title: genomic_DNA_Breast_TDLU_AJP10_0850_157

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_161

status: Public on Dec 08 2011

type: genomic

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

country: USA

institute: NCI

description: Primary

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using the standard Illumina scanner setting.

data_processing:
Cy3, Cy5, Average Beta, and detection p-values were extracted using BeadStudio software.

Unmethylated and methylated signal intensities are available in 'GSE29428_raw_data.txt', which is linked to the Series GSE29428 record as a supplementary file.

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Breast_Primary, ER+

label_protocol: DNA was bisulfite converted, amplified, and labeled.

extract_protocol: Genomic DNA was extracted using standard techniques.

tag: tissue

value: breast

tag: disease state

tag: er status

value: ER+


title: ER-positive placebo-treated patient 28

type: RNA

city: Pittsburgh

first: Soonmuyung

last: Paik

state: PA

address: 1307 Federal Street, Suite 303

department: Pathology

institute: NSABP Foundation

hyb_protocol: After the labeling procedure, the amplified cDNA was purified with the KREA pure columns (Kreatech Biotechnology, Amsterdam, The Netherlands) to remove the dye in excess and was then fragmented using the Affymetrix fragmentation buffer provided with the GeneChip® Sample Cleanup Module Kit (Affymetrix, Santa Clara, CA). Finally, the cDNA was purified with the Clean-up columns, provided as well with the GeneChip® Sample Cleanup Module Kit, an added to the Hybridization Cocktail. The cocktail was then subjected to an overnight pre-hybridization to an used Affymetrix Genechip U133 2.0 Plus. The day after, 900 ng of the unbound labeled cDNA mix removed from the chip were processed as raccomanded by the manufacturer and hybridized to the Agilent Whole Human Genome (4 X 44 k) array. The hybridization was performed at 65 °C for 17 hours at a rotation of 10 revolutions per minute.

scan_protocol: The slides were scanned using a DNA Microarray Scanner ( Agilent Technologies, Santa Clara, CA) and features were extracted using Agilent’s Feature Extraction Software (v 9.5.3.1).

data_processing: Single channel hybridization intensity data were compiled using commercial software (Partek Genomic Suite, St Louis, Missouri). After quantile normalization, genes with mean intensity below 500 were filtred out. Data were log2 transformed for statistical analysis.

molecule: total RNA

source_name: Primary Breast cancer

label_protocol: 3 μg of the WTA product were labeled with a fluorescent dye (Cy3) using a direct chemical labeling method (ULS™ Labeling Kit with Cy3 for Agilent Gene Expression Arrays, Kreatech Biotechnology, Amsterdam, The Netherlands)

extract_protocol: Tumor areas were identified by ER immunostaining with a hematoxylin counter stain. Total RNA was isolated from 3 to 5  five μn unstained sections using the Ambion RecoverAll™ Total Nucleic Acid Isolation Kit (Applied Biosystems, Foster City, CA) and quantified using UV absorption on a spectrophotometer (NanoDrop® ND-1000). 100-200 nanograms of total RNA were converted to cDNA and amplified using a commercial service provided by Rubicon Genomics, Inc. (Ann Arbor, Mi), using the TransPlex™ Whole Transcriptome Amplification (WTA) kit.

treatment_protocol: Excised tumor specimens were formalin fixed paraffin embedeed in a routine process.

tag: histology

value: ductal

tag: ER_status (0 - negarive, 1 - positive)

tag: HER2_status (0 - negarive, 1 - positive)

tag: treatment (1 - placebo, 2- tamoxifen)


