title: H3K27ac,117029 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,117029 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,117029 antibody


title: Liver_KK/HIJ_1105

status: Public on Feb 28 2009

type: RNA

city: Chapel Hill

first: Daniel

middle: M

last: Gatti

state: NC

address: 135 Dauer Dr.

department: Environmental Sciences & Engineering

country: USA

institute: University of Noth Carolina

description: Analysis of mouse liver gene expression.

hyb_protocol: Labeled cRNA was processed and hybridized to Agilent Mouse Toxicology Arrays (catalog# 4121A, about 22,000 features) according the the manufacturer’s protocol. Following hybridization, arrays were washed using a custom protocol developed by Icoria, Inc. Briefly, array gaskets are removed under immersion in Wash Solution 1 (6X SSPE, 0.005% N-Lauroylsarcosine). Arrays were washed with Wash Solution 1 and incubated for one minute with gentle agitation on a magnetic stir plate. A second incubation was performed in Wash Solution 2 (0.06X SSPE, 0.005% N-Lauroylsarcosine).

scan_protocol: Agilent Scanner with Agilent Feature Extraction.

data_processing: Data was processed using the UNC Microarray data base at (http://genome.unc.edu). Loess normalization was performed.

molecule: total RNA

organism: Mus musculus

source_name: Reference

label_protocol: In this study, all RNA samples were hybridized to arrays individually; none were pooled. RNA amplifications and labeling were performed using Low RNA Input Linear Amplification kits (Agilent Technologies). For hybridization, 750 ng of total RNA from each mouse liver was amplified and labeled with fluorescent dye (Cy5). In parallel, 750 ng of a common reference RNA (Icoria Inc., RTP, NC) was labeled with the fluorescent dye, Cy3, in order to standardize analysis of global gene expression between mouse strains.

extract_protocol: Reference RNA from Icoria.

tag: Icoria Reference RNA

tag: C57BL/6J male liver, kidney, lung, brain and spleen

source_name: liver, KK/HIJ

extract_protocol: To eliminate variability in transcript expression that might arise between liver lobes, the left liver lobe was selected for the remainder of the data analysis and gene expression profiling. RNA was extracted from the 30 mg of tissue derived from the left lobe of sample livers using the Qiagen RNeasy kit (Qiagen, Valencia, CA). RNA concentrations were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and quality was verified using the Agilent Bio-Analyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Male mice (aged 7-9 weeks) were obtained from The Jackson Laboratory and housed in polycarbonate cages on Sani-Chips irradiated hardwood bedding (P.J. Murphy Forest Products Corp., Montville, NJ). Animals were fed NTP-2000 wafer feed (Zeigler Brothers, Inc., Gardners, PA) and water ad libitum, and maintained on a 12 h light-dark cycle. Mice utilized in this study comprise 36 inbred strains that are priority strains for the Mouse Phenome Project 13: 129S1/SvImJ, A/J, AKR/J, BALB/cByJ, BTBR T+ tf/J, BUB/BnJ, C3H/HeJ, C57BL/10J, C57BL/6J, C57BLKS/J, C57BR/CdJ, C57L/J, CAST/EiJ, CBA/J, CZECHII/EiJ, DBA/2J, FVB/NJ, JF1/Ms, KK/HlJ, LP/J, MA/MyJ, MSM/Ms, NOD/ShiLtJ (formerly NOD/LtJ), NON/LtJ, NZO/H1LtJ, NZW/LacJ, P/J, PERA/EiJ, PL/J, PWD/PhJ, RIIIS/J, SEA/GnJ, SJL/J, SM/J, SWR/J, and WSB/EiJ. F1 hybrid mice, B6C3F1/J, were also used for phenotypic measurements. Care of mice followed institutional guidelines under a protocol approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill.

tag: Strain

value: KK/HIJ

tag: Gender

value: male


title: MED1,116881 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

status: Public on Mar 01 2009

type: genomic

city: Dallas

first: Gary

middle: Chung

last: Hon

state: TX

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116881 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

hyb_protocol: NimbleGen

scan_protocol: NimbleGen

data_processing: raw data

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116881 antibody

label_protocol: Cy3 input Cy5 ChIP sample

extract_protocol: NimbleGen

tag: cells

value: HeLa

source_name: Input DNA from HeLa cells


title: p300,116781 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against p300,116781 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using p300,116781 antibody


title: Liver_JF1_1061

source_name: liver, JF1


title: Liver_FVB/NJ_1177

source_name: liver, FVB/NJ

value: FVB/NJ


title: MED1,116874 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116874 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116874 antibody


