title: DP31-21%

institute: Gifu University Graduate School of Medicine

description: Gene expression under 21% O2

value: female


title: DP185-3%

status: Public on Sep 03 2013

type: RNA

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

country: Japan

description: Gene expression under 3% O2

hyb_protocol: Following labeling and clean up, the amplified RNA and dye incorporation were quantified using a ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE) and hybridized to Agilent whole human genome 4 × 44 K oligo-DNA microarray (Agilent Technologies). After hybridization, the arrays were washed consecutively by using Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Fluorescence images of the hybridized arrays were generated using the Agilent DNA Microarray Scanner, and the intensities were extracted with Agilent Feature Extraction software ver.10.7.3.1. Each sample was analyzed once.

data_processing: The level of gene expression was determined by using Agilent Feature Extraction Software..

molecule: total RNA

organism: Homo sapiens

label_protocol: After RNA was qualified by the Agilent 2100 Bioanalyzer, 250 ng of total RNA was converted to cDNA, amplified, and labeled with Cy3-labeled CTP using the Low Input Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the protocol supplied by the manufacturer.

growth_protocol: Dental pulp cells were cultured in MSCGM medium (LONZA) under 21% and 3% oxygen concentration atomosphere.

extract_protocol: RNA extraction (RNeasy Plus Mini Kit; Qiagen, Valencia, CA, USA)

tag: tissue

value: dental pulp cells

tag: gender

value: male

tag: age

tag: oxygen concentration


title: HEMa, rep 1

status: Public on Sep 04 2013

city: Houston

first: HAI

last: LONG

state: TX

address: 1515 Holcombe Blvd., Unit 425

department: Leukemia

country: USA

institute: University of Texas MD Anderson Cancer Center

description: replicate 1

hyb_protocol: A total of 750ng of labelled cRNA was prepared for direct hybridization to the Sentrix HumanHT-12 v4 Beadchip as per Illumina’s protocol (Part # 11286340 Rev. A). All the four samples, each in triplicate, were loaded into 12 individual arrays on the same beadchip, and hybridized at 58°C for 16 hours on a rocking platform. After hybridization, the chip was washed, blocked, stained with Cy3 and washed again, and dried before scanning.

scan_protocol: Scanned by Illumina iScan system.

data_processing: Using the scanner operating software, GenomeStudio, signal on the array were converted into a TXT file as raw data. The data were normalized with quantile normalization for analysis.

label: biotin

source_name: Human Epidermal Melanocytes, adult, lightly pigmented donor (HEMa-LP)

label_protocol: For each sample, 500ng of total RNA was amplified and labeled with biotin using the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) as per standard protocol. The quantity of labelled product was determined using NanoDrop 1000 Spectrophotometer, and quality control was performed with Agilent 2100 Bioanalyzer.

growth_protocol: Melanoma cell lines SK-MEL-28 and LOXIMVI were cultured in Dulbecco’s modiﬁed Eagle's minimal essential medium (DMEM) and RPMI 1640 medium, respectively, supplemented with 2 mM L-glutamine and 10% fetal bovine serum. Two normal melanocytes, HEMn-LP and HEMa-LP, were purchased from Invitrogen (Carlsbad, CA) and grown in Medium 254 supplemented with HMGS-2 (Human Melanocyte Growth Supplement-2, PMA-Free) for 3-6 passages before we harvested them for RNA extraction. All cells were grown at 37°C in an atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen) as per manufacturer's protocol. The quantity of total RNA was determined with NanoDrop 1000 Spectrophotometer, and the quality control was performed with Agilent 2100 Bioanalyzer.

value: Male

value: adult

value: normal skin


title: DP31-3%

description: Gene expression under 3% O2


title: HEMn, rep 3

description: replicate 3

source_name: Human Epidermal Melanocytes, neonatal, lightly pigmented donor (HEMn-LP)

value: neonatal


title: HEMn, rep 1

description: replicate 1

data_processing: Using the scanner operating software, GenomeStudio, signals on the array were converted into a TXT file as raw data. The data were normalized with quantile normalization for analysis.


title: DC-7

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

description: gene expression data from cell culture

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade

data_processing:
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
Data were collected using the using the GeneChip operating software (GCOS) v1.4. The data was then analyzed using Partek Genomics Suite software version 6.5 using Robust Mulitchip Average (RMA) for data normalization.

source_name: MCF-7 cells from ATCC

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

growth_protocol: Cells were cultured in DMEM + 10 % Fetal plex media in 6 well plates at 37C, 5% C02 for 7 days total

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

treatment_protocol: Cells were treated daily with fresh media containing 200 uM Lacciac Acid A

tag: cell type

value: breast cancer cells

tag: agent


title: DC-8LA

description: gene expression data from cell culture

value: 200 uM Lacciac Acid A


title: WT-SIB_root-quiescent-center_rep2

city: Hayward

first: Don

middle: R

last: Maszle

state: CA

address: 3935 Point Eden Way

institute: Mendel Biotechnology, Inc.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization Protocol

scan_protocol: Affymetrix Scan Protocol using GCOS and Agilent G2500A Scanner

data_processing: Used R/Bioconductor fitPLM procedure to fit a probe-level model after first performing RMA.2 background correction and quantile normalization

organism: Arabidopsis thaliana

source_name: WT-SIB; root quiescent center; rep 2

label_protocol: Standard Biotin Label

growth_protocol: Stratified seeds were germinated on solid 80% MS medium (80% MS vitamins, 0.3% sucrose, 1% BactoAgar) with a 16:8 L:D photoperiod for 6 d. Seedlings were then transferred to vertical plates containing 80% MS (80% MS vitamins, 0.3% sucrose, 1% BactoAgar for an additional 5 d.

extract_protocol: Primary and lateral root tips from 11 d old seedlings were used for the collection of specific root tissues by laser microdissection. Preparation of paraffin sections (8 ??m) was performed as Jiao et al., 2009, with minor modifications. Tissue sections were imaged by fluorescene microscopy using the PALM MicroBeam System (Carl Zeiss, Germany), and quiescent center cells were were collected into adhesive caps. Three biological replicates, each pooled from 40 to 60 roots, were collected for each sample. Total RNA was prepared from the microdissected tissues using the PicroPure RNA isolation kit, and RiboAmp HS RNA amplification kit (Life Technologies, USA), and cRNA was generated using Turbo labeling Biotin Kit (Life Technologies, USA) according to the manual.

treatment_protocol: Seedlings were not treated.

tag: line

value: WT sibling

value: root quiescent center


title: CB1 CTL, biological replicate 1

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression data from neonatal neutrophils

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (EukGE-Ws2v4).