title: ER-negative placebo-treated patient 32


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_160

description: Primary


title: ER-negative tamoxifen-treated patient 30


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_155

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_156

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_153

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_152

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_154

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_151

description: Primary


title: ER-positive tamoxifen-treated patient 25


title: ER-positive placebo-treated patient 26

value: lobular


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_149

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_148

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_150

description: Primary


title: ER-positive placebo-treated patient 27


title: ER-positive placebo-treated patient 62


title: ER-positive tamoxifen-treated patient 23


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_147

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_145

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_146

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_144

description: Primary


title: ER-positive tamoxifen-treated patient 24


title: ER-negative tamoxifen-treated patient 20


title: ER-positive placebo-treated patient 18


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_142

description: Primary


title: ER-positive tamoxifen-treated patient 15


title: ER-positive placebo-treated patient 16


title: ER-positive placebo-treated patient 19


title: ER-positive placebo-treated patient 21


title: ER-positive tamoxifen-treated patient 14


title: ER-positive placebo-treated patient 11


title: genomic_DNA_Breast_MET_AJP10_0850_139

description: Metastasis

source_name: Breast_Metastasis, ER+


title: ER-positive placebo-treated patient 17


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_138

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_143

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_141

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_135

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_140

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_136

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_137

description: Terminal ductal-lobular unit (TDLU)

source_name: Breast_Terminal ductal-lobular unit (TDLU)

value: TDLU


title: ER-negative placebo-treated patient 13


title: ER-positive placebo-treated patient 12


title: ER-positive tamoxifen-treated patient 10


title: ER-positive tamoxifen-treated patient 9


title: ER-positive placebo-treated patient 7


title: ER-positive placebo-treated patient 22


title: genomic_DNA_Breast_MET_AJP10_0850_131

description: Metastasis


title: ER-positive placebo-treated patient 5


title: ER-positive placebo-treated patient 8


title: genomic_DNA_Breast_TDLU_AJP10_0850_130

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_129

description: Primary


title: ER-negative tamoxifen-treated patient 4


title: genomic_DNA_Breast_MET_AJP10_0850_128

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_133

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_134

description: Primary


title: genomic_DNA_MESENCH_AJP10_0850_132

description: MESENCH

value: MUSCLE


title: genomic_DNA_Breast_MET_AJP10_0850_127

description: Metastasis


title: ER-positive tamoxifen-treated patient 3


title: 13688883 - Col0 T48h Leaf Rep1 vs Ler T48h Leaf Rep1

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

country: France

institute: INRA

description: Several factors affect today a more extended use of microarrays for research and as a diagnosis tool. These factors are the experimental cost, the reproducibility of the measurements and the format of the analyses. This project aims at bringing solutions in these three domains by optimizing multiplexed analyses in order to reduce cost and enhance the number of samples treated simultaneously; by proposing new couples flurophores / slide surface in order to increase the signal precision and by developing new applications such as Comparative Genomic Hybridization (GGH) or Promoter Arrays to bring the plant microarray beyond transcriptome analyses. Altogether, these approaches will allow us to construct an optimized diagnostic tool based on 96 well microplate microarrays. This multidisciplinary project bring together biologists, chemists, physicists and mathematicians to develop innovative solutions for future application of DNA microarrays.

hyb_protocol: Ler T48h Leaf Rep1 Cy5 / Col0 T48h Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: Ler T48h Leaf Rep1

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

growth_protocol: rosette - Media : Agar 0.75% Hygrometry : 70% Light intensity : 150-190 µE.m-2.s-1 Light : short day (8 hours of day/16 hours of night)- beginning of day : 9h, beginning of night : 17h.

extract_protocol: Ler T48h Leaf Rep1:33.76ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Hydroponic culture with Nitrogen deficiency  - limited nitrogen supply - nitrogen concentration,nitrogen deprivation:quantity 0mM time 10day . Hydroponic culture with nitrogen deficiency : At first time, the seeds are sowed in Agar 0.75% (6mM NO3-/2) eppendorfs. When the roots leave out the agar, the plants are transfered on plates with holes for the leafs growth at 6 mM NO3-. The plants grow during 35 days. At 35 days, the plants are put in nitrogen deficiency at 0 mM NO3-.

value: leaf

tag: ecotype

value: Landsberg erecta

tag: age

source_name: Col0 T48h Leaf Rep1

extract_protocol: Col0 T48h Leaf Rep1:38.66ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_125

description: Primary


title: 13689213 - dcl1-9 T0 Root Rep2 vs Ler T0 Root Rep2

hyb_protocol: Ler T0 Root Rep2 Cy5 / dcl1-9 T0 Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T0 Root Rep2

growth_protocol: roots - Media : Agar 0.75% Hygrometry : 70% Light intensity : 150-190 µE.m-2.s-1 Light : short day (8 hours of day/16 hours of night)- beginning of day : 9h, beginning of night : 17h.

