title: Control_wildtype_brown_adipose_7months_replicate_4

description:
replicate 4
Sample name: 280_WT_B_7


title: Control_wildtype_brown_adipose_3months_replicate_5

status: Public on Apr 18 2017

type: RNA

city: Bar Harbor

first: Christoph

last: Preuss

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description:
replicate 5
Sample name: A316_WT_B_3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Brown adipose tissue

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

extract_protocol: RNA was extracted from 3, 7 and 12-month old mice for tumor and non-tumor brown adipose tissue from all four genotypes using the RNeasy Lipid Tissue Mini Kit (QIAGEN, Cat. No.74804). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were raised with a light-dark cycle with lights on at 7am and off at 7pm, and free access to water and food (no. 2019, Teklad Global Rodent, 9% fat; Harlan Laboratories, Madison, WI). For sacrifice, mice were anesthetized with sodium pentobarbital (Somnotol; MTC Pharmaceuticals, Hamilton, Ontario, Canada). After cardiac puncture, organs were rapidly removed, weighed, and frozen. Experiments were approved by the Canadian Council on Animal Care-accredited animal facility committee of CHU Sainte-Justine Hospital.

tag: tissue

value: brown adipose

tag: background strain

tag: genotype

value: Control

tag: age

value: 3 months


title: Control_wildtype_brown_adipose_7months_replicate_2

description:
replicate 2
Sample name: 264_WT_B_7

value: 7 months


title: Control_wildtype_brown_adipose_3months_replicate_3

description:
replicate 3
Sample name: A314_WT_B_3


title: Control_wildtype_brown_adipose_3months_replicate_2

description:
replicate 2
Sample name: A313_WT_B_3


title: Primoridial follicles Post-natal day 3 Repeat 2

city: Chicago

first: and

last: PhD

state: Illinois

address: 5841 South Maryland Avenue, MC 5032 Room AB540

department: Department of Surgery

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol. Samples were randomly hybrized to BeadChips

data_processing: Data were vst transform and rsn normalized, and non-detected probes were removed as indicated in Table S3 (Johnson, Li et al., 2007). Significant genes were identified using limma (Smyth, 2004) and were corrected for multiple comparisons using the false discovery rate (fdr) method (Benjamini & Hochberg, 1995)

label: Biotin

source_name: Entire ovaries were collected at post-natal day 3

label_protocol: mRNA samples were in vitro labeled using the TargetAmp 1-Round Aminoallyl-aRNA Kit (Epicentre, Madison, WI)

growth_protocol: Follicles were isolated directly from mice

extract_protocol: Three different samples were collected from each pooled follicular stage for transcriptomic analysis. RNA was purified from follicles using the Qiagen RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and quantity was assessed both by NanoDrop (Thermo Scientific, Wilmington, DE) and BioAnalyzer 2100 Expert (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment. Diffference between the samples are just ovarian follicle maturation stages

tag: strain background

tag: gender

value: female

value: Ovary

tag: follicle stage

tag: pnd


title: Pre-Antral follicles Repeat 1

source_name: Pre-antral follicles (200‒300 µm) at PND 18

value: Ovarian Follicle

value: PREANTRAL


title: Control_wildtype_brown_adipose_3months_replicate_1

description:
replicate 1
Sample name: A295_WT_B_3


title: Primary follicle Repeat 2

source_name: Primary follicles (70-90 µm in diameter) PND 10

value: PRIMARY


title: Primoridial follicles Post-natal day 3 Repeat 3


title: Control_wildtype_brown_adipose_12months_replicate_3

description:
replicate 3
Sample name: 230_WT_B_12

value: 12 months


title: Antral follicles Repeat 1

source_name: Antral follicles (400‒600 µm) were mechanically isolated from pregnant mare serum gonadotropin (PMSG)-treated mice ovaries at post-natal day 20

value: ANTRAL


title: Antral follicles Repeat 2


title: Primary follicle Repeat 1


title: Two-layer secodary follicle Repeat 3

source_name: Two-layered secondary follicles (100-130 µm) at PND 12


title: Primoridial follicles Post-natal day 3 Repeat 1


title: Multi-layered secondary follicle Repeat 1

source_name: Multi-layer secondary follicles (150‒180 µm) at PND 16

value: MLS


title: Primoridial follicles Post-natal day 4 Repeat 3

source_name: Entire ovaries were collected at post-natal day 4


title: Multi-layered secondary follicle Repeat 2


title: Multi-layered secondary follicle Repeat 3


title: Pre-Antral follicles Repeat 3


title: Pre-Antral follicles Repeat 2


title: Primary follicle Repeat 3


title: Two-layer secodary follicle Repeat 2


title: Primoridial follicles Post-natal day 4 Repeat 2


title: Two-layer secodary follicle Repeat 1


title: Control_wildtype_brown_adipose_3months_replicate_4

description:
replicate 4
Sample name: A315_WT_B_3


title: Antral follicles Repeat 3


title: endothelial cells_young_lansoprazole100μM_rep3

city: Ancona

first: Laura

last: Costarelli

address: Via Birarelli, 8

country: Italy

institute: INRCA - National Institute of Health & Science on Ageing

description: Replicate 3 of 3

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The microarray data analysis was performed by Partek Genomics Suite Version 6.6 (Partek, St Louis, MO, USA). Raw intensity values stored in CEL files were imported into Partek and normalized using the GCRMA method. In order to correct for multiple comparisons and reduce the number of false positives, a false discovery rate (FDR) adjusted P value < 5.00E-2 was used in combination with a fold-change (FC) ≥ 2.

organism: Homo sapiens

source_name: Human coronary artery endothelial cells, young, lansoprazole

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3’IVT Expression Arrays Manual, Affymetrix).

growth_protocol: HCAECs purchased from Clonetics Corporation (Lonza) were cultured at 37°C and 5% CO2 in endothelial cell growth medium EBM-2 supplemented with EGM-2/MV SingleQuots (Clonetics Corporation). Cells were plated at a seeding density of 2.500 cells/cm2 in T25 flasks and the medium was changed every 48 hours. Cell cultures reached confluence after 6-7 days, as assessed by light microscopic examination, and they were passaged at weekly intervals. After trypsinization and before replating, harvested cells were counted using the Trypan blue viability stain.

extract_protocol: Total RNA extraction with Qiagen RNeasy mini kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were serially passaged until they showed phenotypes of senescence. Young (P6) and senescent (P12) cells grown on culture dishes and were exposed to 100μM omeprazole or lansoprazole (Sigma Aldrich, Milano, Italy) and compared with untreated group (CTRL)   .