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

data_processing: The digital data retrieved from the CEL files were processed by Partek Genomic Suite version 6.5 using modified RMA-algorithm.

source_name: neonatal neutrophil

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Two-Cycle cDNA Synthesis Kit and IVT labeling kit).

growth_protocol: PGN induced transcriptional changes in human neonatal neutrophils

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy micro kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: PGN treatment for 4 hours at 10 microgram / microliter

value: neonatal neutrophil

tag: treatment

value: control

tag: source tissue

value: cord blood


title: DP185-21%

description: Gene expression under 21% O2


title: athb17-1_root-quiescent-center_rep4

source_name: athb17-1; root quiescent center; rep 4


title: DC-8

description: gene expression data from cell culture


title: DC-7LA

description: gene expression data from cell culture


title: HEMn, rep 2

description: replicate 2


title: DP54-21%

description: Gene expression under 21% O2


title: DC-5

description: gene expression data from cell culture


title: HEK293  treated  scramble OO-PNA oligo 48hr biological replicate 1

city: Bangkok

first: Chatchawit

last: Aporntewan

address: Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University

country: Thailand

institute: Chulalongkorn University

hyb_protocol: The cDNAs were hybridized using Affymetrix Human Gene 1.0 ST arrays for 18 hours at 45oC with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0007 fluidics protocol.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The scanned images were inspected for hybridization efficiency and CEL files generated from GCOS (GeneChip Operating Software) were imported into Expression Console (EC) 1.2 software for array QC. The matrix was created by Affymetrix Power Tools (APT) -- Release 1.14.3 on Windows 7. The command was apt-probeset-summarize -a rma -d HuGene-1_0-st-v1.r3.cdf -o out --cel-files cel_list.txt.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps
RMA normalization was performed on the samples to generate the quality control (QC) metrics to determine data quality. These include, perfect match mean (PM_Mean), Background mean (Bgd_Mean), positive and negative probes (POS vs NEG AUC), bacterials spike controls, and polyA controls.

source_name: Human Embryonic Kidney 293 cells, treated  scramble OO-PNA oligo, 48hr

label_protocol: DNA/RNA heteroduplex was amplified via SPIA (Single Primer Isothermal Amplification), which produces single stranded anti-sense DNA. Post –SPIA Modification generates sense target cDNA that was fragmented, biotin labeled according to Origen Labs’ Encore Biotin Module.

growth_protocol: HEK 293 cells were grown according to the manufacturer’s protocol in DMEM (Gibco-BRL) supplemented with 2 mM L-glutamine and 10% heat-inactivated fetal calf serum (FCS), and 10 mg/ml antibiotic antimycotic (Invitrogen) as before and after transfection. Cell harvest was performed at 48 hr post-transfection.

extract_protocol: All samples were RNA extracted according to the manufacturer’s protocol using Trizol (Invitrogen). Total RNA was reverse transcribed processed according to the Affymetrix and NuGEN recommended protocols, to produce cDNA/mRNA hybrid molecule, which was subsequently used as a template to create double stranded cDNA with a unique DNA/RNA heteroduplex on one end.

treatment_protocol: HEK293 cells were transfected with  50 nM of OO-A(15) and scramble OO-PNA oligo (OO-acgttcgcgcaacga).

tag: cell line

value: scramble OO-PNA oligo

tag: growth

value: adherent and monolayer


title: HEK293  treated  scramble OO-PNA oligo 48hr biological replicate 2


title: β-catenin siRNA transfection

city: Daegu

first: seung hyun

last: shin

address: 101 Dong-In-Dong, Jung-Gu

country: South Korea

institute: Department of Immunology and Hair Research Center, School of Medicine Kyungpook National University

description: Gene expression data from β-catenin siRNA transfected mouse dermal cells

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Mouse Gene 1.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000 (Affymetrix).

data_processing: The RMA algorithm was used for expression summary and signal calculation of Affymetrix Mouse Gene 1.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

organism: Mus musculus

source_name: β-catenin siRNA transfected dermal cells

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5).

growth_protocol: Freshly isolated dermal cells from the dorsal skins of C57BL/6 neonates (P0) were cultured in DMEM supplemented with 10% fetal bovine serum for 24 hours before siRNA transfection

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

treatment_protocol: Cultured dermal cells were transfected with either control siRNA or β-catenin specific siRNAs (β-catenin siRNA) at a final concentration of 10 nM for 48 hours

tag: strain

value: cultured neonatal dermal cells


title: Control siRNA transfection

description: Gene expression data from control siRNA transfected mouse dermal cells

source_name: control siRNA transfected dermal cells


title: HEK293  treated OO-A(15) 48hr biological replicate 2

source_name: Human Embryonic Kidney 293 cells, treated OO-A(15), 48hr


title: DC-5LA

description: gene expression data from cell culture


title: HEK293  treated OO-A(15) 48hr biological replicate 1


title: L1_control

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic gene expression data from control mouse

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix mouse Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method in R version 2.12.2 with the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set.

source_name: control mouse receiving normal drinking water throughout

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

treatment_protocol: A part of the most infiltrated colon was snap frozen for RNA isolation

value: female

value: 6 weeks

tag: colitis group

value: colon


title: N2_2cyclesrecov

description: Colonic gene expression data from 2 cycles DSS mouse with additional recovery period

source_name: mouse receiving 2 cycles of DSS followed by an additional recovery period of 3 weeks with normal drinking water

value: 2 cycles DSS with additional recovery period


title: G3_3cycles

description: Colonic gene expression data from 3 cycles DSS mouse

source_name: 3 cycles DSS mouse (DSS cycle was repeated three times)

value: 3 cycles DSS


title: M5_2cyclesrecov


title: F5_3cycles


title: E3_2cycles

description: Colonic gene expression data from 2 cycles DSS mouse

source_name: 2 cycles DSS mouse (DSS cycle was repeated twice)

value: 2 cycles DSS


title: L2_control


title: D5_2cycles


title: M1_2cyclesrecov


title: F1_3cycles


title: K3_1cycle

description: Colonic gene expression data from 1 cycle DSS mouse

source_name: 1 cycle DSS mouse (DSS for 7 days followed by a recovery period of 2 weeks with normal drinking water)

value: 1 cycle DSS


title: J5_1cylcle


title: J1_1cylcle


title: G2_3cycles


title: E2_2cycles


title: E4_2cycles


title: Adipocyte_amosite_replicate 2

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

institute: Nagoya University

hyb_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).

scan_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010, Agilent C Scanner Settings).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20110722) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: 3T3-L1 cultured adipocytes treated with amosite fibers

growth_protocol: Mature adipocytes were differentiated from 3T3-L1 preadipocyte cell line. After differentiation, mature adipocytes were maintained in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic (Gibco 15240). The cells were maintained in an incubator with 5% CO2 at 37oC.

extract_protocol: Total RNA was extracted using RNeasy Mini(QIAGEN).

treatment_protocol: Mature adipocytes were treated with different types of asbestos fibers at a concentration of 10 mg/cm2. After 72 hours of incubation, total RNA was isolated from the cells. Physiological saline was used as a control.

value: amosite fibers at 10 mg/cm2 for 72 hours.


title: D4_2cycles


title: M3_2cyclesrecov


title: N3_2cyclesrecov


title: K1_1cycle


title: K2_1cycle


title: F3_3cycles


title: C3_acute

description: Colonic gene expression data from acute colitis mouse

source_name: acute colitis mouse receiving 7 days of DSS without recovery period prior to sacrifice

value: acute colitis


title: B4_acute


title: Adipocytes_amosite_replicate 1

label_protocol: According to the manufacturer’s protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, May 2010).


title: Adipocytes_crocidolite_replicate 1

source_name: 3T3-L1 cultured adipocytes treated with crocidolite fibers

value: crocidolite fibers at 10 mg/cm2 for 72 hours.


title: B3_acute


title: Adipocytes_crocidolite_replicate 2


title: B2_acute


title: A1_control


title: C1_acute


title: Adipocytes_chrysotile_replicate 1

source_name: 3T3-L1 cultured adipocytes treated with chrysotile fibers

value: chrysotile fibers at 10 mg/cm2 for 72 hours.