extract_protocol: Ler T0 Root Rep2:36.5ug. (DNeasy_Plant_Qiagen.pdf)

treatment_protocol: no treatment

value: root

source_name: dcl1-9 T0 Root Rep2

extract_protocol: dcl1-9 T0 Root  Rep2:25.31ug. (DNeasy_Plant_Qiagen.pdf)


title: 13688882 - Ler T48h Leaf Rep1 vs Col0 T48h Leaf Rep1

hyb_protocol: Col0 T48h Leaf Rep1 Cy5 / Ler T48h Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_124

description: Primary


title: ER-positive placebo-treated patient 2


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_126

description: Primary


title: 13757259 - dcl1-9 T48h Leaf Rep2 vs Ler T48h Leaf Rep2

hyb_protocol: Ler T48h Leaf Rep2 Cy5 / dcl1-9 T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T48h Leaf Rep2

extract_protocol: Ler T48h Leaf Rep2:72.96ug. (DNeasy_Plant_Qiagen.pdf)

source_name: dcl1-9 T48h Leaf Rep2

extract_protocol: dcl1-9 T48h Leaf  Rep2:56.02ug. (DNeasy_Plant_Qiagen.pdf)


title: 13688886 - Ler T0 Root Rep2 vs dcl1-9 T0 Root Rep2

hyb_protocol: dcl1-9 T0 Root Rep2 Cy5 / Ler T0 Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757256 - Ler T0 Leaf Rep2 vs dcl1-9 T0 Leaf Rep2

hyb_protocol: dcl1-9 T0 Leaf Rep2 Cy5 / Ler T0 Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl1-9 T0 Leaf Rep2

extract_protocol: dcl1-9 T0 Leaf Rep2:44.69ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Ler T0 Leaf Rep2

extract_protocol: Ler T0 Leaf Rep2:46.36ug. (DNeasy_Plant_Qiagen.pdf)


title: 13757258 - Ler T48h Leaf Rep2 vs dcl1-9 T48h Leaf Rep2

hyb_protocol: dcl1-9 T48h Leaf Rep2 Cy5 / Ler T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_122

description: Primary


title: 13757257 - dcl1-9 T0 Leaf Rep2 vs Ler T0 Leaf Rep2

hyb_protocol: Ler T0 Leaf Rep2 Cy5 / dcl1-9 T0 Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_120

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_121

description: Primary

source_name: Breast_Primary, ER-

value: ER-


title: ER-positive placebo-treated patient 1


title: genomic_DNA_Breast_TDLU_AJP10_0850_123

description: Terminal ductal-lobular unit (TDLU)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_117

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_115

description: Primary


title: genomic_DNA_MESENCH_AJP10_0850_119

description: MESENCH


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_112

description: Primary


title: 13757250 - dcl234 T48h Leaf Rep2 vs Col0 T48h Leaf Rep2

hyb_protocol: Col0 T48h Leaf Rep2 Cy5 / dcl234 T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T48h Leaf Rep2

extract_protocol: Col0 T48h Leaf Rep2:27.11ug. (DNeasy_Plant_Qiagen.pdf)

source_name: dcl234 T48h Leaf Rep2

extract_protocol: dcl234 T48h Leaf Rep2:3.91ug. (DNeasy_Plant_Qiagen.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_114

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_113

description: NOTUMREG

value: NOTUMREG


title: 13757255 - dcl234 T10d Root Rep2 vs Col0 T10d Root Rep2

hyb_protocol: Col0 T10d Root Rep2 Cy5 / dcl234 T10d Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T10d Root Rep2

extract_protocol: Col0 T10d Root Rep2:9.55ug. (DNeasy_Plant_Qiagen.pdf)

source_name: dcl234 T10d Root Rep2

extract_protocol: dcl234 T10d Root Rep2:3.95ug. (DNeasy_Plant_Qiagen.pdf)