title: Liver_NZO/H1LtJ_1181

source_name: liver, NZO/H1LtJ


title: Liver_FVB/NJ_1058


title: Liver_P/J_1107

source_name: liver, P/J

value: P/J


title: Liver_DBA/2J_1049

source_name: liver, DBA/2J


title: MED1,116879 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against MED1,116879 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using MED1,116879 antibody


title: H3K4me3,116769 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,116769 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116769 antibody


title: Liver_CZECHII/EiJ_1114

source_name: liver, CZECHII/EiJ

value: CZECHII/EiJ


title: Liver_DBA/2J_1164


title: Liver_CZECHII/EiJ_1037


title: Liver_CZECHII/EiJ_1113


title: Liver_C57L/J_1174

source_name: liver, C57L/J


title: H3K4me3,116779 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,116779 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116779 antibody


title: Liver_CAST/EiJ_1025

source_name: liver, CAST/EiJ

value: CAST/EiJ


title: Liver_C57BR/CdJ_1185

source_name: Reference

source_name: liver, C57BR/CdJ


title: H3K27ac,126614 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,126614 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,126614 antibody


title: Liver_CBA/J_1139

source_name: liver, CBA/J

value: CBA/J


title: Liver_C57L/J_1101


title: H3K27ac,117041 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K27ac,117041 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K27ac,117041 antibody

source_name: Input DNA from HeLa cells


title: Liver_JF1/Ms_1196

source_name: liver, JF1/Ms


title: Liver_C57BL/6_1082

source_name: liver, C57BL/6


title: H3K4me1,116876 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116876 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116876 antibody


title: Liver_C57BL/6J_1153

source_name: liver, C57BL/6J


title: H3K4me1,116814 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116814 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116814 antibody


title: Liver_KK/HIJ_1184

source_name: liver, KK/HIJ


title: Liver_C57BLKS/J_1134

source_name: liver, C57BLKS/J


title: Liver_C3H/HeJ_1168

source_name: liver, C3H/HeJ


title: Liver_C57BLKS_1013

source_name: liver, C57BLKS


title: Liver_C57BL/10J_1172

source_name: liver, C57BL/10J


title: Liver_C57BR/CdJ_1212


title: Liver_BUB/BnJ_1092

source_name: liver, BUB/BnJ

value: BUB/BnJ


title: Liver_C3H/HeJ_1046

source_name: Reference


title: Liver_BUB/BnJ_1002


title: Liver_CBA/J_1217


title: Liver_BTBR_1034

source_name: liver, BTBR

value: BTBR


title: Liver_BTBR_1203


title: Liver_Balb/cByJ_1160

source_name: liver, Balb/cByJ

value: Balb/cByJ


title: Liver_C57BL/10J_1052


title: Liver_BALB/cByJ_1088

source_name: liver, BALB/cByJ

value: BALB/cByJ


title: Liver_AKR/J_1031

source_name: liver, AKR/J

value: AKR/J


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide3 rep3

type: mixed

city: Nagoya

first: Masaki

last: Ito

address: Chikusa

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description: Tobacco microarray consists of 4 slides. Modification of single channel label data was used. For hybridizations, we used Cy5-labeled cDNA and Cy3-labeled vector sequence. All DNA spots on array contain flanking vector sequence that was introduced by amplification of cDNA inserts by PCR with universal primers (clones in pGEM Te - M13 universal primers, clones in pBKSII - M13 FWD/KS reverse). Using Cy5 (signal) and Cy3 (control), data can be normalized by creating Cy5/Cy3 ratio, thus allowing normalization for amount of spotted DNA on individual slides by microarray spotter.

hyb_protocol: Before use, the DNA on the spotted microarray slides was immobilized by cross-linking the slides under UV light (energy 50 mJ cm2) and slides were prehybridized for 1 h at 55°C in prehybridization buffer [1% bovine serum albumin (BSA), 5× saline sodium citrate (SSC) and 0.1% sodium dodecyl sulfate (SDS)] as described previously [1,2].  Hybridization of microarrays with Cy-5-labeled sample cDNA and Cy-3-labeled DNA sequence as control was performed in ExpressHyb hybridization solution (Clontech, Palo Alto, CA, USA) at 60°C for 4 h as described previously [1]. The protocol described in [1] was later modified with the use of a Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites of the respective vectors (pGEM-Teasy and pBII KS+), instead of the labeled oligo-DNA that was used previously [2].  The hybridized slides were washed in SSC/SDS buffer solutions at 55°C (final wash in 0.1× SSC and 0.1% SDS) and briefly rinsed in water. Slides were dried by centrifugation.  [1]Demura, T., Tashiro, G., Horiguchi, G. et al. (2002) Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl Acad. Sci. USA, 99, 15794–15799.  [2]Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45, 1280–1289.