title: A5_control


title: Adipocytes_chrysotile_replicate 2


title: C5_Icv placebo

city: Dallas

first: Teppei

last: Fujikawa

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UT Southwestern

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data processing was carried out on log2 transformed expression values using CyberT (http://cybert.ics.uci.edu/) with a window size of 51 and Bayesian confidence value of 5.
The complete data set ('cyberT_full_output.txt') contains further processed data generated by CyberT (e.g. ranking, Pvalue, diffMean etc).

source_name: Mouse Liver

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

extract_protocol: RNA was extracted with Trizol reagent, followed by QIAGEN RNeasy mini plus (gDNA eliminator) kit in accordance with the prescribed protocol provided with the kit.

tag: strain background

value: mixed

tag: genotype/variation

value: insulin-deficient mice

tag: sample group

value: icv PBS administration


title: L6_Icv leptin

value: icv leptin administration


title: L5_Icv leptin


title: C1_Icv placebo


title: C6_Icv placebo


title: A2_control

value: control


title: C2_Icv placebo


title: L3_Icv leptin


title: Adipocytes_physiological saline_replicate 1

source_name: 3T3-L1 cultured adipocytes treated with physiological saline

value: physiological saline


title: Adipocytes_physiological saline_replicate 2


title: C4_Icv placebo


title: C3_Icv placebo


title: L1_Icv leptin


title: L2_Icv leptin


title: L4_Icv leptin


title: Bursaphelenchus xylophilus inoculating Pinus thunbergii replicate 2

city: Nanjing

first: Jianren

last: Ye

state: Jiangsu

address: Long Pan Road

country: China

institute: Nanjing Forestry University

description: Biological replicate 2 of 3. Bursaphelenchus xylophilus, gene expression after  7 days inoculating Pinus thunbergii.

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

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Gene Spring software 11.0 (Agilent technologies, Santa Clara, CA, USA) was used for background subtraction and LOWESS normalization.

organism: Bursaphelenchus xylophilus

source_name: Bursaphelenchus xylophilus

label_protocol: 500 ng of total RNA were primed with 0.8 µl of  T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1.2 µl AffinityScript RNase Block Mix, and 5 mM dNTP mix , 0.24µl  Cy3-label

growth_protocol: Two treatments were applied: (i) A suspension of 5000 nematodes (a mixture of adults and juveniles) was used to inoculate a fungus  Botrytis cinerea (the fungus had been incubated at 25°C for 6 days) on potato dextrose agar medium and grown at 25°C for additional 7 days; (ii) The same amount of nematodes was pipetted into wounds (2 cm in length) of P. thunbergii seedlings, about 50 cm above soil level.

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

treatment_protocol: The nematodes were separated from  Botrytis cinerea and Pinus thunbergii seedlings in a Baermann funnel. Then,Bursaphelenchus xylophilus was collected by centrifugation at 3000 rpm for 1 min and frozen in liquid nitrogen for further RNA isolation.

value: day 7


title: BT549_AZD6244 24h_C

city: Nashville

first: Justin

middle: M

last: Balko

state: TN

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

description: SUM159PT cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 24 h before harvest

hyb_protocol: For the Gene 1.1ST Array plate, the requisite amount of target was then added to hybridization cocktail for Gene Titan WT array plates as specified in the GeneChip® WT Terminal Labeling and Hybridization User Manual (P/N 702808 Rev. 2) to give a final target concentration of ~25ng/ul in the hybridization cocktail. The total amount of target hybridized was 2.25ug. The target in hybridization cocktail was heat denatured at 99C for 5 minutes, cooled to 45C for 5 minutes, centrifuged and then loaded on the Affymetrix Array plate arrays for hybridization on the Affymetrix Gene Titan Instrument.

scan_protocol: The Array plate was washed and stained on the Gene Titan instrument using Affymetrix Hybidization Wash and Stain kit reagents for the Gene Titan instrument (P/N 901406). After washing and staining, the array was scanned in the Affymetrix Gene Titan instrument using AGCC v.3.1.1

data_processing: Signal was analyzed with Affymetrix Expression Console, v. 1.1, using an RMA normalization algorithm producing log base 2 results

label_protocol: Affymetrix WT Sense reactions, using the Ambion WT Reaction kit (Catalog#4411974), were assembled and run following the manufacturer’s protocol. Briefly, a sample mix of 100ng total RNA, and poly-A spike in controls (included in Affymetrix WT Terminal Labeling Kit Catalog# 901524), were brought to a 5 ul final volume with nuclease free H2O. First Strand Synthesis Master mix was added to the sample mix and incubated at 25C for 1 hour, followed by incubation at 42 C for 1 hour. Incubations were followed by a cooling to 4 C for 2 minutes. Subsequently, Second Strand Synthesis Master mix was added to the sample mix, and incubated at 16C for 1 hours. The reaction was heatinactivated by 10 minute incubation at 65C. The resulting cDNA was then processed in a 16 hour IVT reaction to generate cRNA. The cRNA was then cleaned using magnetic beads included with the kit, and was used as template in a second first strand synthesis reaction to generate target of the correct sense for hybridization to the Affymetrix Gene and Exon arrays. The Second Cycle cDNA synthesis reaction was set up with 10ug cRNA, random hexamer, and first strand synthesis reagents to make cDNA. The cDNA target was then treated with Rnase H to remove template cRNA and cleaned up over a kit supplied column, or Agencourt SPRI beads, following manufacturer’s protocol (RNAClean, Catalog#000494). A total of 5.5ug of the clean cDNA target was then enzymatically fragmented and end-labeled using the Affymetrix kit reagents (Catalog# 901524). The cRNA, cDNA, and fragmented and end-labeled target were assessed by Agilent bioanalysis to insure that the amplified target met the recommended smear range, and that fragmentation and end-labeling were complete.

growth_protocol: MDA231 cells were grown in DMEM+10% FBS; BT549 cells were grown in RPMI + 10% FBS; SUM159PT cells were grown in DMEM/F12 nutrient mix + 5% FBS + 0.5ug/mL hydrocortisone

extract_protocol: RNEasy kit (QIAGEN)

treatment_protocol: Cells were reverse transfected with 10nM control non targeting siRNA (dharmacon smart pool) or DUSP4-targeted siRNA.  Some control-siRNA treated cells were also treated with 4 or 24 h of 1uM selumetinib prior to harvest.  Remaining cells were treated with DMSO as a control for selumetinib.  All cells were harvested 96h after transfection.

tag: sirna

value: siCONTROL

tag: drug


title: mRNA, mouse postnatal day7, biological rep 5

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

description:
gene expression data from lung tissue of postnatal mice
d7_5

hyb_protocol: Labeled RNA was hybridized for 17 hr at 65C on Agilent 8X60K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters.

source_name: Lung tissue, mouse postnatal, day7, biological rep 5

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 500ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

tag: tissue

value: whole lung

value: 7 days


title: mRNA, mouse postnatal day7, biological rep 4

description:
gene expression data from lung tissue of postnatal mice
d7_4

source_name: Lung tissue, mouse postnatal, day7, biological rep 4

tag: age


title: BT549_AZD6244 24h_A

source_name: SUM159PT cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 24 h before harvest


title: Bursaphelenchus xylophilus inoculating Pinus thunbergii replicate 3

description: Biological replicate 3 of 3. Bursaphelenchus xylophilus, gene expression after  7 days inoculating Pinus thunbergii.