title: 13757249 - Col0 T48h Leaf Rep2 vs dcl234 T48h Leaf Rep2

hyb_protocol: dcl234 T48h Leaf Rep2 Cy5 / Col0 T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757241 - Col0 T0 Root Rep2 vs Col0 T48h Root Rep2

hyb_protocol: Col0 T48h Root Rep2 Cy5 / Col0 T0 Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T48h Root Rep2

extract_protocol: Col0 T48h Root Rep2:22.65ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Col0 T0 Root Rep2

extract_protocol: Col0 T0 Root Rep2:22.33ug. (DNeasy_Plant_Qiagen.pdf)


title: 13757239 - Col0 T48h Root Rep2 vs dcl234 T48h Root Rep2

hyb_protocol: dcl234 T48h Root Rep2 Cy5 / Col0 T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T48h Root Rep2

extract_protocol: dcl234 T48h Root Rep2:12.96ug. (DNeasy_Plant_Qiagen.pdf)


title: 13757254 - Col0 T10d Root Rep2 vs dcl234 T10d Root Rep2

hyb_protocol: dcl234 T10d Root Rep2 Cy5 / Col0 T10d Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757252 - Col0 T10d Leaf Rep2 vs dcl234 T10d Leaf Rep2

hyb_protocol: dcl234 T10d Leaf Rep2 Cy5 / Col0 T10d Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T10d Leaf Rep2

extract_protocol: dcl234 T10d Leaf Rep2:24.13ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Col0 T10d Leaf Rep2

extract_protocol: Col0 T10d Leaf Rep2:7.86ug. (DNeasy_Plant_Qiagen.pdf)


title: 13757246 - Col0 T10d Root Rep2 vs Col0 T48h Root Rep2

hyb_protocol: Col0 T48h Root Rep2 Cy5 / Col0 T10d Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_TDLU_AJP10_0850_111

description: Terminal ductal-lobular unit (TDLU)

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.

source_name: Breast_Terminal ductal-lobular unit (TDLU)

extract_protocol: Genomic DNA was extracted using standard techniques.


title: 13757244 - Col0 T48h Root Rep2 vs Col0 T0 Root Rep2

hyb_protocol: Col0 T0 Root Rep2 Cy5 / Col0 T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757253 - dcl234 T10d Leaf Rep2 vs Col0 T10d Leaf Rep2

hyb_protocol: Col0 T10d Leaf Rep2 Cy5 / dcl234 T10d Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_118

description: Primary

source_name: Breast_Primary, ER+


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_116

description: Primary


title: genomic_DNA_Breast_NOTUMREG_AJP10_0850_109

description: NOTUMREG


title: genomic_DNA_Breast_MET_AJP10_0850_110

description: Metastasis

source_name: Breast_Metastasis, ER+


title: 13757240 - dcl234 T48h Root Rep2 vs Col0 T48h Root Rep2

hyb_protocol: Col0 T48h Root Rep2 Cy5 / dcl234 T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_MET_AJP10_0850_108

description: Metastasis


title: 13757139 - Col0 T0 Leaf Rep1 vs Ler T0 Leaf Rep1

hyb_protocol: Ler T0 Leaf Rep1 Cy5 / Col0 T0 Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T0 Leaf Rep1

extract_protocol: Ler T0 Leaf Rep1:20.41ug. (Qiagen_RNeasy.pdf)

source_name: Col0 T0 Leaf Rep1

extract_protocol: Col0 T0 Leaf Rep1:12.74ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_107

description: Primary


title: 13757245 - Col0 T48h Root Rep2 vs Col0 T10d Root Rep2

hyb_protocol: Col0 T10d Root Rep2 Cy5 / Col0 T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_106

description: Primary


title: 13757138 - Ler T0 Leaf Rep1 vs Col0 T0 Leaf Rep1

hyb_protocol: Col0 T0 Leaf Rep1 Cy5 / Ler T0 Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757133 - Col0 T0 Leaf Rep2 vs dcl234 T0 Leaf Rep2

hyb_protocol: dcl234 T0 Leaf Rep2 Cy5 / Col0 T0 Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T0 Leaf Rep2

extract_protocol: dcl234 T0 Leaf Rep2:8.6ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Col0 T0 Leaf Rep2

extract_protocol: Col0 T0 Leaf Rep2:18.9ug. (DNeasy_Plant_Qiagen.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_105

description: Primary


title: 13757136 - Col0 T0 Root Rep2 vs dcl234 T0 Root Rep2

hyb_protocol: dcl234 T0 Root Rep2 Cy5 / Col0 T0 Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T0 Root Rep2

extract_protocol: dcl234 T0 Root Rep2:26.43ug. (DNeasy_Plant_Qiagen.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_104