scan_protocol: The Cy-5 (sample signal) and Cy-3 (control signal) were obtained by scanning with a GenePix 4000A microarray scanner (Molecular Dynamics). The scans were subsequently analyzed by the MicroArray Suite iplab program (Scananalytics, BD Biosciences, Rockville, MD, USA).

data_processing: Raw signal data were first modified by subtraction of respective background values. Ratio of VALUE means (Cy-5-labeled cDNA signal)/(Cy-3-labeled vector control signal) after background correction are listed in result table.

molecule: polyA RNA

organism: Nicotiana tabacum

source_name: C-truncated NtmybA2 (NtmybA2∆C) overexpressor, tobacco cells, stationary phase

label_protocol: polyA mRNA quality was estimated by Bioanalyzer. 1 μg of mRNA was labeled and used for single-slide hybridizations. Samples were spiked with control Kanamycin mRNA (Promega). Labeling was performed using SuperScript II reverse transcriptase (Invitrogen), random 9-mer primers, poly(A)-specific poly (dT) primers, and Cy-3/Cy-5-labeled dCTP nucleotides (Amersham Biosciences) for first-strand cDNA synthesis. Quality of probe was estimated by gel electrophoresis and subsequent fluoroimaging analysis.

extract_protocol: The cells were collected by filtration and snap-frozen in liquid nitrogen. Total RNA was prepared using TRIzol reagent (Invitrogen) as described in the manufacturer’s protocols. The poly(A)-rich RNA fraction was isolated from total RNA using a GenElute mRNA Miniprep Kit (Sigma) in two subsequent runs of purification following the Miniprep Kit protocol.

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 3 of 4, replicate 3


title: Tobacco pPZP-35S vector control stationary phase slide3 rep3

source_name: pPZP-35S vector control, tobacco cells, stationary phase, control sample

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 3 of 4, replicate 3


title: Tobacco synchronization 14h slide3 expB

source_name: Synchronization, tobacco cells, 14h

treatment_protocol: Seven days old tobacco BY-2 cells after subculture were diluted 10 times with fresh medium, and cultured in the presence of 5 microg/ml aphidicolin for 24 h. Cells were then washed to remove aphidicolin and transferred into fresh medium.

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco NtmybA2 overexpressor stationary phase slide3 rep2

source_name: NtmybA2 overexpressor, tobacco cells, stationary phase

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 3 of 4, replicate 2


title: Tobacco NtmybA2 overexpressor stationary phase slide3 rep3

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 3 of 4, replicate 3


title: H3K4me3,116780 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me3,116780 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me3,116780 antibody

source_name: Input DNA from HeLa cells


title: Tobacco synchronization 12h slide3 expB

source_name: Synchronization, tobacco cells, 12h

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco pPZP-35S vector control stationary phase slide3 rep1

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 3 of 4, replicate 1


title: Tobacco synchronization 10h slide3 expB

source_name: Synchronization, tobacco cells, 10h

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco synchronization 16h slide3 expB

source_name: Synchronization, tobacco cells, 16h

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco pPZP-35S vector control stationary phase slide3 rep2

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 3 of 4, replicate 2


title: H3K4me1,116823 HeLa custom condensed Nimblegen 2.1M Human tiling array of hg17 at 100bp resolution, set 01 of 3

description: Chromatin immunoprecipitation was performed using antibodies against H3K4me1,116823 and formaldehyde crosslinked chromatin from HeLa cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to 3 sub-arrays on 1 physical array containing a total of 2.1 million 50-mer oligonucleotides

source_name: Chromatin immunoprecipitated DNA from HeLa cells using H3K4me1,116823 antibody


title: Liver_A/J_1019

source_name: liver, A/J

value: A/J


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide3 rep1

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 3 of 4, replicate 1


title: Tobacco synchronization 14h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco synchronization 0h slide3 expB

source_name: Synchronization, tobacco cells, 0h

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 3 of 4, experiment B


title: Liver_129S1/SvImJ_1070

source_name: Reference

tag: Icoria Reference RNA

tag: C57BL/6J male liver, kidney, lung, brain and spleen

source_name: liver, 129S1/SvImJ


title: Tobacco synchronization 4h slide3 expB

source_name: Synchronization, tobacco cells, 4h

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco NtmybA2 overexpressor stationary phase slide3 rep1