title: BT549_AZD6244 4h_C

description: SUM159PT cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 4 h before harvest


title: BT549_AZD6244 4h_B

source_name: SUM159PT cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 4 h before harvest


title: mRNA, mouse postnatal day7, biological rep 2

description:
gene expression data from lung tissue of postnatal mice
d7_2

source_name: Lung tissue, mouse postnatal, day7, biological rep 2


title: BT549_AZD6244 24h_B


title: mRNA, mouse postnatal day7, biological rep 3

description:
gene expression data from lung tissue of postnatal mice
d7_3

source_name: Lung tissue, mouse postnatal, day7, biological rep 3


title: Bursaphelenchus xylophilus inoculating Pinus thunbergii replicate 1

description: Biological replicate 1 of 3. Bursaphelenchus xylophilus, gene expression after  7 days inoculating Pinus thunbergii.


title: BT549_AZD6244 4h_A


title: BT549_siDUSP4_B

description: SUM159PT cells transfected with DUSP4 siRNA for 96 h

value: DMSO


title: BT549_siCONTROL_B

description: SUM159PT cells transfected with non-targeting siRNA for 96 h


title: mRNA, mouse postnatal day4, biological rep 5

description:
gene expression data from lung tissue of postnatal mice
d4_5

source_name: Lung tissue, mouse postnatal, day4, biological rep 5

value: 4 days


title: mRNA, mouse postnatal day4, biological rep 2

description:
gene expression data from lung tissue of postnatal mice
d4_2

source_name: Lung tissue, mouse postnatal, day4, biological rep 2


title: BT549_siCONTROL_C

source_name: SUM159PT cells transfected with non-targeting siRNA for 96 h


title: mRNA, mouse postnatal day4, biological rep 1

description:
gene expression data from lung tissue of postnatal mice
d4_1

source_name: Lung tissue, mouse postnatal, day4, biological rep 1


title: BT549_siDUSP4_A

source_name: SUM159PT cells transfected with DUSP4 siRNA for 96 h


title: mRNA, mouse postnatal day4, biological rep 4

description:
gene expression data from lung tissue of postnatal mice
d4_4

source_name: Lung tissue, mouse postnatal, day4, biological rep 4


title: mRNA, mouse postnatal day4, biological rep 3

description:
gene expression data from lung tissue of postnatal mice
d4_3

source_name: Lung tissue, mouse postnatal, day4, biological rep 3


title: BT549_siDUSP4_C


title: mRNA, mouse postnatal day7, biological rep 1

description:
gene expression data from lung tissue of postnatal mice
d7_1

source_name: Lung tissue, mouse postnatal, day7, biological rep 1


title: Bursaphelenchus xylophilus growing on Botrytis cinerea replicate 3

description: Biological replicate 3 of 3. Bursaphelenchus xylophilus, gene expression after  7 days growing on Botrytis cinerea.


title: BT549_siCONTROL_A


title: Bursaphelenchus xylophilus growing on Botrytis cinerea replicate 2

description: Biological replicate 2 of 3. Bursaphelenchus xylophilus, gene expression after  7 days growing on Botrytis cinerea.


title: mRNA, mouse postnatal day1, biological rep 5

description:
gene expression data from lung tissue of postnatal mice
d1_5

source_name: Lung tissue, mouse postnatal, day1, biological rep 5

value: 1 day


title: SUM159PT_AZD6244 24h_C

description: BT549 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 24 h before harvest


title: SUM159PT_AZD6244 4h_C

description: BT549 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 4 h before harvest


title: mRNA, mouse postnatal day1, biological rep 4

description:
gene expression data from lung tissue of postnatal mice
d1_4

source_name: Lung tissue, mouse postnatal, day1, biological rep 4


title: SUM159PT_AZD6244 24h_A

source_name: BT549 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 24 h before harvest


title: mRNA, mouse postnatal day1, biological rep 2

description:
gene expression data from lung tissue of postnatal mice
d1_2

source_name: Lung tissue, mouse postnatal, day1, biological rep 2


title: SUM159PT_AZD6244 24h_B


title: mRNA, mouse postnatal 2 week, biological rep 5

description:
gene expression data from lung tissue of postnatal mice
d14_5

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 5

value: 2 weeks


title: mRNA, mouse postnatal day1, biological rep 3

description:
gene expression data from lung tissue of postnatal mice
d1_3

source_name: Lung tissue, mouse postnatal, day1, biological rep 3


title: Bursaphelenchus xylophilus growing on Botrytis cinerea replicate 1

description: Biological replicate 1 of 3. Bursaphelenchus xylophilus, gene expression after  7 days growing on Botrytis cinerea.

source_name: Bursaphelenchus xylophilus


title: SUM159PT_siCONTROL_A

description: BT549 cells transfected with non-targeting siRNA for 96 h


title: SUM159PT_AZD6244 4h_B

source_name: BT549 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 4 h before harvest


title: SUM159PT_siDUSP4_B

description: BT549 cells transfected with DUSP4 siRNA for 96 h


title: SUM159PT_siCONTROL_C

source_name: BT549 cells transfected with non-targeting siRNA for 96 h


title: SUM159PT_siDUSP4_A

source_name: BT549 cells transfected with DUSP4 siRNA for 96 h


title: mRNA, mouse postnatal 2 week, biological rep 2

description:
gene expression data from lung tissue of postnatal mice
d14_2

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 2


title: MDA231_AZD6244 24h_C

description: MDA231 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 24 h before harvest


title: SUM159PT_siCONTROL_B


title: mRNA, mouse postnatal 2 week, biological rep 1

description:
gene expression data from lung tissue of postnatal mice
d14_1

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 1


title: SUM159PT_AZD6244 4h_A


title: mRNA, mouse postnatal day1, biological rep 1

description:
gene expression data from lung tissue of postnatal mice
d1_1

source_name: Lung tissue, mouse postnatal, day1, biological rep 1


title: mRNA, mouse postnatal 2 week, biological rep 4

description:
gene expression data from lung tissue of postnatal mice
d14_4

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 3


title: mRNA, mouse postnatal 6 week, biological rep 2

description:
gene expression data from lung tissue of postnatal mice
6wk_2

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 2

value: 6 weeks


title: mRNA, mouse postnatal 6 week, biological rep 4

description:
gene expression data from lung tissue of postnatal mice
6wk_4

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 4


title: mRNA, mouse postnatal 2 week, biological rep 3

description:
gene expression data from lung tissue of postnatal mice
d14_3


title: SUM159PT_siDUSP4_C


title: mRNA, mouse postnatal 6 week, biological rep 1

description:
gene expression data from lung tissue of postnatal mice
6wk_1

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 1


title: DP185-3% miRNA

description: Gene expression under 3% O2

hyb_protocol: and then hybridized to Agilent Microarray Sure Print G3 Human miRNA 8 × 60 K miRBase 16.0 using the miRNA Complete Labeling and Hyb Kit (Agilent Technologies).

scan_protocol: Following hybridization for 20 h, the slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies) and scanned using an Agilent Scanner.

data_processing: The images were processed and analyzed with Agilent Feature Extraction Software. The raw data were normalized using quantile normalization and then analyzed in GeneSpring GX software 11.5 (Agilent Technologies).

label_protocol: After dephosphorylation and denaturation, the total RNA was labeled with cyanine 3-pCp,

extract_protocol: Total RNA was isolated using an miRNeasy Mini Kit (Qiagen).

