control

value: BALB/c

value: Liver

value: female

tag: age


title: Mouse LV, akt2-/- 2

description: Gene expression data from mouse heart


title: NKCC1_small intestine

status: Public on Nov 17 2010

city: Cincinnati

first: Gary

last: Shull

state: OH

address: 231 Albert Sabin Way ML0524

institute: University of Cincinnati

description: 6 wild-type and 6 NKCC1-knockout small intestine RNA samples were compared. Total RNA was collected from both male and female 8-week old wild-type and NKCC1-null mice on an inbred FVB\N background. All comparisons were done between wild-type and NHE4-null samples from age- and gender-matched mice.

hyb_protocol: The microarrayed DNA probes were incubated in Prehybridization Buffer (5X SSC, 0.1% SDS, and 1% bovine serum albumin) at 42oC for 90 min.  For hybridization, the microarray slides are spotted with 42 ml Hybridization Buffer  (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target cDNA; covered with glass coverslips (Fisher; Pittsburgh, PA), and placed in humidified hybridization chambers (Corning; Acton, MA).  The hybridization chambers were placed in a water bath at 48°C for 66 hr.  The slides were placed in a slide rack set in a staining dish and washed in 1X SSC with 0.2% SDS for 4 min at 48°C with agitation and transferred to a staining dish with 0.1X SSC and 0.2% SDS and washed with agitation for 4 min at room temperature and two times for 4 min each in 0.1X SSC at room temperature.  The slides were spun-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.  Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.  The Cy3 and Cy5 fluorescence signal intensities were normalized.

data_processing: See: Sartor, et al. BMC Bioinformatics. 2006 Dec 19;7:538.  To test for differentially expressed genes, a hierarchical Bayes procedure, IBMT (Sartor et al., BMC Bioinf, 2006) was used.

source_name: total RNA from whole small intestine

label_protocol: Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.  The cDNA was decorated with monofunctional reactive Cy3 and Cy5 dyes.

growth_protocol: Mice had access to normal chow and water ad libitum, and were aged to 8 weeks old.

extract_protocol: Total RNA was extracted from whole colon using Tri-Reagent as per the manufacturer's instructions.

value: inbred FVBN


title: Mouse LV, WT 1

description: Gene expression data from mouse heart


title: S.x towensendii 3

organism: Sporobolus x townsendii

source_name: RNA leaves, hybrid

value: F1 hybrid

value: 6X ploidy


title: S.x towensendii 4


title: S.x towensendii 5


title: Mouse LV, akt2-/- 3

description: Gene expression data from mouse heart


title: S.alterniflora 5

organism: Sporobolus alterniflorus

source_name: RNA leaves, parents

value: maternal parent


title: Old Chlorella

description: Gene expression data from liver that 50-week-old was intake food including 2.0% Chlorella powder.

source_name: Liver, food including 2.0% Chlorella powder, 50-week-old mouse

value: Chlorella


title: Mouse LV, akt2-/- 1

description: Gene expression data from mouse heart


title: S.x towensendii 2


title: S.x towensendii 1


title: S.maritima 4

organism: Sporobolus maritimus

value: paternal parent


title: S.maritima 3


title: S.alterniflora 4


title: S.alterniflora 1


title: Mouse LV, WT 2

description: Gene expression data from mouse heart


title: S.alterniflora 2


title: S.maritima 1


title: S.maritima 5


title: HPAEC_beta-catenin_siRNA_24hr_rep2

status: Public on Nov 06 2010

city: Baltimore

first: Molong

last: Li

address: 733 N. Broadway

department: School of Medicine

institute: Johns Hopkins University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using an Illumina Beadstation

data_processing: rank invariant normalization using Illumina's BeadStudio software

organism: Homo sapiens

source_name: human pulmonary artery endothelial cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Human PA ECs (ScienCell) were grown in commercial EC media (Sciencell). Cells were subcultured at a 1:6 ratio in gelatin-coated dishes (BD Falcon and Corning) and used at passage 5.

extract_protocol: 250ng of RNA were extracted from each sample using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: PAECs were transfected  with siRNA duplexes specific for βC (L-003482-00; Dharmacon); BMPRII (L-005309-00; Dharmacon), or non-targeting siRNA as control (D-001810-01, Dharmacon) using lipofectamine 2000 (Invitrogen) for 24 hrs. Cells were then starved in basal media (Sciencell) with 0.5% FBS and gentamycin/amphotericin over night before harvesting.