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_103

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_101

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_102

description: Primary


title: 13757134 - dcl234 T0 Leaf Rep2 vs Col0 T0 Leaf Rep2

hyb_protocol: Col0 T0 Leaf Rep2 Cy5 / dcl234 T0 Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_100

description: Primary


title: 13757130 - dcl1-9 T10d Leaf Rep1 vs dcl1-9 T48h Leaf Rep1

hyb_protocol: dcl1-9 T48h Leaf Rep1 Cy5 / dcl1-9 T10d Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl1-9 T48h Leaf Rep1

extract_protocol: dcl1-9 T48h Leaf Rep1:35.37ug. (Qiagen_RNeasy.pdf)

source_name: dcl1-9 T10d Leaf Rep1

extract_protocol: dcl1-9  T10d Leaf Rep1:19.56ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_99

description: Primary

source_name: Breast_Primary, ER-


title: 13757137 - dcl234 T0 Root Rep2 vs Col0 T0 Root Rep2

hyb_protocol: Col0 T0 Root Rep2 Cy5 / dcl234 T0 Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_MET_AJP10_0850_98

description: Metastasis

source_name: Breast_Metastasis, ER-


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_97

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_96

description: Primary


title: 13757128 - dcl234 T48h Leaf Rep1  vs Col0 T48h Leaf Rep1

hyb_protocol: Col0 T48h Leaf Rep1 Cy5 / dcl234 T48h Leaf Rep1  Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T48h Leaf Rep1

extract_protocol: Col0 T48h Leaf Rep1:38.66ug. (Qiagen_RNeasy.pdf)

source_name: dcl234 T48h Leaf Rep1

extract_protocol: dcl234 T48h Leaf Rep1:38.3ug. (Qiagen_RNeasy.pdf)


title: 13757126 - dcl1-9 T0 Leaf Rep1 vs Ler T0 Leaf Rep1

hyb_protocol: Ler T0 Leaf Rep1 Cy5 / dcl1-9 T0 Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl1-9 T0 Leaf Rep1

extract_protocol: dcl1-9 T0 Leaf Rep1:50.01ug. (Qiagen_RNeasy.pdf)


title: 13757127 - Col0 T48h Leaf Rep1 vs dcl234 T48h Leaf Rep1

hyb_protocol: dcl234 T48h Leaf Rep1  Cy5 / Col0 T48h Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13697200 - Col0 T10d Leaf Rep1 vs Ler T10d Leaf Rep1

hyb_protocol: Ler T10d Leaf Rep1 Cy5 / Col0 T10d Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T10d Leaf Rep1

extract_protocol: Ler T10d Leaf Rep1:17.74ug. (Qiagen_RNeasy.pdf)

source_name: Col0 T10d Leaf Rep1

extract_protocol: Col0 T10d Leaf Rep1:13.72ug. (Qiagen_RNeasy.pdf)


title: 13757260 - Ler T10d Leaf Rep1 vs Col0 T10d Leaf Rep1

hyb_protocol: Col0 T10d Leaf Rep1 Cy5 / Ler T10d Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757125 - Ler T0 Leaf Rep1 vs dcl1-9 T0 Leaf Rep1

hyb_protocol: dcl1-9 T0 Leaf Rep1 Cy5 / Ler T0 Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13691693 - Col0 T10d Leaf Rep2 vs Col0 T48h Leaf Rep2

hyb_protocol: Col0 T48h Leaf Rep2 Cy5 / Col0 T10d Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T48h Leaf Rep2

extract_protocol: Col0 T48h Leaf Rep2:27.11ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Col0 T10d Leaf Rep2


title: 13757129 - dcl1-9 T48h Leaf Rep1 vs dcl1-9 T10d Leaf Rep1

hyb_protocol: dcl1-9 T10d Leaf Rep1 Cy5 / dcl1-9 T48h Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_93

description: Primary

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.