value: dental pulp cells

tag: gender

value: male


title: MDA231_AZD6244 24h_B

source_name: MDA231 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 24 h before harvest


title: mRNA, mouse postnatal 6 week, biological rep 3

description:
gene expression data from lung tissue of postnatal mice
6wk_3

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 3


title: DP185-21% miRNA

description: Gene expression under 21% O2


title: MDA231_AZD6244 4h_C

description: MDA231 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 4 h before harvest


title: DP54-3% miRNA

description: Gene expression under 3% O2


title: MDA231_AZD6244 24h_A


title: DP31-3% miRNA

description: Gene expression under 3% O2

value: female


title: siControl HeLa DOX

city: Bunkyo-ku

first: Junya

last: Kawauchi

state: Tokyo

address: Yushima 1-5-45

department: Medical Research Institute

institute: Tokyo Medical & Dental University

description: Gene expression of doxorubicin treated siControl HeLa Cells

hyb_protocol: Samples from the same cell line with siControl or siElonginA were hybridized to the same slide. Labeled cRNA samples were used for hybridization to Agilent 4x44K microarrays.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 44k array slides.

data_processing: Agilent Feature Extraction software; gProcessedSignal; processed Cy3 Signal

source_name: siControl HeLa, 1microM doxorubicin, 3hr , replicate 1

label_protocol: The mRNA samples were labeled and processed following the Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol with a total RNA input of 500 ng.

growth_protocol: DMEM + 10% FBS + antibiotics(penicillin/streptmycin)

extract_protocol: Total RNA extraction was performed using Sepazol RNA I super (Nacalai Tesque) according to the manufacturer's instructions.

treatment_protocol: Cells were treated 1microM Doxorubicin for 3hours.

value: HeLa


title: siEloA HeLa DOX

description: Gene expression of doxorubicin treated siEloA HeLa Cells

source_name: siEloA HeLa, 1microM doxorubicin, 3hr , replicate 1


title: MDA231_siDUSP4_C

description: MDA231 cells transfected with DUSP4 siRNA for 96 h


title: MDA231_AZD6244 4h_A

source_name: MDA231 cells transfected with non-targeting siRNA for 96 h and treated with selumetinib at 1uM 4 h before harvest


title: DP54-21% miRNA

description: Gene expression under 21% O2


title: MDA231_siDUSP4_A

source_name: MDA231 cells transfected with DUSP4 siRNA for 96 h


title: MDA231_AZD6244 4h_B


title: MDA231_siCONTROL_B

description: MDA231 cells transfected with non-targeting siRNA for 96 h


title: Hippocampi Sham, replicate 4

city: Girona

first: Gemma

last: Huguet

address: Campus de Montilivi

country: Spain

institute: Universitat de Girona

description:
Sham-4
Biological replicate 4 of 4. Hippocampi of sham rats versus brain tissue pool of reference.
Sham rats with electrode placement but without stimulation, handling process similar to stimulated animals.

hyb_protocol: After fragmentation, 750 ng of labeled cRNA from each of the two samples were co-hybridized in in situ hybridization buffer (Agilent) for 17 h at 65ºC and washed at rt 1 min in 6X SSPE (Saline Sodium Phosphate-EDTA) pH 7.4 + 0.005% Sarcosine, 1 min at rt in 0.06X SSPE_0.005% Sarcosine, 1 min in Acetonitrile and 30 s in Dye Stabilization and Drying solution (Agilent).

scan_protocol: Scanned on an Agilent G2565AA scanner at 10 µm resolution and quantified using GenePix 6.0 (Molecular Dynamics). Spots with signal intensities twice above the local background, not saturated and not flagged by GenePix were considered reliable and with a weight of 1 for normalization purposes, whereas the rest were given weights of 0.01.

data_processing: Raw data were processed using a web implementation of limma (Smyth, G. K. (2004). Raw data was corrected for background noise using the normexp method. Global lowess normalization was applied (intra-chip normalization). A further scaling of the normalized log2 ratios (inter-chip normalization) was applied to assure comparability across samples.

organism: Rattus norvegicus

source_name: Hippocampi of sham rats

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy5-CTP or Cy3-CTP using the Low Input RNA labeling kit (Agilent) and purified using RNeasy columns (Qiagen, Hilden, Germany).

extract_protocol:
Ipsilateral hippocampi, with respect to the electrode, dissected from slices between Bregma levels -2.56 and -3.60.

Tissues were conserved in RNAlater (Ambion, Austin, TX) for 48 h at 4ºC. Total RNAs were prepared with an RNeasy Lipid Tissue Mini kit according to the manufacturer's protocol (Qiagen, Valencia, CA).

treatment_protocol: Rats were implanted with a monopolar stainless steel electrode aimed at the lateral hypothalamus. After a post-surgery recovery period (7 days), the animals were trained in ICSS to establish the individual optimum current intensity of ICSS for 20 min on two consecutive days. Electrical brain stimulation consisted of 0.3-s trains of 50 Hz sinusoidal waves at intensities ranging from 10 and 400 µA. Rats in the Sham group were handled and allowed to explore the ICSS box for 20 min on two consecutive days, but without ICSS. Twenty-four hours after the last ICSS establishment session, animals in the ICSS group were allowed to self-administer 2500 trains of electrical stimulation. Animals in the Sham group were equally placed in the ICSS box for 40 min but did not receive stimulation (sham session).

value: Wistar

value: 13 weeks

value: hippocampus

value: sham

tag: sample type

value: pool from three rats

source_name: PollRef

extract_protocol:
Brain pooled tissue consisting of hippocampal, thalamic and cortical contralateral brain tissue with respect to the electrode placement.

Tissues were conserved in RNAlater (Ambion, Austin, TX) for 48 h at 4ºC. Total RNAs were prepared with an RNeasy Lipid Tissue Mini kit according to the manufacturer's protocol (Qiagen, Valencia, CA).

value: hippocampus, thalamus, and cortex of brain

value: reference pool from ICSS (n=3) and Sham rats (n=3)


title: MDA231_siCONTROL_A

source_name: MDA231 cells transfected with non-targeting siRNA for 96 h

value: siCONTROL


title: Hippocampi Sham, replicate 3

description:
Sham-3
Biological replicate 3 of 4. Hippocampi of sham rats versus brain tissue pool of reference.
Sham rats with electrode placement but without stimulation, handling process similar to stimulated animals.


title: Hippocampi Sham, replicate 1

description:
Sham-1
Biological replicate 1 of 4. Hippocampi of sham rats versus brain tissue pool of reference.
Sham rats with electrode placement but without stimulation, handling process similar to stimulated animals.


title: Hippocampi ICSS, replicate 4

description:
ICSS-4
Biological replicate 4 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.
ICSS rats subjected to acute self-stimulation (2500 stimulation trains). Electrode placement at lateral hypothalamus unilateraly in the right hemisphere.

source_name: Hippocampi of stimulated rats

value: intracranial self-stimulation (ICSS)


title: Hippocampi Sham, replicate 2

description:
Sham-2
Biological replicate 2 of 4. Hippocampi of sham rats versus brain tissue pool of reference.
Sham rats with electrode placement but without stimulation, handling process similar to stimulated animals.


title: Hippocampi ICSS, replicate 1

description:
ICSS-1
Biological replicate 1 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.
ICSS rats subjected to acute self-stimulation (2500 stimulation trains). Electrode placement at lateral hypothalamus unilateraly in the right hemisphere.