value: pulmonary artery endothelial cells

tag: source

value: ScienCell


title: S.alterniflora 3

value: leaves


title: S.maritima 2


title: HPAEC_BMPRII_siRNA_24hr_rep2

description: replicate 2


title: HPAEC_BMPRII_siRNA_24hr_rep1

description: replicate 1


title: HPAEC_beta-catenin_siRNA_24hr_rep3

description: replicate 3


title: HPAEC_control_siRNA_24hr_rep1

description: replicate 1


title: HPAEC_beta-catenin_siRNA_24hr_rep4

description: replicate 4


title: HPAEC_BMPRII_siRNA_24hr_rep3

description: replicate 3


title: HPAEC_control_siRNA_24hr_rep4

description: replicate 4


title: HPAEC_control_siRNA_24hr_rep2

description: replicate 2


title: HPAEC_beta-catenin_siRNA_24hr_rep1

description: replicate 1


title: HPAEC_control_siRNA_24hr_rep3

description: replicate 3


title: CD36+EPC-Control-48h-rep2

status: Public on Nov 03 2010

first: Ning

last: zhi

address: 9000 Rockville Pike

department: hematology

description: CD36+ EPCs generated from CD34+ stem cells

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16h

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation (''S10 transform).

source_name: Control transduced for 48h

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: CD36+ EPCs were generated form CD34+ stem cells and maintained in the AMEM contained several growth factors

extract_protocol: Qiagen miRNA extraction with minElute columns

treatment_protocol: CD36+ EPCs were transduced with NS1 or control-lentivirus, and harvested at different time point

tag: cell type

value: CD36+ Erythoid Progenitor Cells (EPCs)


title: CD36+EPC-Control-48h-rep3


title: CD36+EPC-Control-24h-rep3

source_name: Control transduced for 24h


title: CD36+EPC-Control-24h-rep2


title: CD36+EPC-NS1-48h-rep2

source_name: NS1 transduced for 48h


title: CD36+EPC-Control-48h-rep1


title: CD36+EPC-Control-24h-rep1


title: CD36+EPC-Control-12h-rep3

source_name: Control transduced for 12h


title: CD36+EPC-Control-12h-rep2


title: CD36+EPC-NS1-48h-rep1


title: CD36+EPC-NS1-24h-rep2

source_name: NS1 transduced for 24h


title: CD36+EPC-NS1-24h-rep1


title: CD36+EPC-Control-12h-rep1


title: CD36+EPC-NS1-24h-rep3


title: Old Control

description: Gene expression data from liver that 50-week-old was intake normal food.

source_name: Liver, normal food, 50-week-old mouse


title: CD36+EPC-NS1-12h-rep1

source_name: NS1 transduced for 12h


title: ADAR2 brain_rep4

status: Public on Nov 01 2010

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

value: male

value: 19 weeks

tag: strain ADAR-/-/GluR-BR/R

value: brain

source_name: Wt RNA pool brain

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

tag: type

value: rna pool

tag: mouse ids


title: ADAR2 brain_rep8

label_protocol: For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.


title: ADAR2 brain_rep7


title: Nogo-A KO C57Bl/6 Adult Spinal Cord 2

city: Zurich

first: Laura

last: Montani

address: Winterthurerstrasse 190

department: Neuromorphology

country: Switzerland

institute: Brain Research Institute - UZH/ETHZ - Zurich

description: Doesn't apply

hyb_protocol: The botin-labeled cRNA sample (10 μg) was fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) andmixed in 300 μl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 array for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 FS450_0001 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Raw data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signedrank call algorithm (Liu et al., 2002). The efficiency of the labelling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes (GAPDH and ACO7), for the poly A spikein controls and the prokaryotic control (BIOB, BIOC, CREX, BIODN).

label: Biotin

source_name: Naïve Nogo-A KO adult spinal cord

label_protocol: Total RNA was reverse-transcribed into double-stranded cDNA with One-Cycle cDNASynthesis Kit (Affymetrix Inc., P/N 900431, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA was in vitro transcribed in presence of biotin-labeled nucleotides using a IVTLabeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and Bioanalyzer 2100 (Agilent, Waldbronn, Germany).

growth_protocol: Doesn't apply

extract_protocol: Animal was sacrificed and spinal cord immediately explanted and transferred into RNA later stabilization solution (Ambion) and stored at -20C, up to collection of all the experimental samples. On the same day, total RNA extraction was performed with was performed with an RNeasy micro kit (Qiagen, CA, USA) according to manufacturer’s protocol with the addition of an on-column DNase digestion step to more efficiently remove remaining DNA contamination. The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany).