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 3 of 4, replicate 1


title: Liver_A/J_1141

tag: Strain

tag: Gender


title: Tobacco synchronization 8h slide3 expB

source_name: Synchronization, tobacco cells, 8h

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide3 rep2

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 3 of 4, replicate 2


title: Tobacco synchronization 2h slide3 expB

source_name: Synchronization, tobacco cells, 2h

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco synchronization 6h slide3 expB

source_name: Synchronization, tobacco cells, 6h

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 3 of 4, experiment B


title: Tobacco synchronization 12h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco synchronization 8h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco synchronization 16h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 3 of 4, experiment A


title: Liver_129S1/SvImJ_1162


title: Tobacco synchronization 4h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco synchronization 0h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide4 rep2

source_name: C-truncated NtmybA2 (NtmybA2∆C) overexpressor, tobacco cells, stationary phase

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 4 of 4, replicate 2


title: Tobacco synchronization 2h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco pPZP-35S vector control stationary phase slide4 rep3

source_name: pPZP-35S vector control, tobacco cells, stationary phase, control sample

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 4 of 4, replicate 3


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide2 rep3

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 2 of 4, replicate 3


title: Tobacco NtmybA2 overexpressor stationary phase slide4 rep1

source_name: NtmybA2 overexpressor, tobacco cells, stationary phase

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 4 of 4, replicate 1


title: Tobacco pPZP-35S vector control stationary phase slide2 rep3

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 2 of 4, replicate 3


title: Tobacco NtmybA2 overexpressor stationary phase slide4 rep3

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 4 of 4, replicate 3


title: Tobacco pPZP-35S vector control stationary phase slide2 rep2

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 2 of 4, replicate 2


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide2 rep2

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 2 of 4, replicate 2


title: Tobacco synchronization 6h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco NtmybA2 overexpressor stationary phase slide2 rep2

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 2 of 4, replicate 2


title: Tobacco NtmybA2 overexpressor stationary phase slide4 rep2

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 4 of 4, replicate 2


title: Tobacco synchronization 12h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco synchronization 16h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide4 rep3

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 4 of 4, replicate 3


title: Tobacco synchronization 14h slide4 expB

source_name: Synchronization, tobacco cells, 14h

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide2 rep1

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 2 of 4, replicate 1


title: Tobacco pPZP-35S vector control stationary phase slide4 rep2

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 4 of 4, replicate 2


title: Tobacco NtmybA2 overexpressor stationary phase slide2 rep3

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 2 of 4, replicate 3


title: Tobacco synchronization 10h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco pPZP-35S vector control stationary phase slide2 rep1

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 2 of 4, replicate 1


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide4 rep1

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 4 of 4, replicate 1


title: Tobacco pPZP-35S vector control stationary phase slide4 rep1

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 4 of 4, replicate 1


title: Tobacco synchronization 10h slide3 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 3 of 4, experiment A


title: Tobacco NtmybA2 overexpressor stationary phase slide2 rep1

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 2 of 4, replicate 1


title: Tobacco synchronization 16h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 6h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco synchronization 8h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco synchronization 0h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco synchronization 12h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 4h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco synchronization 6h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 10h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 2h slide4 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 4 of 4, experiment B


title: Tobacco synchronization 8h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 16h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 12h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 14h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 10h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 6h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 16h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 10h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 2h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 4h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 14h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 4h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 12h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 0h slide2 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 2 of 4, experiment B


title: Tobacco synchronization 8h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 2h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 8h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 4h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 0h slide4 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 4 of 4, experiment A


title: Tobacco synchronization 2h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide1 rep3

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 1 of 4, replicate 3


title: Tobacco NtmybA2 overexpressor stationary phase slide1 rep3

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 1 of 4, replicate 3


title: Tobacco pPZP-35S vector control stationary phase slide1 rep3

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 1 of 4, replicate 3


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide1 rep1

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 1 of 4, replicate 1


title: Tobacco NtmybA2 overexpressor stationary phase slide1 rep1

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 1 of 4, replicate 1


title: Tobacco synchronization 0h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 14h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco C-truncated NtmybA2 (NtmybA2∆C) overexpressor stationary phase slide1 rep2

tag: Tobacco cells overexpressig C-truncated form of NtmybA2 (NtmybA∆C), stationary phase, slide 1 of 4, replicate 2


title: Tobacco pPZP-35S vector control stationary phase slide1 rep1

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 1 of 4, replicate 1


title: Tobacco synchronization 0h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco synchronization 10h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco synchronization 2h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco synchronization 4h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco synchronization 8h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco synchronization 16h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco pPZP-35S vector control stationary phase slide1 rep2