title: MDA231_siDUSP4_B

value: DMSO


title: P2 VICs cultured on TCPS, treated with TGF-beta1 at 5ng/ml for 8 hours, biological replicate 2

status: Public on Sep 02 2013

city: Beijing

first: Huan

last: Wang

address: Peking University Health Science Center, No. 38 Xueyuan Road, Haidian District

department: Basic Medical Sciences

institute: Peking University

description: Gene expression data from P2 VICs cultured on TCPS treated with TGFβ1 at 5ng/ml for 8 hours.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Spotfire (TIBCO) using default analysis settings and GCRMA as normalization method.

organism: Sus scrofa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA based on the GeneChip 3' IVT express kit.

growth_protocol: Valvular interstitial cells (VICs) were isolated from porcine aortic valves based on collagenase II digestion and cultured with standard tissue culture using media 199 supplemented with 15% fetal bovine serum.

extract_protocol: Total RNA was extracted based on RNeasy mini kit from Qiagen according to the manufacturer's protocol.

treatment_protocol: P0 VICs were freshly isolated cells without any treatment. P2 VICs were passaged twice and cultured in media 199 with 1% fetal bovine serum. P2 VICs were treated with or without porcine TGF-β1 (5 ng/ml) for 8 hours or 24 hours, but all of them were in culture for a total duration of 3 days.

tag: developmental stage

value: adult

value: aortic valve

tag: cell type

value: valvular interstitial cells (VICs)

tag: culture

value: TCPS

tag: number passages

tag: treatment duration

value: 8 hrs


title: MDA231_siCONTROL_C

tag: cell line


title: P2 VICs cultured on TCPS, treated with TGF-beta1 at 5ng/ml for 24 hours, biological replicate 3

description: Gene expression data from P2 VICs cultured on TCPS treated with TGFβ1 at 5ng/ml for 24 hours.

tag: treatment

value: 24 hrs


title: P2 VICs cultured on TCPS, no treatment, biological replicate 2

description: Gene expression data from P2 VICs cultured on TCPS with low serum media.

source_name: P2 VICs cultured on TCPS, no treatment


title: Hippocampi ICSS, replicate 2

description:
ICSS-2
Biological replicate 2 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.
ICSS rats subjected to acute self-stimulation (2500 stimulation trains). Electrode placement at lateral hypothalamus unilateraly in the right hemisphere.

tag: strain

value: male


title: P2 VICs cultured on TCPS, treated with TGF-beta1 at 5ng/ml for 8 hours, biological replicate 1


title: P2 VICs cultured on TCPS, treated with TGF-beta1 at 5ng/ml for 24 hours, biological replicate 1


title: P0 VICs without treatment, biological replicate 3

description: Gene expression data from freshly isolated and non-treated P0 VICs isolated from adult pig aortic valves.

source_name: P0 VICs without treatment


title: P0 VICs without treatment, biological replicate 1


title: DP31-21% miRNA

description: Gene expression under 21% O2

value: dental pulp cells

value: female


title: P2 VICs cultured on TCPS, no treatment, biological replicate 1


title: P2 VICs cultured on TCPS, treated with TGF-beta1 at 5ng/ml for 8 hours, biological replicate 3


title: Hippocampi ICSS, replicate 3

description:
ICSS-3
Biological replicate 3 of 4. Hippocampi of stimulated rats versus brain tissue pool of reference.
ICSS rats subjected to acute self-stimulation (2500 stimulation trains). Electrode placement at lateral hypothalamus unilateraly in the right hemisphere.

value: Wistar

value: 13 weeks

value: hippocampus


title: P2 VICs cultured on TCPS, treated with TGF-beta1 at 5ng/ml for 24 hours, biological replicate 2


title: CSE-WT(HFD+)

city: Yufu

first: Toshihide

last: Kimura

state: Oita

address: 1-1 Idaigaoka, Hasamamachi

department: Department of Pharmacology

institute: Oita University, Faculty of Medicine

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8×60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: beta-cell, high fat diet, wild type

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: wild type

value: 6 months

tag: diet

value: high-fat diet

value: beta-cell


title: PBMC - Untreated - Biological Replicate 10

city: Roma

first: Federica

last: Moschella

address: Viale Regina Elena 299

department: Cell Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

description: Biological replicate 10 of 10. Control PBMC, untreated

hyb_protocol: Labeled samples, diluted in Hybridization buffer (5X SSC; 50% Formamide; salmon sperm-DNA 100 ng/ul; 0.1% SDS), were applied to microarrays enclosed in Corning hybridization chambers - 50°C over night.

scan_protocol: Slides were scanned on GenePix® 4200A instrument (Axon Instruments) - Images were quantified using GenePix Pro 6.0

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. BRBArrayTools software was used.

source_name: PBMC, untreated patient

label_protocol: aRNA were obtained using the Ambion Amino Allyl MessageAmp™ II aRNA Amplification Kit, according to the manufacturer's instructions. 12 µg of aRNA were labeled with Amersham Cy5 (RNA samples) or Cy3 (Reference RNA)

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: Patients were treated with 3-4 g/m2 cyclophosphamide, blood was drawn at the indicated time point, PBMC were obtained by Ficoll grandient separation

value: Peripheral blood mononuclear cells (PBMC)

tag: patient's tumor

value: Chronic lymphocytic leukemia

tag: cyclophosphamide dosage

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: pool of 10 human cell lines


title: P2 VICs cultured on TCPS, no treatment, biological replicate 3

value: adult

value: aortic valve

value: valvular interstitial cells (VICs)


title: CSE-KO(HFD+)

source_name: beta-cell, high fat diet, knockout

tag: genotype/variation

value: CSE knockout


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 8

description: Biological replicate 8 of 8. PBMC, 2 days following Cyclophosphamide

source_name: PBMC, 2 days following Cyclophosphamide

tag: tissue


title: PBMC - Untreated - Biological Replicate 9

description: Biological replicate 9 of 10. Control PBMC, untreated

value: Multiple myeloma


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 6

description: Biological replicate 6 of 8. PBMC, 2 days following Cyclophosphamide


title: P0 VICs without treatment, biological replicate 2


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 9

description: Biological replicate 9 of 10. PBMC, 1 day following Cyclophosphamide

source_name: PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 10

description: Biological replicate 10 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 7

description: Biological replicate 7 of 8. PBMC, 2 days following Cyclophosphamide


title: PBMC - Untreated - Biological Replicate 8

description: Biological replicate 8 of 10. Control PBMC, untreated


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 7

description: Biological replicate 7 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 8

description: Biological replicate 8 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Untreated - Biological Replicate 7

description: Biological replicate 7 of 10. Control PBMC, untreated


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 5

description: Biological replicate 5 of 8. PBMC, 2 days following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 6

description: Biological replicate 6 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 5 - Biological Replicate 5

description: Biological replicate 5 of 5. PBMC, 5 days following Cyclophosphamide

source_name: PBMC, 5 days following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 5

description: Biological replicate 5 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Untreated - Biological Replicate 6

description: Biological replicate 6 of 10. Control PBMC, untreated


title: PBMC - Untreated - Biological Replicate 5

description: Biological replicate 5 of 10. Control PBMC, untreated


title: PBMC - Cyclophosphamide-treated - day 5 - Biological Replicate 4

description: Biological replicate 4 of 5. PBMC, 5 days following Cyclophosphamide

value: Plasma cell leukemia


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 4

description: Biological replicate 4 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 2