treatment_protocol: Untreated sample from naive Nogo-A KO animal

tag: Strain

value: Nogo-A KO C57Bl/6

tag: Gender

value: Male

tag: Age

value: Adult,  4 months old

tag: Tissue

value: Spinal Cord


title: ADAR2 brain_rep2

tag: gender

tag: tissue

tag: rna pool; male, age


title: Nogo-A KO C57Bl/6 Adult Spinal Cord 1

description: Doesn't apply

value: Nogo-A knockout C57Bl/6


title: Wildtype C57Bl/6 Adult Spinal Cord 2

description: Doesn't apply

source_name: Naive wildtype adult spinal cord

treatment_protocol: Untreated sample from naive animal

value: C57Bl/6 Gender:Male Age:Adult, 4 months Tissue:Spinal cord


title: CD36+EPC-NS1-12h-rep3


title: ADAR2 brain_rep6


title: Nogo-A KO C57Bl/6 Adult Spinal Cord 3

description: Doesn't apply

source_name: Naïve Nogo-A knockout adult spinal cord


title: CD36+EPC-NS1-48h-rep3


title: Wildtype C57Bl/6 Adult Spinal Cord 3

description: Doesn't apply


title: Wildtype C57Bl/6 Adult Spinal Cord 1

description: Doesn't apply

value: Adult, 4 months

value: Spinal cord


title: 16

city: Charlottesville

first: Carol

middle: A

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

department: Medicine

institute: University of Virginia

description: Gene expression data from a single laser captured  trophozoite

hyb_protocol: After biotinylation, 2 μg of cRNA was hybridized to the E_his-1a520285 Affymetrix custom array that has been described elsewhere (Gilchrist et al., 2006). The arrays were washed and stained with streptavidin-phycoerythrin (Molecular Probes, Carlsbad, CA), following the standard Affymetrix protocol for eukaryotic targets

scan_protocol: The arrays were scanned with an Affymetrix Gene Chip scanner 3000l

data_processing: Affymetrix® GeneChip®  Operating Software (GCOS) (http://www.affymetrix.com/products/software/specific/gcos.affx) was used to determine the detection call (present, marginal, absent) for each probe set.

organism: Entamoeba histolytica

source_name: Single cell capture 16

label_protocol: The  WT-Ovation™ Pico System (NuGEN, San Carlos, CA) was used for cDNA synthesis and amplification.  The quantity of cDNA obtained from one amplification cycle was insufficient for microarray analysis. Therefore one cycle amplified cDNA (1C) was subjected to a second cycle of amplification 2C from a single cell was used for biotinylated cRNA synthesis.

growth_protocol: E. histolytica trophozoites, strain HM-1:IMSS, were grown axenically at 37°C in complete TYI-S-33 medium containing 100 U/ml of penicillin and 100 μg/ml streptomycin (Invitrogen, Carlsbad, CA) (Diamond, 1961).  For all experiments, trophozoites were harvested during log-phase growth by a 10-min incubation on ice.

extract_protocol: RNA was purified from a single ameba using the PicoPure™ RNA Isolation Kit (Molecular Devices, Sunnyvale, CA).

treatment_protocol: For laser capture microdissection analysis, harvested trophozoites were allowed to adhere to metal framed PEN membrane slides (Molecular Devices, Sunnyvale, CA) for 15 mins at 37°C in TYI-S-33 media.  Subsequently, single cells were captured from the PEN slides using a Pix Cell II laser capture microdissection system equipped with an Olympus microscope (Arcturus Engineering, Mountain View, CA).

tag: strain


title: ADAR2 brain_rep3


title: chondrocytes at E18.5, transgenic, biological rep2 Hoxc8

status: Public on Oct 15 2010

city: Baton Rouge

first: Claudia

last: Kappen

state: LA

address: 6400 Perkins Road

department: Developmental Biology

institute: Pennington Biomedical Research Center

hyb_protocol: GeneChip arrays were hybridized overnight in the Affymetrix hybridization oven at 42oC. Washing and scanning was performed using the Affymetrix GeneChip Fluidics Station 450.

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 and global scaling as normalization method.

source_name: Mouse rib chondrocytes

label_protocol: Biotin-labeled samples were generated using the Affymetrix Eukaryotic One-Cycle Target Labeling Assay.

growth_protocol: Pregnant dams were single housed, the morning with presence of a vaginal plug being counted as 0.5 days.