tag: pPZP211-35S vector transformed (control) tobacco cells, stationary phase, slide 1 of 4, replicate 2


title: Tobacco synchronization 6h slide2 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 2 of 4, experiment A


title: Tobacco synchronization 12h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco NtmybA2 overexpressor stationary phase slide1 rep2

tag: Tobacco cells overexpressig full-length NtmybA2, stationary phase, slide 1 of 4, replicate 2


title: Tobacco synchronization 16h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 16h after release from aphidicolin block, slide 1 of 4, experiment A


title: Tobacco synchronization 14h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 1 of 4, experiment A


title: Tobacco synchronization 6h slide1 expB

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 1 of 4, experiment B


title: Tobacco synchronization 10h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 10h after release from aphidicolin block, slide 1 of 4, experiment A


title: C.elegans_Temperature 20 degrees_3

city: Tsukuba

first: Akira

last: Higashibata

state: Ibaraki

department: Department of Space Biology and Microgravity Sciences

institute: Japan Aerospace Exploration Agency

description: This study focused on temperature, profiling the altered gene expression that develops under four thermal conditions (10, 15, 20, and 25°C) in C. elegans.

hyb_protocol: Labeled cRNA (1.65 µg/sample) was hybridized to a C. elegans oligo microarray using a gene expression hybridization kit at 60 °C for 17 hours.

scan_protocol: Chips were scanned with an Agilent Scanner and processed with Agilent Feature Extraction Software (Version 9.1.3.1).

data_processing: Microarray data were analyzed using Gene Spring software (Agilent Technologies). Log ratios are derived by per Chip (Normalize to 50th percentile) and per Gene.

organism: Caenorhabditis elegans

source_name: control (20 degrees)

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Cy3 labeled cRNA was produced according to manufacturer's protocol.

growth_protocol: The Bristol N2 strain was pre-cultured in C. elegans maintenance medium (CeMM) for 1 month at 20 °C. Approximately 5000 worms of mixed larval stage were transferred into 5 mL culture bags containing fresh CeMM at 10 for 2 weeks.

extract_protocol: Worms were homogenized with four rounds of 20-second beating at 5000 rpm in a Micro SmashTM MS-100 bead beater with 3 minutes of cooling on ice between rounds. Total RNA was extracted using an Isogen RNA purification kit following the manufacturer’s protocol.

tag: C.elegans_Temperature 10 degrees_1


title: C.elegans_Temperature 25 degrees_3

source_name: 25 degrees

tag: Ceanorhabditis elegans, N2 wild type


title: C.elegans_Temperature 20 degrees_2


title: C.elegans_Temperature 25 degrees_1


title: C.elegans_Temperature 25 degrees_2


title: Tobacco synchronization 12h slide1 expA

source_name: Synchronization, tobacco cells, 12h

tag: Tobacco cells synchronized by aphidicolin treatment, 12h after release from aphidicolin block, slide 1 of 4, experiment A


title: C.elegans_Temperature 20 degrees_1


title: Tobacco synchronization 8h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 8h after release from aphidicolin block, slide 1 of 4, experiment A


title: C.elegans_Temperature 15 degrees_3

source_name: 15 degrees


title: C.elegans_Temperature 15 degrees_2


title: Tobacco synchronization 4h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 4h after release from aphidicolin block, slide 1 of 4, experiment A


title: Tobacco synchronization 6h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 6h after release from aphidicolin block, slide 1 of 4, experiment A


title: Tobacco synchronization 2h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 2h after release from aphidicolin block, slide 1 of 4, experiment A


title: Tobacco synchronization 0h slide1 expA

tag: Tobacco cells synchronized by aphidicolin treatment, 0h after release from aphidicolin block, slide 1 of 4, experiment A


title: C.elegans_Temperature 15 degrees_1


title: C.elegans_Temperature 10 degrees_3

source_name: 10 degrees


title: 13756848 - mkkkc5_b vs Control_b

status: Public on Feb 15 2009

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: The mkkkC5 mutant, a knockout line of MAPKKKC5, shows changes in growth and development, as well as an altered Alternaria sensitivity. t was shown by Brader and Djamei et al.(2007) that Alternaria brassicicola sensitivity is also influenced by MKK2-activity. Aim of this experiment is to access the transcriptional changes in the mkkkc5plants as well as in plants overexpressing a constitutively active MKK2-version (MKK2EE). The second part of the experiment addresses transcriptional changes in these plants after Alternaria brassicicola infection.

hyb_protocol: Control_b Cy5 / mkkkc5_b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,460V,laser power 35%, Cy5:635nm,pmt voltage 460V,laser power 30%