tag: cells

value: young (p6)

tag: treatment

value: lansoprazole


title: HM_NSsiRNA

city: Hong Kong

first: Kit Yan

last: To

address: Pokfulam Road

department: School of Biological Sciences

country: Hong Kong

institute: The University of Hong Kong

description: NS-siRNA

hyb_protocol: Biotinylated RNA were hybridized on GeneChip miRNA 4.0 Array according to the instructions of the FlashTag Biotin HSR RNA Labelling kit (Affymetrix) . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were processed with Expression Console using the RMA + DABG (with quantile normalization) algorithm.
affymetrix-algorithm-name = rma : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: HM cells transfected with NS siRNA

label_protocol: RNA were biotinylated using the FlashTag Biotin HSR RNA Labelling kit (Affymetrix) with 800ng total RNA as input.

growth_protocol: HEYA8 HM cells were cultured in RPMI 1640 medium supplemented with 5% fetal bovine serum and 1% penicillin and streptomycin at 37C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: Transfection of NS or β-catenin targeting siRNA were performed using siLectfect (Bio-Rad) for 48 h according to manufacturer's protocol. The siRNA were purchased from Dharmacon.

tag: cell line source

tag: cell type

value: highly metastatic (HM) ovarian cancer cells

tag: transfected with

value: non-specific (NS) siRNA


title: endothelial cells_old_lansoprazole100μM_rep3

description: Replicate 3 of 3

source_name: Human coronary artery endothelial cells, old,  lansoprazole

value: old (p12)


title: Primoridial follicles Post-natal day 4 Repeat 1


title: endothelial cells_young_lansoprazole100μM_rep2

description: Replicate 2 of 3


title: HM_β-catenin

description: Bcat-siRNA

source_name: HM cells transfected with β-catenin siRNA

value: β-catenin-specific siRNA


title: endothelial cells_old_lansoprazole100μM_rep2

description: Replicate 2 of 3


title: Pep3M Time 24 Hours rep3

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

description: SAMPLE 19

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to8x60K whole human genome oligonucleotide microarray (Agilent G4851B, grid ID 039494), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.7 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09).

data_processing:
The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Then differential gene lists were obtained from filtered data using Microsoft Excel. Differentially expressed genes were identified in Excel by T-test  and Log2 foldchange threshold and by functional analysis using Ingenuity Pathway Analysis software.
Data are in Log2 scale filtered and each sample is normalized to the 75th percentile.

source_name: HCT116_Pep3M_24 hrs

label_protocol: The cyanine 3-CTP labeled cRNA was prepared using the Agilent Low Input Linear Amplification Kit, following the standard one-color Agilent protocol

growth_protocol: HCT116 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS, Life Technology), 2 mM L-glutamine, and 1% penicillin and streptomycin in a fully-humidified incubator containing 5% CO2 at 37˚C.

extract_protocol: Cells were harvested after the different treatments and total RNA was isolated from each sample using RNA Purification columns (Norgen, Purification Plus kit).

treatment_protocol: For experiments, cells were seeded at a density of 8×10^3 cells/cm2. The following day, one dish of cells was harvested (NT time-0 condition) and the other cells were treated with DMSO, Peptide-3 or Peptide-3M at a concentration of 10 µM by adding the tretaments directly to the growth medium. Cells were then collected at 24 or 48 hours after tretament. One dish of untreated cells was collected at 24hours.

tag: cell line

value: Human colon cancer cell line

tag: cell line info.

value: Originally provided by Dr. B. Vogelstein. Last validation on Dec 2013 by genomic analysis of 18 loci marker (Kit PowerPlex 18D System) verified

tag: treated with

value: control peptide (Pep3M)

tag: time after treatment

value: 24 hrs


title: DMSOTime 48 Hours rep3

description: SAMPLE 23

source_name: HCT116_DMSO_48 hrs

value: DMSO

value: 48 hrs


title: endothelial cells_old_lansoprazole100μM_rep1

description: Replicate 1 of 3


title: endothelial cells_young_lansoprazole100μM_rep1

description: Replicate 1 of 3


title: Pep3MTime 48 Hours rep3

description: SAMPLE 24

source_name: HCT116_Pep3M_48 hrs


title: endothelial cells_old_omeprazole100μM_rep3

description: Replicate 3 of 3

source_name: Human coronary artery endothelial cells, old, omeprazole

value: omeprazole


title: Pep3 Time 24 Hours rep3

description: SAMPLE 22

source_name: HCT116_Pep3_24 hrs

value: peptide-3 (Pep3)


title: Pep3 Time 48 Hours rep3

description: SAMPLE 20

source_name: HCT116_Pep3_48 hrs


title: NT Time 0 rep3

description: SAMPLE 17

value: none (untreated control)

value: 0hr; the starting point of the treatment


title: NT Time 24 Hours rep3

description: SAMPLE 21

source_name: HCT116_NT_24 hrs


title: DMSOTime 48 Hours rep2

description: SAMPLE 15


title: endothelial cells_old_omeprazole100μM_rep2

description: Replicate 2 of 3


title: DMSO Time 24 Hours rep3

description: SAMPLE 18

source_name: HCT116_DMSO_24 hrs


title: Pep3 Time 24 Hours rep2

description: SAMPLE 14


title: HSLAKO_brown_adipose_12months_replicate4

description:
replicate 4
Sample name: 3495_HAKO_B_12

source_name: Brown adipose tissue

tag: tissue

value: brown adipose

value: HSL Single Knockout

value: 12 months


title: endothelial cells_old_omeprazole100μM_rep1

description: Replicate 1 of 3


title: Pep3MTime 48 Hours rep2

description: SAMPLE 16


title: endothelial cells_young_omeprazole100μM_rep3

description: Replicate 3 of 3

source_name: Human coronary artery endothelial cells, young, omeprazole

value: young (p6)


title: DMSO Time 24 Hours rep2

description: SAMPLE 10


title: Pep3 Time 48 Hours rep2

description: SAMPLE 12


title: Pep3M Time 24 Hours rep2

description: SAMPLE 11


title: endothelial cells_young_omeprazole100μM_rep2

description: Replicate 2 of 3

source_name: Human coronary artery endothelial cells, young,omeprazole


title: NT Time 0 rep2

description: SAMPLE 9


title: endothelial cells_old_control_rep3

description: Replicate 3 of 3

source_name: Human coronary artery endothelial cells, old, control

value: untreated


title: endothelial cells_young_control_rep3

description: Replicate 3 of 3

source_name: Human coronary artery endothelial cells, young, control


title: Pep3 Time 24 Hours rep1

description: SAMPLE 6


title: endothelial cells_old_control_rep2

description: Replicate 2 of 3

value: old (p12)


title: BufoBoreas-Spleen_control_rep5

city: Berkeley

first: Thomas

last: Poorten

state: CA

address: 54 Mulford Hall

department: Environmental Science, Policy, and Management

institute: UC Berkeley

description:
NA
Bb10E

hyb_protocol: Hybridization was performed by University of Idaho Genomic Resources Core following the Nimblegen standard operating protocol.

scan_protocol: Scanning was performed by University of Idaho Genomic Resources Core following the Nimblegen standard operating protocol. The chips were scanned on an Axon GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) using GenePix Pro v6.1 software (Molecular Devices, Sunnyvale, CA). For scanning, the PMT gain was adjusted for optimal saturation.