description: Biological replicate 2 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 2

description: Biological replicate 2 of 8. PBMC, 2 days following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 1

description: Biological replicate 1 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Untreated - Biological Replicate 2

description: Biological replicate 2 of 10. Control PBMC, untreated


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 3

description: Biological replicate 3 of 8. PBMC, 2 days following Cyclophosphamide


title: Liver_mPER2_KO_rep4

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

institute: University of Trento

hyb_protocol: Standard Agilent protocol using suggested blocking agent, fragmentation buffer and hybridization buffer. Hybridization run for 17 hours at 65°C. (Manual:One-Color Microarray-Based Gene Expression Analysis)

scan_protocol: Scanning was performed using Agilnet scanner at 5 uM resolution, green dye channel

data_processing: Signal was extracted using feature expression and data were nornalized to the 75th percentile of of all of non-control probes on the microarray using genespring software

label: Cyanine 3-CTP

source_name: Liver

label_protocol: Standard Agilent protocol that uses T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP (Manual:One-Color Microarray-Based Gene Expression Analysis)

extract_protocol: Standard single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction

value: mixed background 129sv and C57Bl/6

value: liver

value: mper2brdm1 mutant (PMID:10408444)


title: stomach_P60_rep2

first: Xiao

last: Yang

address: 20 Dongdajie

institute: Beijing Institute of Biotechnology

description: Biological replicate 2 of 2

hyb_protocol: Hybridization was performed overnight on a μParaflo™ microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 μL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing:
In the raw data files, 'Sample A' always corresponds to control, and 'Sample B' to tumor tissue. To remove the interference from different fluorescence (Cy3/Cy5), we labeled 'sample A' with Cy3 and 'sample B' with Cy5 in duplicate 1, and labeled 'sample A' with Cy5 and 'sample B' with Cy3 in duplicate 2.
Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
For two color experiments, the ratio of the two sets of detected signals (log2 transformed, balanced) and p-values of the t-test were calculated; differentially detected signals were those with less than 0.01 p-values.
In the data table, a VALUE of 'null' means that one or both signals of mutant and control could not be detected, leading to no correct ratio.

source_name: control stomach P60

label_protocol: An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments

value: stomach

tag: age

value: 60 days

tag: tumor

value: No

value: control

source_name: mutant stomach P60

value: advanced stage tumor

value: Pten mutant


title: stomach_P20_rep2

description: Biological replicate 2 of 2

source_name: control stomach P20

value: 20 days

source_name: mutant stomach P20

value: Early stage tumor


title: stomach_P60_rep1

description: Biological replicate 1 of 2


title: Liver_WT_rep2

value: WT


title: Liver_WT_rep1


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 1

description: Biological replicate 1 of 8. PBMC, 2 days following Cyclophosphamide

value: Peripheral blood mononuclear cells (PBMC)

value: pool of 10 human cell lines


title: PBMC - Cyclophosphamide-treated - day 1 - Biological Replicate 3

description: Biological replicate 3 of 10. PBMC, 1 day following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 2 - Biological Replicate 4

description: Biological replicate 4 of 8. PBMC, 2 days following Cyclophosphamide


title: Liver_WT_rep4


title: Blood_tumour induction_week6 [SAMPLE 506]

status: Public on Sep 01 2013

city: Galway

first: Róisín

last: Dwyer

address: Costelloe Road

country: Ireland

institute: National University of Ireland Galway

description: microRNA expression data comparing early to late stage disease

data_processing: The cycle threshold (Ct) was quantified using the Sequence Detector System (SDS) software version 2.2.2 (Applied Biosystem, Foster City, CA). Data were normalized using U6 readings on each card

label: FAM dye

source_name: Blood from animal bearing established tumor

extract_protocol: Total RNA was extracted from 50 µL of blood using TRI Reagent BD technique (Molecular Research Centre, Inc.)

treatment_protocol: Female athymic nude mice (Harlan Sprague-Dawley, Indianapolis, IN) received an injection of MDA-MB-231 cells in 0.2 ml 50% Matrigel medium. Blood sampling was carried out on all animals from the lateral tail vein at weeks 1 and 6 following tumor induction

tag: sample

value: Whole Blood

tag: timepoint

value: Week 6

tag: disease

value: Human breast cancer

tag: Sex

value: Female


title: PBMC - Cyclophosphamide-treated - day 5 - Biological Replicate 1

description: Biological replicate 1 of 5. PBMC, 5 days following Cyclophosphamide

value: Multiple myeloma


title: PBMC - Untreated - Biological Replicate 3

description: Biological replicate 3 of 10. Control PBMC, untreated


title: PBMC - Cyclophosphamide-treated - day 5 - Biological Replicate 2

description: Biological replicate 2 of 5. PBMC, 5 days following Cyclophosphamide


title: PBMC - Cyclophosphamide-treated - day 5 - Biological Replicate 3

description: Biological replicate 3 of 5. PBMC, 5 days following Cyclophosphamide


title: Liver_WT_rep3

value: mixed background 129sv and C57Bl/6

value: liver


title: Blood_tumour induction_week6 [SAMPLE 406]


title: PBMC - Untreated - Biological Replicate 1

description: Biological replicate 1 of 10. Control PBMC, untreated


title: Blood_tumour induction_week1 [SAMPLE 401]

source_name: Blood taken at breast tumor induction stage

value: Week 1


title: PBMC - Untreated - Biological Replicate 4

description: Biological replicate 4 of 10. Control PBMC, untreated

value: Plasma cell leukemia


title: Blood_tumour induction_week1 [SAMPLE 501]


title: Blood_tumour induction_week6 [SAMPLE 306]


title: Blood_tumour induction_week1 [SAMPLE 301]


title: stomach_P20_rep1

description: Biological replicate 1 of 2

value: stomach

value: No

value: control


title: Blood_tumour induction_week6 [SAMPLE 206]


title: Blood_tumour induction_week6 [SAMPLE 106]


title: Blood_tumour induction_week1 [SAMPLE 201]


title: Blood_tumour induction_week1 [SAMPLE 101]


title: Liver_mPER2_KO_rep3

value: mper2brdm1 mutant (PMID:10408444)


title: Liver_mPER2_KO_rep2


title: Liver_mPER2_KO_rep1


title: Dose 1-2

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

description: Biological replicate 2 of 3.