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

organism: Arabidopsis thaliana

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

growth_protocol: leaf - Media: soil Temperature: 21 Light: 12h

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  - harvest date:15-11-07

tag: Arabidopsis thaliana (col-0)  mutant (at5g58954-) - harvest date:15-11-07


title: 13756846 - Control_b vs mkkkc5_b

hyb_protocol: mkkkc5_b Cy5 / Control_b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756845 - mkkkc5_a vs Control_a

hyb_protocol: Control_a Cy5 / mkkkc5_a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697187 - Control_b vs MKK2EE_b

hyb_protocol: MKK2EE_b Cy5 / Control_b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (pGreen::MKK2EE-myc) - harvest date:15-11-07


title: 13697183 - MKK2EE_a vs Control_a

hyb_protocol: Control_a Cy5 / MKK2EE_a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C.elegans_Temperature 10 degrees_1


title: 13697182 - Control_a vs MKK2EE_a

hyb_protocol: MKK2EE_a Cy5 / Control_a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C.elegans_Temperature 10 degrees_2


title: 13697188 - MKK2EE_b vs Control_b

hyb_protocol: Control_b Cy5 / MKK2EE_b Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688392 - Control_a_0d vs MKK2EE_a_0d

hyb_protocol: MKK2EE_a_0d Cy5 / Control_a_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: leaf - Media:soil Temperature:21°C Light:12h

treatment_protocol: Name:Alternaria brassicicola infection - environmental treatment - pathogen infection,alternaria brassicicola:. 5-7 true leaves of 25 day old plants grown in soil were infected with 5 ul of Alternaria spore suspension (5x100.000 per ml in potato-dextrose media) after wounding the infection site with a pipette tip. Mock treatment with 5ul potato-dextrose-media.


title: 13688386 - Control_b_2d vs mkkkc5_b_2d

hyb_protocol: mkkkc5_b_2d Cy5 / Control_b_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (at5g58951-) - harvest date:17-11-07

tag: Arabidopsis thaliana (col-0)  - harvest date:17-11-07


title: 13688378 - Control_a_0d vs mkkkc5_a_0d

hyb_protocol: mkkkc5_a_0d Cy5 / Control_a_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (at5g58951-) - harvest date:15-11-07


title: 13688387 - mkkkc5_a_2d vs Control_a_2d

hyb_protocol: Control_a_2d Cy5 / mkkkc5_a_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688390 - Control_a_2d vs mkkkc5_a_2d

hyb_protocol: mkkkc5_a_2d Cy5 / Control_a_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13756844 - Control_a vs mkkkc5_a

hyb_protocol: mkkkc5_a Cy5 / Control_a Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757025 - MKK2EE_b_0d vs Control_b_0d

hyb_protocol: Control_b_0d Cy5 / MKK2EE_b_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688334 - Control_b_2d vs MKK2EE_b_2d

hyb_protocol: MKK2EE_b_2d Cy5 / Control_b_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (pGreen::MKK2EE-myc) - harvest date:17-11-07


title: 13688393 - MKK2EE_a_0d vs Control_a_0d

hyb_protocol: Control_a_0d Cy5 / MKK2EE_a_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688336 - Control_b_0d vs MKK2EE_b_0d

hyb_protocol: MKK2EE_b_0d Cy5 / Control_b_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688389 - mkkkc5_b_2d vs Control_b_2d

hyb_protocol: Control_b_2d Cy5 / mkkkc5_b_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688335 - MKK2EE_b_2d vs Control_b_2d

hyb_protocol: Control_b_2d Cy5 / MKK2EE_b_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688340 - mkkkc5_b_1d vs Control_b_1d

hyb_protocol: Control_b_1d Cy5 / mkkkc5_b_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  - harvest date:16-11-07

tag: Arabidopsis thaliana (col-0)  mutant (at5g58951-) - harvest date:16-11-07


title: Tobacco synchronization 14h slide2 expB

hyb_protocol: Before use, the DNA on the spotted microarray slides was immobilized by cross-linking the slides under UV light (energy 50 mJ cm2) and slides were prehybridized for 1 h at 55°C in prehybridization buffer [1% bovine serum albumin (BSA), 5× saline sodium citrate (SSC) and 0.1% sodium dodecyl sulfate (SDS)] as described previously [1,2].  Hybridization of microarrays with Cy-5-labeled sample cDNA and Cy-3-labeled DNA sequence as control was performed in ExpressHyb hybridization solution (Clontech, Palo Alto, CA, USA) at 60°C for 4 h as described previously [1]. The protocol described in [1] was later modified with the use of a Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites of the respective vectors (pGEM-Teasy and pBII KS+), instead of the labeled oligo-DNA that was used previously [2].  The hybridized slides were washed in SSC/SDS buffer solutions at 55°C (final wash in 0.1× SSC and 0.1% SDS) and briefly rinsed in water. Slides were dried by centrifugation.  [1]Demura, T., Tashiro, G., Horiguchi, G. et al. (2002) Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl Acad. Sci. USA, 99, 15794–15799.  [2]Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45, 1280–1289.