data_processing: Each tissue type (skin, liver, and spleen) was analyzed separately.  Using the R package "oligo", each array was background corrected and normalized using the quantile normalization procedure. Each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure (Irizarry et al. Biostatistics 4(2):249). The median polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed

organism: Anaxyrus boreas

source_name: Spleen

label_protocol: Cy3 labeling was performed by performed by University of Idaho Genomic Resources Core following the Nimblegen standard operating protocol.

growth_protocol: Prior to the experiment the frogs were housed communally, but for the experiement they were each kept in individual tanks.  The frogs were kept in a room maintained at 18 degrees C with 12:12 light:dark photoperiod.  The frogs were fed crickets twice per week ad libitum with a water change. For both species (Bufo marinus, Bufo boreas), ten out of twenty frogs were experimentally exposed to the chytrid pathogen Batrachochytrium dendrobatidis for 24 hours. The experiement ended 18 days after inoculation, when all frogs were sacrificed and tissues were collected and preserved in liquid nitrogen. Gene expression was analysed in sample size of 6 replicates per species and tissue type.

extract_protocol: Total RNA was extracted using a routine Trizol/Chloroform protocol. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer (minimum RIN score = 8.0).

tag: excluded from analyses based on qc

value: Spleen

value: Wild-type

tag: phenotype

value: normal

tag: subject id

tag: pathogen infection intensity (zoospore equivalents) for subject

tag: slide id

tag: cy3 pmt


title: BufoMarinus-Spleen_Bd-infected_rep1

description:
NA
Bm1E

organism: Rhinella marina

tag: genotype


title: Pep3 Time 48 Hours rep1

description: SAMPLE 4

value: Human colon cancer cell line

value: Originally provided by Dr. B. Vogelstein. Last validation on Dec 2013 by genomic analysis of 18 loci marker (Kit PowerPlex 18D System) verified


title: BufoMarinus-Spleen_control_rep1

description:
incidental co-infection with intradermal nematode
Bm3E


title: NT Time 24 Hours rep2

description: SAMPLE 13

value: 24 hrs


title: NT Time 24 Hours rep1

description: SAMPLE 5


title: DMSOTime 48 Hours rep1

description: SAMPLE 7

value: DMSO

value: 48 hrs


title: endothelial cells_young_omeprazole100μM_rep1

description: Replicate 1 of 3

tag: cells

value: omeprazole


title: Pep3MTime 48 Hours rep1

description: SAMPLE 8

value: control peptide (Pep3M)


title: endothelial cells_old_control_rep1

description: Replicate 1 of 3

tag: treatment


title: endothelial cells_young_control_rep1

description: Replicate 1 of 3


title: Leaf_treated_15°C_in_a_brightly_lit_field_3_hr

city: Suita

first: Yoshihisa

last: Nakazawa

state: Osaka

address: 8, Yamadaoka-2

department: Graduate School of Engineering

country: Japan

institute: Osaka University

description: Gene expression of leaf treated 15°C in a brightly lit field, 3 hr of E.ulmoides

hyb_protocol: Hybridization and washing were conducted according to the manufacture's protocols (Agilent).

scan_protocol: Slides were scanned using Agilent DNA Microarray Scanner (G2505B) at resolution of 5um at 532 mm wavelength (Cy3).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 020871_D_F_20080702) to obtain background subtracted and spatially detrended Processed Signal intensities. The data were normalized on the 75th percentile for further analysis

organism: Eucommia ulmoides

source_name: Leaf treated 15°C in a brightly lit field, 3 hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) as following the procedures described in the manual. The resultant probe was analysed by RNA 6000 Nano Assay kit (Agilent)

growth_protocol: All samples were obtained from wild individuals planted at a factory of Hitachi Zosen Corporation, Osaka, Japan

extract_protocol: Total RNA was prepared from each frozen sample. Each sample was grained into powder using a motor and pestle, and about 200 mg of the sample was used for total RNA extraction by using RNeasy Plant Mini Kit (Qiagen). The extracted RNA was treated by DNase I using RNase-Free DNase Set (Qiagen). RNA quantity and quality were checked by NanoDrop 1000 (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100 electrophoresis system (Agilent Technologies), respectively.

treatment_protocol: Treatment protocols differed among samples. The RNA of 5 kinds of samples (inner stem, outer stem, immature fruit, flower, and leaf) were extracted after  sampling. The other fruit and leaf were used for hormon (IAA, NPA, ABA) treatments and combinations of light (dark, bright field) & temperature (27, 37, 42°C) from 0 to 24 hours, respectively.

value: Stress treated leaf

tag: Sex

value: Male

tag: sampling date


title: Leaf_treated_15°C_in_a_brightly_lit_field_24_hr

description: Gene expression of leaf treated 15°C in a brightly lit field, 24 hr of E.ulmoides

source_name: Leaf treated 15°C in a brightly lit field, 24 hr


title: DMSO Time 24 Hours rep1

description: SAMPLE 2

tag: cell type


title: Leaf_treated_15°C_in_a_brightly_lit_field_0_hr

description: Gene expression of leaf treated 15°C in a brightly lit field, 0 hr of E.ulmoides

source_name: Leaf treated 15°C in a brightly lit field, 0 hr


title: BufoBoreas-Skin_control_rep6

description:
NA
Bb13A

source_name: Skin

value: Skin


title: Leaf_treated_42°C_in_a_brightly_lit_field_24_hr

description: Gene expression of leaf treated 42°C in a brightly lit field, 24 hr of E.ulmoides

source_name: Leaf treated 42°C in a brightly lit field, 24 hr


title: BufoMarinus-Skin_control_rep1

description:
incidental co-infection with intradermal nematode
Bm3A


title: NT Time 0 rep1

description: SAMPLE 1

tag: cell line

value: none (untreated control)

value: 0hr; the starting point of the treatment


title: Pep3M Time 24 Hours rep1

description: SAMPLE 3

source_name: HCT116_Pep3M_24 hrs

tag: cell line info.