source_name: Breast_Primary, ER+


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_92

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_95

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_91

description: Primary


title: 13691692 - Col0 T48h Leaf Rep2 vs Col0 T10d Leaf Rep2

hyb_protocol: Col0 T10d Leaf Rep2 Cy5 / Col0 T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_90

description: Primary


title: 13691688 - Ler T48h Root Rep2 vs Ler T10d Root Rep2

hyb_protocol: Ler T10d Root Rep2 Cy5 / Ler T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T10d Root Rep2

extract_protocol: Ler T10d Root Rep2:6.27ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Ler T48h Root Rep2

extract_protocol: Ler T48h Root Rep2:65.17ug. (DNeasy_Plant_Qiagen.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_88

description: Primary


title: 13691690 - Col0 T0 Leaf Rep2 vs Col0 T48h Leaf Rep2

hyb_protocol: Col0 T48h Leaf Rep2 Cy5 / Col0 T0 Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_89

description: Primary


title: 13691691 - Col0 T48h Leaf Rep2 vs Col0 T0 Leaf Rep2

hyb_protocol: Col0 T0 Leaf Rep2 Cy5 / Col0 T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13691687 - Ler T48h Root Rep2 vs Ler T0 Root Rep2

hyb_protocol: Ler T0 Root Rep2 Cy5 / Ler T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T0 Root Rep2

extract_protocol: Ler T0 Root Rep2:36.5ug. (DNeasy_Plant_Qiagen.pdf)


title: 13691686 - Ler T0 Root Rep2 vs Ler T48h Root Rep2

hyb_protocol: Ler T48h Root Rep2 Cy5 / Ler T0 Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_94

description: Primary

extract_protocol: Genomic DNA was extracted using standard techniques.


title: 13691689 - Ler T10d Root Rep2 vs Ler T48h Root Rep2

hyb_protocol: Ler T48h Root Rep2 Cy5 / Ler T10d Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13691684 - Ler T48h Leaf Rep2 vs Ler T10d Leaf Rep2

hyb_protocol: Ler T10d Leaf Rep2 Cy5 / Ler T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T10d Leaf Rep2

extract_protocol: Ler T10d Leaf Rep2:7.01ug. (DNeasy_Plant_Qiagen.pdf)

source_name: Ler T48h Leaf Rep2

extract_protocol: Ler T48h Leaf Rep2:72.96ug. (DNeasy_Plant_Qiagen.pdf)


title: 13689216 - Ler T48h Leaf Rep2 vs Ler T0 Leaf Rep2

hyb_protocol: Ler T0 Leaf Rep2 Cy5 / Ler T48h Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Ler T0 Leaf Rep2

extract_protocol: Ler T0 Leaf Rep2:46.36ug. (DNeasy_Plant_Qiagen.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_83

description: Primary


title: 13689215 - Ler T0 Leaf Rep2 vs Ler T48h Leaf Rep2

hyb_protocol: Ler T48h Leaf Rep2 Cy5 / Ler T0 Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ER-positive tamoxifen-treated patient 6

hyb_protocol: After the labeling procedure, the amplified cDNA was purified with the KREA pure columns (Kreatech Biotechnology, Amsterdam, The Netherlands) to remove the dye in excess and was then fragmented using the Affymetrix fragmentation buffer provided with the GeneChip® Sample Cleanup Module Kit (Affymetrix, Santa Clara, CA). Finally, the cDNA was purified with the Clean-up columns, provided as well with the GeneChip® Sample Cleanup Module Kit, an added to the Hybridization Cocktail. The cocktail was then subjected to an overnight pre-hybridization to an used Affymetrix Genechip U133 2.0 Plus. The day after, 900 ng of the unbound labeled cDNA mix removed from the chip were processed as raccomanded by the manufacturer and hybridized to the Agilent Whole Human Genome (4 X 44 k) array. The hybridization was performed at 65 °C for 17 hours at a rotation of 10 revolutions per minute.