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

treatment_protocol: Rib cages were dissected from E18.5 embryos and washed in PBS. Cells were dissociated by enzymatic digestion with 0.25% Collagenase and 0.25% Trypsin/EDTA for 1h at 37oC. The rib cages were washed, and fresh 0.25% Collagenase in PBS was added for 1h at 37oC. Enzymatic reaction was stopped by adding an equal volume of tissue culture medium containing 10% FCS. The cells were filtered through a 70 micrometer cell strainer and pelleted (1200rpm for 10min). Pellets were washed with PBS and stored in Trizol reagent.

value: FVB

value: primary chondrocytes

tag: genome/variation

value: Hoxc8 transgenic


title: chondrocytes at E18.5, transgenic, biological rep4 Hoxc8


title: ADAR2 brain_rep5


title: MSC_d42_TGF

city: Philadelphia

first: Alice

middle: H

last: Huang

state: PA

address: 424 Stemmler Hall, 3450 Hamilton Walk

department: Bioengineering

institute: University of Pennsylvania

hyb_protocol: 5 ug of cDNA was added to hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to 5 Bovine GeneChips (Affymetrix Inc., Santa Clara, CA). The microarrays were then washed at low (6X SSPE) and high (100 mM MES, 0.1 M NaCl) stringency and stained with streptavidin-phycoerythrin.

scan_protocol: To amplify fluorescence, biotinylated anti-streptavidin and streptavidin-phycoerythrin stain were added, and fluorescent signals were recorded after excitation at 570 nm by the Affymetrix Gene Chip Scanner 3000 (Affymetrix Inc., Santa Clara, CA).

data_processing: Data was normalized with MAS5.0

organism: Bos taurus

source_name: mesenchymal stem cells from bone marrow, chondrogenic, 42 days

label_protocol: Following second-strand cDNA synthesis, ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) was carried out for linear amplification of each transcript and the resulting cDNA was fragmented and biotinylated.

growth_protocol: MSCs were encapsulated in agarose and cultured for 42 days in defined media with TGF-beta3

extract_protocol: Total RNA was extracted by two sequential isolations in TRIZOL-chloroform and quantified (ND-1000, Nanodrop Technologies, Wilmington, DE).  Quality assessment of total RNA and synthesized cDNA was performed by Agilent Bioanalyzer.  All protocols were conducted as described in the NuGEN Ovation manual and the Affymetrix GeneChip Expression Analysis Technical Manual.

tag: sample type

value: mesenchymal stem cells from bone marrow were encapsulated in agarose and cultured for 42 days in defined media with TGF-beta3

value: mesenchymal stem cell


title: MSC_d21_noTGF

source_name: mesenchymal stem cells from bone marrow, undifferentiated, 21 days

growth_protocol: MSCs were encapsulated in agarose and cultured for 21 days in defined media without TGF-beta3

value: mesenchymal stem cells from bone marrow were encapsulated in agarose and cultured for 21 days in defined media without TGF-beta3


title: MSC_d42_noTGF

source_name: mesenchymal stem cells from bone marrow, undifferentiated, 42 days

growth_protocol: MSCs were encapsulated in agarose and cultured for 42 days in defined media without TGF-beta3

value: mesenchymal stem cells from bone marrow were encapsulated in agarose and cultured for 42 days in defined media without TGF-beta3


title: ADAR2 brain_rep1

value: male

value: 19 weeks

value: brain


title: chondrocytes at E18.5, transgenic, biological rep3 Hoxc8


title: MSC_d3_noTGF

source_name: mesenchymal stem cells from bone marrow, undifferentiated, 3 days

growth_protocol: MSCs were encapsulated in agarose and cultured for 3 days in defined media without TGF-beta3

value: undifferentiated mesenchymal stem cells encapsulated in agarose and cultured for 3 days in defined media without TGF-beta3


title: chondrocytes at E18.5, control, biological rep2

value: wild type


title: MSC_d21_TGF

source_name: mesenchymal stem cells from bone marrow, chondrogenic, 21 days

growth_protocol: MSCs were encapsulated in agarose and cultured for 21 days in defined media with TGF-beta3

value: mesenchymal stem cells from bone marrow were encapsulated in agarose and cultured for 21 days in defined media with TGF-beta3


title: HealthyEpidermis_T4vsT1_rep6

status: Public on Aug 31 2010

city: Toulouse

first: Nicolas

last: Mattiuzzo

address: CHU Purpan, place du Dr Baylac, TSA40031

department: UMR CNRS-UPS (Univ. Paul Sabatier) 5165

institute: Centre National de la Recherche Scientifique (CNRS, France)

description:
test (T4) and reference (T1) are obtained from the same biological sample
ASN006

hyb_protocol: cDNA were deposited on previously re-hydrated and blocked microarrays under coverslip, and slides were placed into hybridization chamber for 16 hours at 50°C. After 4 washes (2x SSC + 0.1% SDS ; 1x/0.2x/0.05x SCC) and drying, slides were scanned.