title: endothelial cells_young_control_rep2

description: Replicate 2 of 3

value: young (p6)

value: untreated


title: BufoMarinus-Liver_Bd-infected_rep1

description:
NA
Bm1D

source_name: Liver

value: Liver


title: BufoMarinus-Liver_control_rep1

description:
incidental co-infection with intradermal nematode
Bm3D

value: Wild-type


title: Leaf_treated_42°C_in_a_brightly_lit_field_3_hr

description: Gene expression of leaf treated 42°C in a brightly lit field, 3 hr of E.ulmoides

source_name: Leaf treated 42°C in a brightly lit field, 3 hr


title: BufoMarinus-Skin_Bd-infected_rep1

description:
NA
Bm1A

value: normal


title: BufoMarinus-Liver_control_rep4

description:
NA
Bm7D


title: BufoBoreas-Liver_Bd-infected_rep3

description:
NA
Bb7D


title: Leaf_treated_27°C_in_the_dark_3_hr 1

description: Gene expression of leaf treated 27°C in the dark, 3 hr of E.ulmoides

source_name: Leaf treated 27°C in the dark, 3 hr


title: Leaf_treated_27°C_in_the_dark_24_hr 1

description: Gene expression of leaf treated 27°C in the dark, 24 hr of E.ulmoides

source_name: Leaf treated 27°C in the dark, 24 hr


title: Leaf_treated_27°C_in_the_dark_0_hr 1

description: Gene expression of leaf treated 27°C in the dark, 0 hr of E.ulmoides

source_name: Leaf treated 27°C in the dark, 0 hr


title: Leaf_treated_27°C_in_the_dark_0_hr 2


title: Leaf_treated_37°C_in_the_dark_24_hr

description: Gene expression of leaf treated 37°C in the dark, 24 hr of E.ulmoides

source_name: Leaf treated 37°C in the dark, 24 hr


title: Leaf_treated_27°C_in_a_brightly_lit_field_0_hr

description: Gene expression of leaf treated 27°C in a brightly lit field, 0 hr of E.ulmoides

source_name: Leaf treated 27°C in a brightly lit field, 0 hr


title: MUG-CC1_2

city: Ulm

first: Kevin

last: Mellert

address: Albert-Einstein-Allee 23

department: Institute of Pathology

country: Germany

institute: University Hospital Ulm

hyb_protocol: 100 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 25 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human 4x44K Whole Genome Microarray (G412F) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.1.1(Agilent) using Default Parameters (protocol GE1_1200_Jun14 and grid: 014850_D_F_20080627) to obtain Background subtracted and spatially detrended processed signal intensities.

source_name: Clivus chordoma_MUG-CC1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer

growth_protocol: The cell lines were cultured in Iscove’s Modified Dulbecco’s Medium/RPMI 1640 (4:1; Lonza, Basel, Switzerland) with 10 % fetal bovine serum (Biochrom AG, Berlin, Germany), 2 mM glutamine, and penicillin/streptomycin

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The cell lines were not treated with any reagents.

value: Clivus chordoma

value: stable chordoma cell line


title: Leaf_treated_27°C_in_the_dark_24_hr 2


title: Leaf_treated_27°C_in_a_brightly_lit_field_3_hr

description: Gene expression of leaf treated 27°C in a brightly lit field, 3 hr of E.ulmoides

source_name: Leaf treated 27°C in a brightly lit field, 3 hr


title: BufoBoreas-Spleen_control_rep4

description:
NA
Bb9E

data_processing: Each tissue type (skin, liver, and spleen) was analyzed separately.  Using the R package oligo, each array was background corrected and normalized using the quantile normalization procedure. Each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure (Irizarry et al. Biostatistics 4(2):249). The median polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed

value: Spleen


title: Leaf_treated_27°C_in_a_brightly_lit_field_24_hr

description: Gene expression of leaf treated 27°C in a brightly lit field, 24 hr of E.ulmoides

source_name: Leaf treated 27°C in a brightly lit field, 24 hr


title: Leaf_treated_27°C_in_the_dark_3_hr 2


title: MUG-CC1_3


title: UM-Chor1_3

source_name: Clivus chordoma_UM-Chor1


title: BufoBoreas-Spleen_Bd-infected_rep4

description:
NA
Bb8E

source_name: Spleen


title: BufoMarinus-Spleen_control_rep4

description:
NA
Bm7E


title: UM-Chor1_1


title: BufoMarinus-Spleen_Bd-infected_rep5

description:
NA
Bm14E


title: UM-Chor1_2


title: U-CH14_3

source_name: Clivus chordoma_U-CH14


title: Leaf_treated_42°C_in_a_brightly_lit_field_0_hr

description: Gene expression of leaf treated 42°C in a brightly lit field, 0 hr of E.ulmoides

source_name: Leaf treated 42°C in a brightly lit field, 0 hr


title: BufoBoreas-Spleen_control_rep6

description:
NA
Bb13E


title: Leaf_treated_37°C_in_the_dark_3_hr

description: Gene expression of leaf treated 37°C in the dark, 3 hr of E.ulmoides

source_name: Leaf treated 37°C in the dark, 3 hr


title: BufoBoreas-Spleen_Bd-infected_rep5

description:
NA
Bb12E


title: MUG-CC1_1


title: Leaf_treated_37°C_in_the_dark_0_hr

description: Gene expression of leaf treated 37°C in the dark, 0 hr of E.ulmoides

source_name: Leaf treated 37°C in the dark, 0 hr


title: Leaf_treated_37°C_in_a_brightly_lit_field_24_hr

description: Gene expression of leaf treated 37°C in a brightly lit field, 24 hr of E.ulmoides

source_name: Leaf treated 37°C in a brightly lit field, 24 hr


title: BufoMarinus-Spleen_Bd-infected_rep4

description:
NA
Bm8E


title: Leaf_treated_37°C_in_a_brightly_lit_field_3_hr

description: Gene expression of leaf treated 37°C in a brightly lit field, 3 hr of E.ulmoides

source_name: Leaf treated 37°C in a brightly lit field, 3 hr


title: U-CH14_2


title: U-CH14_1


title: Leaf_treated_37°C_in_a_brightly_lit_field_0_hr

description: Gene expression of leaf treated 37°C in a brightly lit field, 0 hr of E.ulmoides

source_name: Leaf treated 37°C in a brightly lit field, 0 hr


title: BufoMarinus-Spleen_Bd-infected_rep6

description:
NA
Bm20E


title: Fruit_treated_with_10_μM_ABA_for_12_hr

description: Gene expression of fruit treated with 10 μm ABA for 12 hr of E.ulmoides

source_name: Fruit treated with 10 μM ABA for 12 hr

value: Hormon treated fruit

value: Female


title: BufoBoreas-Spleen_Bd-infected_rep6

description:
NA
Bb14E


title: Fruit_treated_with_10_μM_ABA_for_0_hr

description: Gene expression of fruit treated with 10 μm ABA for 0 hr of E.ulmoides

source_name: Fruit treated with 10 μM ABA for 0 hr


title: Fruit_treated_with_20_μM_NPA_for_24_hr

description: Gene expression of fruit treated with 20 μm NPA for 24 hr of E.ulmoides

source_name: Fruit treated with 20 μM NPA for 24 hr


title: Fruit_treated_with_10_μM_ABA_for_24_hr

description: Gene expression of fruit treated with 10 μm ABA for 24 hr of E.ulmoides

source_name: Fruit treated with 10 μM ABA for 24 hr


title: Fruit_treated_with_20_μM_NPA_for_12_hr

description: Gene expression of fruit treated with 20 μm NPA for 12 hr of E.ulmoides