tag: Tobacco cells synchronized by aphidicolin treatment, 14h after release from aphidicolin block, slide 2 of 4, experiment B


title: 13688383 - Control_a_1d vs Control_a_2d

hyb_protocol: Control_a_2d Cy5 / Control_a_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688337 - Control_b_1d vs mkkkc5_b_1d

hyb_protocol: mkkkc5_b_1d Cy5 / Control_b_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688327 - Control_b_0d vs mkkkc5_b_0d

hyb_protocol: mkkkc5_b_0d Cy5 / Control_b_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688329 - Control_b_2d vs Control_b_1d

hyb_protocol: Control_b_1d Cy5 / Control_b_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688325 - MKK2EE_b_1d vs Control_b_1d

hyb_protocol: Control_b_1d Cy5 / MKK2EE_b_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (col-0)  mutant (pGreen::MKK2EE-myc) - harvest date:16-11-07


title: 13688328 - Control_a_1d vs Control_a_0d

hyb_protocol: Control_a_0d Cy5 / Control_a_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688440 - Control_b_1d vs MKK2EE_b_1d

hyb_protocol: MKK2EE_b_1d Cy5 / Control_b_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688333 - Control_a_2d vs Control_a_1d

hyb_protocol: Control_a_1d Cy5 / Control_a_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688324 - Control_a_2d vs MKK2EE_a_2d

hyb_protocol: MKK2EE_a_2d Cy5 / Control_a_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688323 - Control_b_1d vs Control_b_2d

hyb_protocol: Control_b_2d Cy5 / Control_b_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688322 - Control_b_1d vs Control_b_0d

hyb_protocol: Control_b_0d Cy5 / Control_b_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688388 - Control_a_1d vs MKK2EE_a_1d

hyb_protocol: MKK2EE_a_1d Cy5 / Control_a_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688321 - Control_b_0d vs Control_b_1d

hyb_protocol: Control_b_1d Cy5 / Control_b_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688320 - mkkkc5_a_1d vs Control_a_1d

hyb_protocol: Control_a_1d Cy5 / mkkkc5_a_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688331 - Control_a_0d vs Control_a_1d

hyb_protocol: Control_a_1d Cy5 / Control_a_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688332 - MKK2EE_a_1d vs Control_a_1d

hyb_protocol: Control_a_1d Cy5 / MKK2EE_a_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688319 - Control_a_1d vs mkkkc5_a_1d

hyb_protocol: mkkkc5_a_1d Cy5 / Control_a_1d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688385 - mkkkc5_a_0d vs Control_a_0d

hyb_protocol: Control_a_0d Cy5 / mkkkc5_a_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688379 - mkkkc5_b_0d vs Control_b_0d

hyb_protocol: Control_b_0d Cy5 / mkkkc5_b_0d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13688326 - MKK2EE_a_2d vs Control_a_2d

hyb_protocol: Control_a_2d Cy5 / MKK2EE_a_2d Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CD4 5

status: Public on Feb 01 2009

city: Bethesda

first: John

last: Brady

state: MD

institute: NCI

description: negative selection

hyb_protocol: cRNA samples were hybridized for 16 hours at 45C.  The arrays were processed using the GeneChip Hybridization Wash and Stain kit.  The wash protocol used was Midi_euk2v3.

scan_protocol: Arrays were scanned with GeneChip Scanner 3000.

data_processing: All data were processed using GeneChip Operating System MAS5.0.

label: biotin

source_name: PBL, control

label_protocol: Biotin labeled cRNA was prepared using the Affymetrix protocol with GeneChip Expression 3' Amplification One-Cycle Target Labeling and Control Reagent.

growth_protocol: ATL peripheral blood lymphocytes (PBLs) were purified from apheresis samples.  Control CD4+ lymphocytes were purified by positive or negative selection (Dynal, Oslo, Norway).

extract_protocol: Total RNA was isolated from lymphocytes using RNA-Bee reagent (Tel-Test, TX), followed by purification using Rneasy Mini-columns (Qiagen, Inc., CA).