scan_protocol: Slides were scanned on a GenePix 4000A scanner and image intensity data were extracted with GenePix Pro 6.0 analysis software

data_processing: Median intensities of each spot, local background substraction, log transformation and lowess normalization using Bioplot software. Spots with signal intensity greater than average signal for all buffer spots plus 2 SD and detected by more than half of the samples (i.e. with 4 values at least) were analyzed, other were removed from analysis. Note that the array design includes for a very few genes (including negative controls and ACTB / GAPD housekeeping genes) multiple spot replicates; when several of the spot replicates were positive, corresponding ratios where merged, and by convention the ID mentioned in the Matrix corresponds to the ID of the first spot in the GPL1946 table registered in GEO. Note also that ID in .gpr raw data files do NOT correspond to ID in GPL1946 Table, but to the INTERNAL_ID.

source_name: T1 cell fraction (basal keratinocytes) [reference from sample 6]

label_protocol: Reverse transcription of 10-20µg of total RNA with Superscript II enzyme and oligo-dT12-18 primers (Invitrogen) in the presence of aminoallyl-dUTP (Sigma-Aldrich), purification with cleanup module of Labelstar Array kit (Qiagen), labelling with monofunctional NHS ester Cy3 or Cy5 dye (Amersham), purification, pooling of samples to compare and concentration under vacuum followed by addition of 50µl of hybridization buffer containing 2x SSC, 0.1% SDS and 0.1% salmon sperm DNA (Invitrogen)

growth_protocol: Cells were not cultured (direct processing from ex vivo samples)

extract_protocol: Total RNA extraction with QIAGEN RNeasy mini or midi kits

value: Female

tag: health state

value: healthy

source_name: T4 cell fraction (granular keratinocytes) [test from sample 6]


title: HealthyEpidermis_T4vsT1_rep4

description:
test (T4) and reference (T1) are obtained from the same biological sample
AQQ010 and AQQ011

label: Cy3 on AQQ010 slide, Cy5 on swap-array AQQ011

source_name: T1 cell fraction (basal keratinocytes) [reference from sample 4]

label: Cy5 on AQQ010 slide, Cy3 on swap-array AQQ011

source_name: T4 cell fraction (granular keratinocytes) [test from sample 4]


title: chondrocytes at E18.5, transgenic, biological rep4

tag: age

value: Hoxd4 transgenic


title: chondrocytes at E18.5, control, biological rep4 Hoxc8


title: chondrocytes at E18.5, transgenic, biological rep3


title: HealthyEpidermis_T4vsT1_rep3

description:
test (T4) and reference (T1) are obtained from the same biological sample
AQQ008

source_name: T1 cell fraction (basal keratinocytes) [reference from sample 3]

source_name: T4 cell fraction (granular keratinocytes) [test from sample 3]


title: chondrocytes at E18.5, transgenic, biological rep2


title: chondrocytes at E18.5, control, biological rep1 Hoxc8


title: chondrocytes at E18.5, control, biological rep2 Hoxc8


title: HealthyEpidermis_T4vsT1_rep5

description:
test (T4) and reference (T1) are obtained from the same biological sample
ASN005

source_name: T1 cell fraction (basal keratinocytes) [reference from sample 5]

source_name: T4 cell fraction (granular keratinocytes) [test from sample 5]


title: HealthyEpidermis_T4vsT1_rep1

description:
test (T4) and reference (T1) are obtained from the same biological sample
AQQ002 and AQQ003

label: Cy3 on AQQ002 slide, Cy5 on swap-array AQQ003

source_name: T1 cell fraction (basal keratinocytes) [reference from sample 1]

label: Cy5 on AQQ002 slide, Cy3 on swap-array AQQ003

source_name: T4 cell fraction (granular keratinocytes) [test from sample 1]


title: chondrocytes at E18.5, control, biological rep3


title: chondrocytes at E18.5, control, biological rep4


title: MSC_d42_TGF_dynamic_loading

source_name: mesenchymal stem cells from bone marrow, chondrogenic, 42 days, dynamically loaded

growth_protocol: MSCs were encapsulated in agarose and cultured for 21 days in defined media with TGF-beta3, then subjected to 21 more days of dynamic compressive loading in the presence of TGF-beta3

value: mesenchymal stem cells from bone marrow were encapsulated in agarose and cultured for 21 days in defined media with TGF-beta3, following this pre-culture time, dynamic compression was applied to constructs for 21 more days in defined media with TGF-beta3