source_name: Fruit treated with 20 μM NPA for 12 hr


title: BufoMarinus-Spleen_control_rep6

description:
NA
Bm11E


title: Fruit_treated_with_10_μM_ABA_for_3_hr

description: Gene expression of fruit treated with 10 μm ABA for 3 hr of E.ulmoides

source_name: Fruit treated with 10 μM ABA for 3 hr


title: Fruit_treated_with_20_μM_NPA_for_3_hr

description: Gene expression of fruit treated with 20 μm NPA for 3 hr of E.ulmoides

source_name: Fruit treated with 20 μM NPA for 3 hr


title: BufoBoreas-Spleen_control_rep1

description:
NA
Bb3E


title: BufoMarinus-Spleen_control_rep5

description:
NA
Bm9E


title: BufoMarinus-Spleen_Bd-infected_rep3

description:
NA
Bm6E


title: BufoBoreas-Spleen_Bd-infected_rep2

description:
NA
Bb2E


title: Fruit_treated_with_20_μM_NPA_for_0_hr

description: Gene expression of fruit treated with 20 μm NPA for 0 hr of E.ulmoides

source_name: Fruit treated with 20 μM NPA for 0 hr


title: BufoBoreas-Spleen_control_rep3

description:
NA
Bb6E


title: Fruit_treated_with_20_μM_NPA_for_6_hr

description: Gene expression of fruit treated with 20 μm NPA for 6 hr of E.ulmoides

source_name: Fruit treated with 20 μM NPA for 6 hr


title: BufoMarinus-Spleen_control_rep2

description:
NA
Bm4E

source_name: Spleen


title: Fruit_treated_with_10_μM_IAA_+_20_mM_NPA_for_24_hr

description: Gene expression of fruit treated with 10 μm iAA + 20 mm NPA for 24 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA + 20 mM NPA for 24 hr


title: Fruit_treated_with_10_μM_IAA_+_20_mM_NPA_for_12_hr

description: Gene expression of fruit treated with 10 μm iAA + 20 mm NPA for 12 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA + 20 mM NPA for 12 hr


title: BufoBoreas-Skin_control_rep5

description:
NA
Bb10A

source_name: Skin


title: BufoMarinus-Spleen_Bd-infected_rep2

description:
NA
Bm2E


title: Fruit_treated_with_10_μM_ABA_for_6_hr

description: Gene expression of fruit treated with 10 μm ABA for 6 hr of E.ulmoides

source_name: Fruit treated with 10 μM ABA for 6 hr


title: BufoBoreas-Spleen_Bd-infected_rep1

description:
NA
Bb1E


title: Fruit_treated_with_10_μM_IAA_+_20_mM_NPA_for_6_hr

description: Gene expression of fruit treated with 10 μm iAA + 20 mm NPA for 6 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA + 20 mM NPA for 6 hr


title: BufoBoreas-Spleen_Bd-infected_rep3

description:
NA
Bb7E


title: BufoMarinus-Spleen_control_rep3

description:
NA
Bm5E


title: Untreated_fruit_24_hr_control

description: Gene expression of untreated fruit, 24 hr (control) of E.ulmoides

source_name: Untreated fruit, 24 hr (control)


title: Fruit_treated_with_10_μM_IAA_+_20_mM_NPA_for_3_hr

description: Gene expression of fruit treated with 10 μm iAA + 20 mm NPA for 3 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA + 20 mM NPA for 3 hr


title: Fruit_treated_with_10_μM_IAA_for_0_hr

description: Gene expression of fruit treated with 10 μm iAA for 0 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA for 0 hr


title: Fruit_treated_with_10_μM_IAA_+_20_mM_NPA_for_0_hr

description: Gene expression of fruit treated with 10 μm iAA + 20 mm NPA for 0 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA + 20 mM NPA for 0 hr


title: Untreated_fruit_12_hr_control

description: Gene expression of untreated fruit, 12 hr (control) of E.ulmoides

source_name: Untreated fruit, 12 hr (control)


title: BufoMarinus-Skin_control_rep5

description:
NA
Bm9A


title: BufoBoreas-Skin_Bd-infected_rep4

description:
NA
Bb8A


title: Fruit_treated_with_10_μM_IAA_for_24_hr

description: Gene expression of fruit treated with 10 μm iAA for 24 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA for 24 hr


title: BufoMarinus-Skin_control_rep4

description:
NA
Bm7A


title: Untreated_fruit_6_hr_control

description: Gene expression of untreated fruit, 6 hr (control) of E.ulmoides

source_name: Untreated fruit, 6 hr (control)


title: BufoBoreas-Skin_Bd-infected_rep5

description:
NA
Bb12A


title: Fruit_treated_with_10_μM_IAA_for_3_hr

description: Gene expression of fruit treated with 10 μm iAA for 3 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA for 3 hr


title: BufoBoreas-Skin_control_rep4

description:
NA
Bb9A


title: BufoBoreas-Skin_Bd-infected_rep6

description:
NA
Bb18A


title: BufoBoreas-Skin_Bd-infected_rep2

description:
NA
Bb2A


title: BufoBoreas-Skin_Bd-infected_rep1

description:
NA
Bb1A


title: BufoMarinus-Skin_control_rep2

description:
NA
Bm4A


title: BufoMarinus-Skin_Bd-infected_rep5

description:
NA
Bm14A


title: BufoBoreas-Skin_Bd-infected_rep3

description:
NA
Bb7A


title: Untreated_fruit_3_hr_control

description: Gene expression of untreated fruit, 3 hr (control) of E.ulmoides

source_name: Untreated fruit, 3 hr (control)


title: Fruit_treated_with_10_μM_IAA_for_12_hr

description: Gene expression of fruit treated with 10 μm iAA for 12 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA for 12 hr


title: Untreated_fruit_0_hr_control

description: Gene expression of untreated fruit, 0 hr (control) of E.ulmoides

source_name: Untreated fruit, 0 hr (control)


title: BufoMarinus-Skin_Bd-infected_rep6

description:
NA
Bm18A


title: Leaf 19

description: Gene expression of leaf of E.ulmoides

source_name: Leaf

value: Female leaf


title: BufoBoreas-Skin_control_rep2

description:
NA
Bb4A


title: BufoMarinus-Skin_Bd-infected_rep4

description:
NA
Bm8A


title: Leaf 18

description: Gene expression of leaf of E.ulmoides


title: BufoMarinus-Skin_control_rep3

description:
NA
Bm5A


title: Leaf 16

description: Gene expression of leaf of E.ulmoides


title: Leaf 15

description: Gene expression of leaf of E.ulmoides


title: Fruit_treated_with_10_μM_IAA_for_6_hr

description: Gene expression of fruit treated with 10 μm iAA for 6 hr of E.ulmoides