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (MetricSet in use: GE2_QCMT_Feb07 ).

data_processing: Sample data tables are the log10 red/green data from the Agilent Feature Extraction files. Limma (Bioconductor) processed data are on the Series record.

organism: Daphnia magna

source_name: Complete organism

label_protocol: Agilent Quick-AMP kit 2 color protocol

growth_protocol: Environment Canada test method (1990).  20oC, 16 hr light/8 hr dark photoperiod; fed daily on green algae and YCT preparation

extract_protocol: RNEasy Plus Mini kit (Qiagen); Experion Automated Electrophoresis System (BioRad)

treatment_protocol: OECD Guidelines 2008; 21-day exposures

tag: dose

source_name: Reference

value: Pooled controls


title: Dose 2-1

description: Biological replicate 1 of 3.


title: Dose self-rep

description: Self-replicate for QC purposes


title: Dose 1-3

description: Biological replicate 3 of 3.


title: Dose 1-1

description: Biological replicate 1 of 3.


title: HT1080_pLXSN_rep4

city: Moscow

first: Andrei

last: Komelkov

address: Kashirskoye shosse, 24

department: Institute of Carcinogenesis

country: Russia

institute: N.N.Blokhin Russian Cancer research Center

description: HT1080 human fibrosarcoma cell line transfected with empty pLXSN vector

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

scan_protocol: Scanning was performed by Axon GenePix 4400A High Resolution Microarray Scanner (Molecular Devices).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: HT1080 fibrosarcoma cell line, empty pLXSN vector

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

growth_protocol:
Human fibrosarcoma cell line HT-1080 (ATCC# CCL-121) were cultivated in Dulbecco's modified Eagle's medium (Paneco, Russia) supplemented with 10% fetal bovine serum (PAA laboratories) with penicillin and streptomycin (Paneco, Russia).
All cell lines were maintained in standard conditions (37 C, 5% CO2 atmosphere).

extract_protocol: RNA was isolated using Trizol reagent (Invitrogen, USA) according to  manufacturer’s protocol. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: transfection

value: Transfected with empty pLXSN retrovector


title: HT1080_CRABP1_rep3

description: HT1080 human fibrosarcoma cell line transfected with CRABP1 gene

source_name: HT1080 fibrosarcoma cell line, CRABP1 gene

tag: cell line

value: Transfected with human CRABP1 gene


title: HT1080_CRABP1-R131A_rep4

description: HT1080 human fibrosarcoma cell line transfected with CRABP1 R131A mutant

source_name: HT1080 fibrosarcoma cell line, CRABP1 R131A mutant

value: Transfected with R131A CRABP1 mutant unable to bind retinoic acid


title: HT1080_CRABP1_rep4


title: Dose 2-2

description: Biological replicate 2 of 3.


title: Methanol 1

description: Biological replicate 1 of 3.

value: Methanol control


title: HT1080_pLXSN_rep3


title: Dose 3-3

description: Biological replicate 3 of 3.


title: Dose 3-1

description: Biological replicate 1 of 3.


title: Dose 3-2

description: Biological replicate 2 of 3.


title: Control 3

description: Biological replicate 3 of 3.

value: Culture media only


title: HT1080_CRABP1-R131A_rep3


title: Methanol 3

description: Biological replicate 3 of 3.


title: Control 2

description: Biological replicate 2 of 3.


title: HT1080_CRABP1_rep2


title: HT1080_CRABP1-R131A_rep2

description: HT1080 human fibrosarcoma cell line, transfected with CRABP1 R131A mutant


title: Dose 2-3

description: Biological replicate 3 of 3.


title: 14286606 - C58tral_2days_BR2 vs C58WT_2days_BR2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the functions and the regulatory pathways of the bacterial quorum-sensing system in the context of Agrobacterium/Arabidopsis interactions?

hyb_protocol: C58WT_2days_BR2 Cy5 / C58tral_2days_BR2 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: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

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

growth_protocol: stem - Media=soil hygrometry=greenhouse Temperature Light=greenhouse

treatment_protocol: Name:wounding + C58 WT infection 2days - wounding - infection,c58 wt:time 2day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).

tag: ecotype

value: columbia (Col0)

tag: dev.stage (boyes et al. plant cell 2001)

treatment_protocol: Name:wounding + C58 tral infection 2days - wounding - infection,c58 tral:time 2day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: HT1080_CRABP1-R131A_rep1


title: 14286413 - C58WT_2days_BR2 vs C58tral_2days_BR2

hyb_protocol: C58tral_2days_BR2 Cy5 / C58WT_2days_BR2 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: Methanol 2

description: Biological replicate 2 of 3.


title: Control 1

description: Biological replicate 1 of 3.


title: HT1080_CRABP1_rep1


title: HT1080_pLXSN_rep1


title: HT1080_pLXSN_rep2


title: 14286613 - C58accR_2days_BR2 vs C58WT_2days_BR2

hyb_protocol: C58WT_2days_BR2 Cy5 / C58accR_2days_BR2 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:wounding + C58 accR infection 2days - wounding - infection,c58 accr:time 2day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286612 - C58WT_2days_BR2 vs C58accR_2days_BR2

hyb_protocol: C58accR_2days_BR2 Cy5 / C58WT_2days_BR2 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: 14286423 - C58WT_18days_BR3 vs Control_18days_BR3

hyb_protocol: Control_18days_BR3 Cy5 / C58WT_18days_BR3 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:wounding 18days - wounding - wounding,wounding:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle.

treatment_protocol: Name:wounding+C58 WT infection 18days - wounding - infection,c58 wt:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286609 - C58tral_2days_BR3 vs C58WT_2days_BR3

hyb_protocol: C58WT_2days_BR3 Cy5 / C58tral_2days_BR3 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: 14286424 - Control_18days_BR3 vs C58WT_18days_BR3

hyb_protocol: C58WT_18days_BR3 Cy5 / Control_18days_BR3 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: 14286427 - C58WT_18days_BR2 vs C58tral_18days_BR2

hyb_protocol: C58tral_18days_BR2 Cy5 / C58WT_18days_BR2 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:wounding+C58 tral infection 18days - wounding - infection,c58 tral:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286425 - C58WT_18days_BR1 vs C58tral_18days_BR1

hyb_protocol: C58tral_18days_BR1 Cy5 / C58WT_18days_BR1 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: 14286430 - C58tral_18days_BR1 vs C58accR_18days_BR1

hyb_protocol: C58accR_18days_BR1 Cy5 / C58tral_18days_BR1 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:wounding+C58 accR infection 18days - wounding - infection,c58 accr:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286600 - C58accR_2days_BR3 vs C58WT_2days_BR3

hyb_protocol: C58WT_2days_BR3 Cy5 / C58accR_2days_BR3 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: 14286436 - C58accR_18days_BR3 vs C58tral_18days_BR3

hyb_protocol: C58tral_18days_BR3 Cy5 / C58accR_18days_BR3 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: 14286607 - C58WT_2days_BR3 vs C58tral_2days_BR3

hyb_protocol: C58tral_2days_BR3 Cy5 / C58WT_2days_BR3 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: 14286602 - C58accR_2days_BR1 vs C58tral_2days_BR1

hyb_protocol: C58tral_2days_BR1 Cy5 / C58accR_2days_BR1 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: 14286610 - C58WT_2days_BR1 vs C58accR_2days_BR1

hyb_protocol: C58accR_2days_BR1 Cy5 / C58WT_2days_BR1 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: 14286611 - C58accR_2days_BR1 vs C58WT_2days_BR1

hyb_protocol: C58WT_2days_BR1 Cy5 / C58accR_2days_BR1 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: 14286419 - Control_18days_BR1 vs C58WT_18days_BR1

hyb_protocol: C58WT_18days_BR1 Cy5 / Control_18days_BR1 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: 14286433 - C58tral_18days_BR2 vs C58accR_18days_BR2

hyb_protocol: C58accR_18days_BR2 Cy5 / C58tral_18days_BR2 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: 14286603 - C58WT_2days_BR1 vs C58tral_2days_BR1

hyb_protocol: C58tral_2days_BR1 Cy5 / C58WT_2days_BR1 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: 14286428 - C58tral_18days_BR2 vs C58WT_18days_BR2

hyb_protocol: C58WT_18days_BR2 Cy5 / C58tral_18days_BR2 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: 14286421 - Control_18days_BR2 vs C58WT_18days_BR2

hyb_protocol: C58WT_18days_BR2 Cy5 / Control_18days_BR2 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.