title: chondrocytes at E18.5, control, biological rep1

source_name: Mouse rib chondrocytes

value: FVB


title: HealthyEpidermis_T4vsT1_rep2

description:
test (T4) and reference (T1) are obtained from the same biological sample
AQQ004 and AQQ005

label: Cy3 on AQQ004 slide, Cy5 on swap-array AQQ005

source_name: T1 cell fraction (basal keratinocytes) [reference from sample 2]

label: Cy5 on AQQ004 slide, Cy3 on swap-array AQQ005

source_name: T4 cell fraction (granular keratinocytes) [test from sample 2]


title: chondrocytes at E18.5, transgenic, biological rep1 Hoxc8

value: primary chondrocytes


title: CD36+EPC-NS1-12h-rep2

source_name: NS1 transduced for 12h

value: CD36+ Erythoid Progenitor Cells (EPCs)


title: chondrocytes at E18.5, control, biological rep3 Hoxc8


title: HH 2

status: Public on Aug 24 2010

city: Jacksonville

first: Tushar

last: Patel

state: FL

address: 4500 San Pablo Road

institute: Mayo Clinic

description: ucRNA profiling from human hepatocytes cells

hyb_protocol: Labeled targets from 5 μg of total RNA was used for hybridization on a custom microarray (OSU-CCC 4.0), which includes sense and antisense probes to all 481 human ultraconserved reported by Bejerano et al . All probes on these microarrays are 40-mer oligonucleotides spotted by contacting technologies and covalently attached to a polymeric matrix. The microarrays were hybridized in 6× SSPE (0.9 M sodium chloride/60 mM sodium phosphate/8 mM EDTA, pH 7.4)/30% formamide at 25°C for 18 h, washed in 0.75× TNT (Tris·HCl/sodium chloride/Tween 20) at 37°C for 40 min, and processed by using direct detection of the biotin-containing transcripts by Streptavidin-Alexa647 conjugate. Processed slides were scanned by using a PerkinElmer ScanArray XL5K Scanner with the laser set to 635 nm, at power 80 and PMT 70 settings, and a scan resolution of 10 μm.

scan_protocol: Biotin-containing transcripts were detected using streptavidin–Alexa647 conjugate, scanned and analyzed using an Axon 4000B scanner and the GenePix 6.0 software (Axon Instruments, Downingtown, PA)

data_processing: The mean fluorescence intensity of replicate spots were subtracted from background and normalized using the global median method. We selected ucRNAs measured as present in all the three replicates. Differentially expressed ucRNAs were identified using the Class Comparison Analysis of BRB tools version 3.6.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html).  The criterion for inclusion of a gene in the gene list was a p-value < 0.05.

source_name: human hepatocytes

label_protocol: Five micrograms of total RNA were separately added to reaction mix in a final volume of 12 μl, containing 1 μg of [3′-(N)8-(A)12-biotin-(A)12-biotin-5′] oligonucleotide primer. The mixture was incubated for 10 min at 70°C and chilled on ice. With the mixture remaining on ice, 4 μl of 5× first-strand buffer, 2 μl of 0.1 M DTT, 1 μl of 10 mM dNTP mix, and 1 μl of SuperScript II RNaseH- reverse transcriptase (200 units/μl) was added to a final volume of 20 μl, and the mixture was incubated for 90 min in a 37°C water bath. After incubation for first-strand cDNA synthesis, 3.5 μl of 0.5 M NaOH/50 mM EDTA was added into 20 μl of first-strand reaction mix and incubated at 65°C for 15 min to denature the RNA/DNA hybrids and degrade RNA templates. Then, 5 μl of 1 M Tris·HCI (pH 7.6, Sigma) was added to neutralize the reaction mix, and labeled targets were stored in 28.5 μl at -80°C until chip hybridization.

extract_protocol: trizol protocol

treatment_protocol: cells were cultures in 100 mm dishes and collected for RNA extraction

tag: cell line

value: normal human hepatocytes


title: chondrocytes at E18.5, transgenic, biological rep1


title: 18

source_name: Single cell capture 18


title: HH 1


title: 13969346 - Col0 3 vs HB6 oe 3

status: Public on Aug 01 2010

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

institute: INRA

description: The aim is to determine downstream target of HB6 transcription factor involved in plant development

hyb_protocol: HB6 oe 3 Cy5 / Col0 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,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: HB6 oe 3