source_name: Fruit treated with 10 μM IAA for 6 hr


title: Leaf 14

description: Gene expression of leaf of E.ulmoides


title: Leaf 13

description: Gene expression of leaf of E.ulmoides


title: BufoMarinus-Skin_Bd-infected_rep3

description:
NA
Bm6A


title: Leaf_bud 2

description: Gene expression of leaf bud of E.ulmoides

source_name: Leaf bud


title: Leaf 17

description: Gene expression of leaf of E.ulmoides


title: Leaf 12

description: Gene expression of leaf of E.ulmoides


title: Leaf 8

description: Gene expression of leaf of E.ulmoides

value: Male leaf


title: Leaf 10

description: Gene expression of leaf of E.ulmoides


title: Leaf 11

description: Gene expression of leaf of E.ulmoides


title: Leaf 6

description: Gene expression of leaf of E.ulmoides


title: BufoBoreas-Liver_Bd-infected_rep4

description:
NA
Bb8D

source_name: Liver


title: BufoMarinus-Liver_Bd-infected_rep4

description:
NA
Bm8D


title: BufoBoreas-Liver_control_rep6

description:
NA
Bb13D


title: BufoBoreas-Liver_control_rep4

description:
NA
Bb9D


title: BufoMarinus-Skin_Bd-infected_rep2

description:
NA
Bm2A

source_name: Skin


title: BufoMarinus-Liver_control_rep6

description:
NA
Bm11D


title: BufoBoreas-Liver_Bd-infected_rep5

description:
NA
Bb12D


title: BufoBoreas-Skin_control_rep1

description:
NA
Bb3A


title: Leaf 7

description: Gene expression of leaf of E.ulmoides


title: BufoBoreas-Skin_control_rep3

description:
NA
Bb6A


title: BufoMarinus-Liver_Bd-infected_rep5

description:
NA
Bm14D


title: BufoMarinus-Liver_Bd-infected_rep6

description:
NA
Bm20D


title: Leaf 9

description: Gene expression of leaf of E.ulmoides


title: BufoMarinus-Liver_control_rep5

description:
NA
Bm9D


title: Leaf 5

description: Gene expression of leaf of E.ulmoides


title: BufoBoreas-Liver_Bd-infected_rep6

description:
NA
Bb14D


title: BufoBoreas-Liver_Bd-infected_rep1

description:
NA
Bb1D


title: Leaf 3

description: Gene expression of leaf of E.ulmoides


title: Leaf 4

description: Gene expression of leaf of E.ulmoides


title: Leaf 2

description: Gene expression of leaf of E.ulmoides


title: BufoBoreas-Liver_control_rep5

description:
NA
Bb10D


title: Male_flower 1

description: Gene expression of male flower of E.ulmoides

source_name: Male flower

value: Male flower


title: BufoBoreas-Liver_control_rep2

description:
NA
Bb4D


title: BufoMarinus-Liver_Bd-infected_rep2

description:
NA
Bm2D


title: Female_flower 2

description: Gene expression of female flower of E.ulmoides

source_name: Female flower

value: Female flower/fruit


title: Female_flower 5


title: BufoMarinus-Liver_control_rep2

description:
NA
Bm4D


title: Leaf 1

description: Gene expression of leaf of E.ulmoides

value: Male


title: Female_flower 3


title: Female_flower 4


title: BufoBoreas-Liver_Bd-infected_rep2

description:
NA
Bb2D


title: Male_flower 3


title: BufoBoreas-Liver_control_rep1

description:
NA
Bb3D


title: BufoMarinus-Liver_Bd-infected_rep3

description:
NA
Bm6D


title: Male_flower 2


title: Immature_fruit_without_wing

description: Gene expression of immature fruit without wing of E.ulmoides

source_name: Immature fruit without wing


title: Female_flower 6


title: Female_flower 1


title: Immature_fruit 12

description: Gene expression of immature fruit of E.ulmoides

source_name: Immature fruit


title: Wing_of_immature_fruit

description: Gene expression of wing of immature fruit of E.ulmoides

source_name: Wing of immature fruit


title: BufoBoreas-Liver_control_rep3

description:
NA
Bb6D


title: BufoMarinus-Liver_control_rep3

description:
NA
Bm5D


title: P3

city: Guangzhou

first: Xin

last: Wang

address: Duobao Road, No. 63

department: Department of Obstetrics and Gynecology

country: China

institute: Third Affiliated Hospital of Guangzhou Medical University

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. The labeled cRNAs were hybridized onto the OE Biotech Human lncRNA Microarray V4.0 (4 × 180 K, Agilent), containing the global profiling of 78,243 human lncRNAs and 32776 coding transcripts which are derived from authoritative databases, including Agilent_human G3V2, broadlincRNA, Ensembl, frnadb v3.4, NONCODE v4, RefSeq, UCR and UCSC lincRNA transcript.

scan_protocol: After washing, the arrays were scanned with the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to analyze array images and extract the raw data. Genespring (Version 12.5, Agilent Technologies) was employed to finish the basic analysis of the raw data. Next, the raw data were normalized with the quantile algorithm. The probes that had at least 1 condition out of 2 conditions flagged as “P” were chosen for further data analysis. Differentially expressed lncRNAs were then identified through fold-change (FC) as well as P values calculated with t-test. The threshold for a dysregulated lncRNA was set as a fold-change (FC) value of 2.0 or greater and a p value less than 0.05. Afterwards, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were applied to explore the roles of these differentially expressed lncRNAs and all mRNAs

source_name: placenta

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA was transcribed to double strand cDNA after removal of rRNA by using an mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre Biotechnologies, USA), then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Placental tissues from late-onset PE patients and matched controls (4 samples per group, 8 samples total) were used for microarray analysis, which was performed in the laboratory of the OE Biotechnology Company in Shanghai, People’s Republic of China. The mirVana TM RNA Isolation Kit (Ambion, Foster City, CA, United States) was applied to extract total RNA from frozen samples, according to the manufacturer’s protocols, which were then eluted with 100 ml of nuclease-free water. Total RNA was quantified with the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). For each sample, the RNA Integrity Number (RIN) was greater than or equal to 7, the value of 28S/18S was greater than or equal to 0.7, and the total RNA can meet 2 or more than 2 experiments.