treatment_protocol: RNA was isolated from non-cultured lymphocytes.


title: CD4 7

description: positive selection


title: CD4 4

description: negative selection


title: ATL34

source_name: PBL, ATL

tag: acute leukemia


title: ATL32


title: ATL20


title: CD4 1

description: positive selection


title: ATL2


title: CD4 6

description: positive selection


title: ATL3A

description: patient was drug treated

tag: acute leukemia (post Zenapax)


title: ATL5A

description: progression from lymphomatis disease


title: ATL1


title: ATL15


title: ATL31


title: ATL8

tag: lymphoma


title: ATL19-2


title: ATL12

description: progression from lymphomatis disease


title: CD4 2

description: negative selection


title: ATL2A

description: patient was drug treated


title: Tiling array analysis for Streptococcus pneumoniae

status: Public on Feb 10 2009

city: starkville

first: Ranjit

last: Kumar

state: MS

address: 240 Wise Center Drive,PO Box 6100

department: Dept of Basic Science

institute: MSU

description: Nimblegen provided the raw intensity data after scan.

hyb_protocol: Hibridization was performed by Nimblegen Systems, Inc. www.nimblegen.com

scan_protocol: Scan was performed by Nimblegen Systems, Inc.

data_processing: Array spatial effects were removed by using NMPP package(specifc for Nimblegen arrays), the data was log transformed.The data was normalized using quantile normalization through the Affy package(present in  htp://www.bioconductor.org  and  http://pbil.univ-lyon1.fr/library/affy/html/normalize.quantiles.html).

organism: Streptococcus pneumoniae

source_name: Streptococcus pneumoniae TIGR4_mid log phase(OD600 nm, 0.4–0.6)

label_protocol: One microgram of total RNA was used by Nimblegen systems for labeling and hybridization. Samples were labeled by Nimblegen Systems, Inc.

growth_protocol: S. pneumoniae strain TIGR4 (ref) was grown in THYmedium, Todd-Hewitt broth supplemented with 0.5% yeast extract.

extract_protocol: Cells were harvested from duplicate cultures from mid-log phase (OD600 nm, 0.4–0.6) of growth by centrifugation.The harvested pellets were washed twice in sterile PBS (pH 7.0) and stored at -80°C. RNA was purified from frozen bacterial pellets using Qiagen RNeasy kit by following the manufacturer’s protocol. Isolated RNA was treated with DNase to remove genomic DNA contamination, and purity was checked by performing a one-step RT-PCR using primers specific for 16S rRNA in presence or absence of reverse transcriptase. RNA concentration and quality were determined by using Agilent Bioanalyzer. Purified RNA was stored in nuclease free water at -80°C.


title: CD4 3

description: negative selection


title: ATL18C

description: patient was drug treated

tag: acute leukemia (72hrs post bortezomib)


title: 1672_MMF

city: Amsterdam

first: Oscar

middle: Leonard

last: Volger

state: Noor Holland

address: Meibergdreef 15

department: Cardiology

country: Netherlands

institute: Academic Medical Center

description: All hybridizations were performed according to the manufacturer's specifications.

hyb_protocol: 750ng of biotinylated cRNA was hybridized onto the HumanRef-8 Expression BeadChips according to the Manufacturer.

scan_protocol: According to the Manufacturer, performed by ServiceXS http://www.servicexs.com).

data_processing: Gene expression analysis was performed by using Illumina's Beadstudio v3 software, followed by a quantile inter-array normalization (R, Bioconductor).

label: Biotin

source_name: Carotid Endarterectomy, MMF-treated

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion) was used for the linear amplification of mRNA molecules into antisense biotinylated cRNAs.

extract_protocol: Total RNA molecules were isolated from N=5 consecutive 6 micron thick frozen cross-sections of the endarterectomy sample by using Trizol reagent (Invitrogen), followed by column purification with DNase-I treatment, RNeasy Micro kit (Qiagen).

treatment_protocol: The patient was randomly assigned to treatment with 1000 mg mycophenolate mofetil (MMF), 2 weeks before carotid endarterectomy surgery.

tag: Tissue

value: human carotid endarterectomy from patient with a carotid artertery stenosis (>70% diameter stenosis on angiography) as defined by the North American Symptomatic Carotid Endarterectomy Trial (NACET).


title: 1673_MMF


title: 1668_MMF


title: ATL18A

description: progression from lymphomatis disease


title: ATL19-1


title: ATL18B

description: patient was drug treated

tag: acute leukemia (3hrs post bortezomib)


title: 1663_MMF


title: 1589_MMF


title: 1658_MMF