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

growth_protocol: plantlet - Seeds were surface-sterilized and sown on MS/2 agar plates. Plates were put at 4°C for 5 days to synchronize the germination then placed in growth chamber (16h photoperiod 22°C) for 5 days.

extract_protocol: HB6 oe 3:30ug.

treatment_protocol: no treatment

tag: genotype

value: (col-0)  mutant (hb6-)

source_name: Col0 3


title: 13969341 - Col0 2 vs bpm kd 2

hyb_protocol: bpm kd 2 Cy5 / Col0 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.

source_name: bpm kd 2

extract_protocol: bpm kd 2:30ug.

source_name: Col0 2


title: 13969342 - bpm kd 2 vs Col0 2

hyb_protocol: Col0 2 Cy5 / bpm kd 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: 13969345 - bpm kd 3 vs Col0 3

hyb_protocol: Col0 3 Cy5 / bpm kd 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.

source_name: bpm kd 3

extract_protocol: bpm kd 3:30ug.


title: 13969337 - HB6 oe 2 vs Col0 2

hyb_protocol: Col0 2 Cy5 / HB6 oe 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.

source_name: HB6 oe 2

extract_protocol: HB6 oe 2:30ug.


title: 13970004 - wat1 T6h 1leaf vs Col0 T6h 1leaf

description: identification of the role of the plant cell wall in the interactions between plants and pathogenic agents

hyb_protocol: Col0 T6h 1leaf Cy5 / wat1 T6h 1leaf 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 T6h 1leaf

growth_protocol: leaf - day 16h/22°C night 8h/20°C relative humidity 70%

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6h 1leaf:27.8ug.

treatment_protocol: Name:Ralstonia infection 6h - abiotic stress - abiotic stress,ralstonia solanacearum gmi 1000 strain:time 6hour .

tag: ecotype

tag: genotype/variation

value: wild-type

tag: time point

tag: agent

value: Ralstonia solanacearum gmi 1000

source_name: wat1 T6h 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6h 1leaf:32.5ug.

value: mutant (wat1-)


title: 13970006 - wat1 T6h 2leaf vs Col0 T6h 2leaf

hyb_protocol: Col0 T6h 2leaf Cy5 / wat1 T6h 2leaf 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 T6h 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6h 2leaf:31.1ug.

source_name: wat1 T6h 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6h 2leaf:31.4ug.


title: 13969999 - wat1 T0h 1leaf vs Col0 T0h 1leaf

hyb_protocol: Col0 T0h 1leaf Cy5 / wat1 T0h 1leaf 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 T0h 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T0h 1leaf:38.7ug.

treatment_protocol: Name:H20 - control - control,h2o:.

value: H2O, control

source_name: wat1 T0h 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T0h 1leaf:27.8ug.


title: 13969998 - Col0 T0h 1leaf vs wat1 T0h 1leaf

hyb_protocol: wat1 T0h 1leaf Cy5 / Col0 T0h 1leaf 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: 13969347 - HB6 oe 3 vs Col0 3

hyb_protocol: Col0 3 Cy5 / HB6 oe 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: 13969985 - wat1 T6h 2root vs Col0 T6h 2root

hyb_protocol: Col0 T6h 2root Cy5 / wat1 T6h 2root 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 T6h 2root

growth_protocol: root - day 16h/22°C night 8h/20°C relative humidity 70%

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6h 2root:20.4ug.

source_name: wat1 T6h 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6h 2root:23.8ug.


title: 13969335 - HB6 oe 1 vs Col0 1

hyb_protocol: Col0 1 Cy5 / HB6 oe 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.

source_name: Col0 1

source_name: HB6 oe 1

extract_protocol: HB6 oe 1:30ug.


title: 13970002 - Col0 T6h 1leaf vs wat1 T6h 1leaf

hyb_protocol: wat1 T6h 1leaf Cy5 / Col0 T6h 1leaf 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: 13969989 - wat1 T0h 2root vs Col0 T0h 2root

hyb_protocol: Col0 T0h 2root Cy5 / wat1 T0h 2root 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 T0h 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T0h 2root:24.8ug.

source_name: wat1 T0h 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T0h 2root:31ug.


title: 13969344 - Col0 3 vs bpm kd 3

hyb_protocol: bpm kd 3 Cy5 / Col0 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.

source_name: Col0 3


title: 13969658 - wat1 T1d 1root vs Col0 T1d 1root

hyb_protocol: Col0 T1d 1root Cy5 / wat1 T1d 1root 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 T1d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T1d 1root:22.7ug.

treatment_protocol: Name:Ralstonia infection 1d - abiotic stress - abiotic stress,ralstonia solanacearum gmi 1000 strain:time 1day .