value: placenta

tag: gender

value: female

tag: disease state

value: LOPE


title: IgM BL.10.5

type: protein

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Serum is incubated with autoantigen array

hyb_protocol: Autoantigen array  protocol (microarray core, University of Texas Southwestern Medical Center, Dallas, TX

scan_protocol: Genepix Pro 6.0 software is used to analyze the image and generate the .GPR file (GenePix Results Format)

data_processing: Heatmap was generated using Cluster and treeview software (http://rana.lbl.gov/EisenSoftware.htm)

label: IgM

molecule: protein

source_name: Serum

label_protocol: autoantibodies binding to the antigens on the array detected with laser wavelengths 532nm (cy3 labeled anti-IgG)

extract_protocol: Sera were collected from NOD.B10Sn-H2b/J female mice and age and gender-matched C57BL/10 controls

tag: strain

tag: concentration

value: 0.5 mg/mL


title: Immature_fruit 10

tag: tissue


title: IgM BL.10.3


title: P4


title: P2


title: Immature_fruit 11


title: P1


title: IgM BL.10.4


title: IgM BL.10.2


title: Immature_fruit 9


title: N2


title: IgM BL.10.1


title: BufoMarinus-Skin_control_rep6

description:
NA
Bm11A

tag: excluded from analyses based on qc

value: Skin

tag: phenotype

tag: subject id


title: N4


title: IgM NOD.B10.5


title: Immature_fruit 6


title: IgM NOD.B10.4


title: Immature_fruit 7


title: Immature_fruit 8


title: Immature_fruit 5


title: Immature_fruit 4


title: N3


title: SAMPLE 8 2_4_clone treated with RA

description:
source: from internal cell line repository
ChAT-expressing 2/4 clone treated with Retinoic Acid

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole mouse genome oligonucleotide microarray (Agilent grid ID 028005), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

data_processing: Data filtering and normalization was performed using the Agilent GeneSpring GX 11.0 software. All the features with the flag gIsWellAboveBG=0 (too close to background) were filtered out and excluded from the following analysis. Filtered samples were normalized (aligned) to the 75th percentile. Then differential gene lists were obtained from filtered data using Microsoft Excel: expressed genes were selected by a fold change threshold = 2.0 in linear scale and a minimum absolute fluorescence level >100. The experiment was performed in duplicate and expression values with a coefficient of variation > 2.0 were filtered out and excluded from further analysis.

source_name: N18TG2 murine neuroblastoma cell line

label_protocol: 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: Both N18TG2 murine neuroblastoma cell lines and ChAT-expressing 2/4 clone  were grown in DMEM medium (Sigma) supplemented with 10% FBS (Hyclone), 2 mM L-glutamine, 100 U/L penicillin and 100 μg/L streptomycin at 37˚C and maintained in a humidified incubator containing 10% CO2. 2/4 clone was maintained in the presence of 200 μg/mL G418.

extract_protocol: Total RNA was extracted from hippocampus  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: For differentiation experiments N18TG2 cells and 2/4 cells were seeded at a density of 5×103 cells/cm2. The following day, the cells were induced to differentiate with 1 μM retinoic acid (All-trans retinoic acid, designated RA throughout the paper; Sigma) in a “differentiation medium” composed of DMEM + 1% FBS. RA was dissolved in dimethyl sulphoxide (DMSO; Sigma) and stored as a stock solution at -80˚C. Because of the light sensitivity of RA, all incubations were performed under subdued lighting. The DMSO concentration in each experiment was always ≤0.01%, which was not toxic and did not induce differentiation. For agonist and antagonist treatments N18TG2 cells and 2/4 cells were seeded at a density of 5×103 cells/cm2. After 24h cells were exposed to carbachol (Sigma-Aldrich) 10-4M, atropine (Sigma-Aldrich) 10-5M and mecamylamine (Sigma-Aldrich) 10-5M. Samples were collected at 1, 6 and 12h after the exposure.

tag: genotype/variation

value: ChAT-expressing 2/4 clone

value: treated with RA


title: SAMPLE 6 2_4_clone treated with RA


title: SAMPLE 7 N18TG2 untreated

description:
source: from internal cell line repository
mouse neuroblastoma N18TG2 cells, untreated

value: N18TG2 parental cells


title: SAMPLE 5 N18TG2 untreated


title: SAMPLE 4 2_4_clone untreated

description:
source: from internal cell line repository
ChAT-expressing 2/4 clone, untreated


title: IgM NOD.B10.1


title: IgM NOD.B10.3


title: N1

value: normal


title: IgM NOD.B10.2


title: Immature_fruit 2


title: Immature_fruit 1


title: Outer_stem_tissue_current_year 5

description: Gene expression of outer stem tissue, current year of E.ulmoides

source_name: Outer stem tissue, current year

value: Outer stem tissue


title: Outer_stem_tissue_current_year 4


title: IgG BL.10.4

label: IgG

value: 1.5 mg/mL


title: IgG BL.10.3


title: IgG BL.10.2


title: IgG BL.10.5


title: IgG BL.10.1


title: Outer_stem_tissue_current_year 3


title: Immature_fruit 3

value: Female


title: Outer_stem_tissue_2nd_year

description: Gene expression of outer stem tissue, 2nd year of E.ulmoides

source_name: Outer stem tissue, 2nd year


title: IgG NOD.B10.5

value: 4 mg/mL


title: Outer_stem_tissue_current_year 2


title: Outer_stem_tissue_current_year 1


title: NGFwt_DRG 1

description: Cell cultures from dissociated Dorsal Root Ganglia of neonatal rat

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K Agilent whole rat  genome oligonucleotide microarray (grid ID 028279), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Then differential gene lists were obtained from filtered data using Microsoft Excel. Differentially expressed genes were identified by a combination of T test and foldchange.

organism: Rattus norvegicus

source_name: Cell Culture from Dorsal Root Ganglia

growth_protocol: All procedures were approved by the Italian Ministry of Health (Rome, Italy) and performed in compliance with the guidelines of the US National Institutes of Health and the Italian Ministry of Health (D.L.116/92). DRGs were prepared from neonatal (0-5 days) Wistar rats (Charles River) from both sex, as reported in (Taneda et al., 2010).  DRGs were collected, incubated for 1 hour at 37°C with 0.125% collagenase (Sigma, St. Louis, MO, USA), mechanically dissociated and plated onto coverslips or Petri dishes pretreated with 10 μg/mL poly-L-lysine (Sigma-Aldrich, St Louis, MO), at a density of 50000 cells/well of a 48 well tissue culture plate. The DRG cultures were maintained in serum-free medium, consisting of Dulbecco’s modified Eagle’s medium (DMEM)/F12 (Invitrogen, Carlsbad, CA, USA) supplemented with 87.5 ng/mL 5-fluoro-2′-deoxyuridine, 37.5 ng/mL uridine, 50 U/mL penicillin and 50 μg/mL streptomycin (all from Sigma) and 0.05% N2 supplement (Invitrogen, Carlsbad, CA, USA) at 37 °C in 5% CO2.

extract_protocol: At the end of the incubation period, media and cells were collected for RNA extraction and microarray analysis. Total RNA was extracted from DRGs  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: After 2–3 days in vitro, DRG cultures were stimulated for further experimental procedures using either double mutant hNGFP61S/R100E (n=3 replicates), single mutant hNGFP61S (n=3 replicates) or hNGF wild type (n=2 replicates) at 100 ng/ml concentration for 5 days.

value: Dorsal Root Ganglion from neonatal rats

tag: age

value: 0-5 days

value: hNGF wild type at 100 ng/ml

value: pooled male and female cells


title: IgG NOD.B10.4


title: SAMPLE 2 2_4_clone untreated


title: NGF61_100_DRG 3

value: hNGFP61S/R100E at 100 ng/ml


title: NGFwt_DRG 2


title: SAMPLE 1 N18TG2 treated with RA

description:
source: from internal cell line repository
mouse neuroblastoma N18TG2 cells treated with Retinoic Acid


title: SAMPLE 3 N18TG2 treated with RA


title: NGF61_DRG 3

value: hNGFP61S at 100 ng/ml


title: NGF61_100_DRG 2


title: IgG NOD.B10.3


title: NGF61_100_DRG 1


title: Inner_stem_tissue_current_year 5

description: Gene expression of inner stem tissue, current year of E.ulmoides

source_name: Inner stem tissue, current year

value: Inner stem tissue

value: Male


title: Inner_stem_tissue_2nd_year

description: Gene expression of inner stem tissue, 2nd year of E.ulmoides

source_name: Inner stem tissue, 2nd year


title: IgG NOD.B10.2


title: Inner_stem_tissue_current_year 4


title: IgG NOD.B10.1


title: Inner_stem_tissue_current_year 1


title: Inner_stem_tissue_current_year 2


title: Inner_stem_tissue_current_year 3


title: NGF61_DRG 2


title: Leaf_bud 1

value: Male leaf


title: NGF61_DRG 1


title: NHEK_poly(I:C)

status: Public on Apr 17 2017

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Gene expression data from NHEKs treated with or without poly(I:C)

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: Normal cultured primary human epidermal keratinocytes

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: Normal human epidermal keratinocytes (NHEKs) were harvested from neonatal foreskins and cultured in KGM-GOLD for up to 3 passages before use.

extract_protocol: Total RNA was isolated from cells using the RNeasy kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Cells were treated with vehicle or 30 ug/ml poly(I:C) for 24 hours, followed by 72 hours recovery time in KGM-GOLD.

value: epidermal keratinocytes

value: Treated keratinocytes with poly(I:C)

value: neonatal


title: NHEK_vehicle

value: Normal keratinocyte control without poly(I:C)


title: 561965A12 - 77_TREATMENT5_24H_REP3 vs 71_WATER_24H_REP3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 77_TREATMENT5_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Vitis vinifera

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: caulin leaf - peat+perlite (4:1). RH 65%. 20+/-2°C. Daylight + HQI light

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:.

tag: vitis vinifera  - age

treatment_protocol: Name:T5_24H - compound based treatment - plant defense activation ,water:.


title: 561965A06 - 74_TREATMENT2_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 74_TREATMENT2_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T2_24H - compound based treatment - plant defense activation ,water inoculation:.


title: 561965A09 - 71_WATER_24H_REP3 vs 76_TREATMENT4_24H_REP3

hyb_protocol: 76_TREATMENT4_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T4_24H - compound based treatment - plant defense activation ,water:.


title: 561891A10 - 62_TREATMENT4_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 62_TREATMENT4_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: no treatment


title: 561965A02 - 72_ADJ_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 72_ADJ_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:ADJUVANT_24H - compound based treatment - control,adjuvant:.


title: 561965A07 - 71_WATER_24H_REP3 vs 75_TREATMENT3_24H_REP3

hyb_protocol: 75_TREATMENT3_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol.

treatment_protocol: Name:T3_24H - compound based treatment - plant defense activation ,water:.


title: 561965A01 - 71_WATER_24H_REP3 vs 72_ADJ_24H_REP3

hyb_protocol: 72_ADJ_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A11 - 57_WATER_24H_REP2 vs 63_TREATMENT5_24H_REP2

hyb_protocol: 63_TREATMENT5_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A08 - 61_TREATMENT3_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 61_TREATMENT3_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561965A10 - 76_TREATMENT4_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 76_TREATMENT4_24H_REP3 Cy3 : 30mmol. (Hybridization_Protocol.txt) 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: 561965A05 - 71_WATER_24H_REP3 vs 74_TREATMENT2_24H_REP3

hyb_protocol: 74_TREATMENT2_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A12 - 63_TREATMENT5_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 63_TREATMENT5_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561965A08 - 75_TREATMENT3_24H_REP3 vs 71_WATER_24H_REP3

hyb_protocol: 71_WATER_24H_REP3 Cy5 / 75_TREATMENT3_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A10 - 48_TREATMENT4_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 48_TREATMENT4_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A09 - 57_WATER_24H_REP2 vs 62_TREATMENT4_24H_REP2

hyb_protocol: 62_TREATMENT4_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A08 - 47_TREATMENT3_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 47_TREATMENT3_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:. Name: - compound based treatment - plant defense activation ,water:.


title: 561891A05 - 57_WATER_24H_REP2 vs 60_TREATMENT2_24H_REP2

hyb_protocol: 60_TREATMENT2_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A07 - 57_WATER_24H_REP2 vs 61_TREATMENT3_24H_REP2

hyb_protocol: 61_TREATMENT3_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A09 - 43_WATER_24H_REP1 vs 48_TREATMENT4_24H_REP1

hyb_protocol: 48_TREATMENT4_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A04 - 59_TREATMENT1_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 59_TREATMENT1_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:T1_24H - compound based treatment - plant defense activation ,water inoculation:.


title: 561856A11 - 43_WATER_24H_REP1 vs 49_TREATMENT5_24H_REP1

hyb_protocol: 49_TREATMENT5_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A02 - 58_ADJ_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 58_ADJ_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A07 - 43_WATER_24H_REP1 vs 47_TREATMENT3_24H_REP1

hyb_protocol: 47_TREATMENT3_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561965A11 - 71_WATER_24H_REP3 vs 77_TREATMENT5_24H_REP3

hyb_protocol: 77_TREATMENT5_24H_REP3 Cy5 / 71_WATER_24H_REP3 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A03 - 57_WATER_24H_REP2 vs 59_TREATMENT1_24H_REP2

hyb_protocol: 59_TREATMENT1_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A06 - 60_TREATMENT2_24H_REP2 vs 57_WATER_24H_REP2

hyb_protocol: 57_WATER_24H_REP2 Cy5 / 60_TREATMENT2_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561891A01 - 57_WATER_24H_REP2 vs 58_ADJ_24H_REP2

hyb_protocol: 58_ADJ_24H_REP2 Cy5 / 57_WATER_24H_REP2 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A12 - 49_TREATMENT5_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 49_TREATMENT5_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A06 - 46_TREATMENT2_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 46_TREATMENT2_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A05 - 43_WATER_24H_REP1 vs 46_TREATMENT2_24H_REP1

hyb_protocol: 46_TREATMENT2_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A03 - 43_WATER_24H_REP1 vs 45_TREATMENT1_24H_REP1

hyb_protocol: 45_TREATMENT1_24H_REP1 Cy5 / 43_WATER_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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: 561856A04 - 45_TREATMENT1_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 45_TREATMENT1_24H_REP1 Cy3 : 30pmol. (Hybridization_Protocol.txt) 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.