source_name: wat1 T1d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T1d 1root:22ug.


title: 13969338 - Col0 1 vs bpm kd 1

hyb_protocol: bpm kd 1 Cy5 / Col0 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.

source_name: bpm kd 1

extract_protocol: bpm kd 1:30ug.


title: 13969339 - bpm kd 1 vs Col0 1

hyb_protocol: Col0 1 Cy5 / bpm kd 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: 13970005 - Col0 T6h 2leaf vs wat1 T6h 2leaf

hyb_protocol: wat1 T6h 2leaf Cy5 / Col0 T6h 2leaf 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: 13969984 - Col0 T1d 1root vs wat1 T1d 1root

hyb_protocol: wat1 T1d 1root Cy5 / Col0 T1d 1root 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: 13969986 - Col0 T6h 2root vs wat1 T6h 2root

hyb_protocol: wat1 T6h 2root Cy5 / Col0 T6h 2root 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: 13970001 - wat1 T0h 2leaf vs Col0 T0h 2leaf

hyb_protocol: Col0 T0h 2leaf Cy5 / wat1 T0h 2leaf 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 T0h 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T0h 2leaf:36.5ug.

source_name: wat1 T0h 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T0h 2leaf:32.2ug.


title: 13969988 - Col0 T6h 1root vs wat1 T6h 1root

hyb_protocol: wat1 T6h 1root Cy5 / Col0 T6h 1root 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: wat1 T6h 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6h 1root:44ug.

source_name: Col0 T6h 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6h 1root:19.4ug.


title: 13969987 - wat1 T6h 1root vs Col0 T6h 1root

hyb_protocol: Col0 T6h 1root Cy5 / wat1 T6h 1root 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: 13969657 - Col0 T1d 2root vs wat1 T1d 2root

hyb_protocol: wat1 T1d 2root Cy5 / Col0 T1d 2root 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: wat1 T1d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T1d 2root:18.5ug.

source_name: Col0 T1d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T1d 2root:21.5ug.


title: 13969336 - Col0 2 vs HB6 oe 2

hyb_protocol: HB6 oe 2 Cy5 / Col0 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.

source_name: HB6 oe 2

extract_protocol: HB6 oe 2:30ug.

source_name: Col0 2


title: 13969334 - Col0 1 vs HB6 oe 1

hyb_protocol: HB6 oe 1 Cy5 / Col0 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: 13969656 - wat1 T1d 2root vs Col0 T1d 2root

hyb_protocol: Col0 T1d 2root Cy5 / wat1 T1d 2root 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: 13969648 - wat1 T4d 2root vs Col0 T4d 2root

hyb_protocol: Col0 T4d 2root Cy5 / wat1 T4d 2root 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 T4d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T4d 2root:13.1ug.

treatment_protocol: Name:Ralstonia infection 4d - abiotic stress - abiotic stress,ralstonia solanacearum gmi 1000 strain:time 4day .

source_name: wat1 T4d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T4d 2root:10.3ug.


title: 13969990 - Col0 T0h 2root vs wat1 T0h 2root

hyb_protocol: wat1 T0h 2root Cy5 / Col0 T0h 2root 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: 13969647 - Col0 T0h 1root vs wat1 T0h 1root

hyb_protocol: wat1 T0h 1root Cy5 / Col0 T0h 1root 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: wat1 T0h 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T0h 1root:14ug.

source_name: Col0 T0h 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T0h 1root:39ug.


title: 13969642 - wat1 T1d 2leaf vs Col0 T1d 2leaf

hyb_protocol: Col0 T1d 2leaf Cy5 / wat1 T1d 2leaf 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 T1d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T1d 2leaf:21.5ug.

source_name: wat1 T1d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T1d 2leaf:28.2ug.


title: 13969646 - wat1 T0h 1root vs Col0 T0h 1root

hyb_protocol: Col0 T0h 1root Cy5 / wat1 T0h 1root 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: 13969645 - Col0 T1d 1leaf vs wat1 T1d 1leaf

hyb_protocol: wat1 T1d 1leaf Cy5 / Col0 T1d 1leaf 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: wat1 T1d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T1d 1leaf:38.7ug.

source_name: Col0 T1d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T1d 1leaf:28.7ug.


title: 13969650 - wat1 T4d 1root vs Col0 T4d 1root

hyb_protocol: Col0 T4d 1root Cy5 / wat1 T4d 1root 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 T4d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T4d 1root:22ug.

source_name: wat1 T4d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T4d 1root:11ug.