source_name: Primary Breast cancer

extract_protocol: Tumor areas were identified by ER immunostaining with a hematoxylin counter stain. Total RNA was isolated from 3 to 5  five μn unstained sections using the Ambion RecoverAll™ Total Nucleic Acid Isolation Kit (Applied Biosystems, Foster City, CA) and quantified using UV absorption on a spectrophotometer (NanoDrop® ND-1000). 100-200 nanograms of total RNA were converted to cDNA and amplified using a commercial service provided by Rubicon Genomics, Inc. (Ann Arbor, Mi), using the TransPlex™ Whole Transcriptome Amplification (WTA) kit.


title: 13688888 - Ler T48h Root Rep2 vs dcl1-9 T48h Root Rep2

hyb_protocol: dcl1-9 T48h Root Rep2 Cy5 / Ler T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl1-9 T48h Root Rep2

extract_protocol: dcl1-9 T48h Root  Rep2:18.74ug. (DNeasy_Plant_Qiagen.pdf)


title: 13689212 - Ler T10d Leaf Rep2 vs dcl1-9 T10d Leaf Rep2

hyb_protocol: dcl1-9 T10d Leaf Rep2 Cy5 / Ler T10d Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl1-9 T10d Leaf Rep2

extract_protocol: dcl1-9 T10d Leaf Rep2:3.83ug. (DNeasy_Plant_Qiagen.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_87

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_84

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_80

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_82

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_81

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_79

description: Primary


title: 13688889 - dcl1-9 T48h Root Rep2 vs Ler T48h Root Rep2

hyb_protocol: Ler T48h Root Rep2 Cy5 / dcl1-9 T48h Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13691685 - Ler T10d Leaf Rep2 vs Ler T48h Leaf Rep2

hyb_protocol: Ler T48h Leaf Rep2 Cy5 / Ler T10d Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_75

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_74

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_73

description: Primary


title: 13688890 - Ler T10d Root Rep2 vs dcl1-9 T10d Root Rep2

hyb_protocol: dcl1-9 T10d Root Rep2 Cy5 / Ler T10d Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl1-9 T10d Root Rep2

extract_protocol: dcl1-9 T10d Root Rep2:5.5ug. (DNeasy_Plant_Qiagen.pdf)


title: 13689214 - dcl1-9 T10d Root Rep2 vs Ler T10d Root Rep2

hyb_protocol: Ler T10d Root Rep2 Cy5 / dcl1-9 T10d Root Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757124 - Col0 T0 Leaf Rep1 vs dcl234 T0 Leaf Rep1

hyb_protocol: dcl234 T0 Leaf Rep1 Cy5 / Col0 T0 Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T0 Leaf Rep1

extract_protocol: dcl234 T0 Leaf Rep1:14.59ug. (Qiagen_RNeasy.pdf)

source_name: Col0 T0 Leaf Rep1

extract_protocol: Col0 T0 Leaf Rep1:12.74ug. (Qiagen_RNeasy.pdf)


title: 13688885 - dcl1-9 T10d Leaf Rep2 vs Ler T10d Leaf Rep2

hyb_protocol: Ler T10d Leaf Rep2 Cy5 / dcl1-9 T10d Leaf Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_85

description: Primary

hyb_protocol: DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_86

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_72

description: Primary


title: 13757023 - Col0 T0 Root Rep1 vs dcl234 T0 Root Rep1

hyb_protocol: dcl234 T0 Root Rep1 Cy5 / Col0 T0 Root Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T0 Root Rep1

extract_protocol: dcl234 T0 Root Rep1:15.15ug. (Qiagen_RNeasy.pdf)

source_name: Col0 T0 Root Rep1

extract_protocol: Col0 T0 Root Rep1:13.19ug. (Qiagen_RNeasy.pdf)


title: 13757024 - dcl234 T0 Root Rep1 vs Col0 T0 Root Rep1

hyb_protocol: Col0 T0 Root Rep1 Cy5 / dcl234 T0 Root Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757115 - dcl234 T48h Root  Rep1  vs Col0 T48h Root Rep1

hyb_protocol: Col0 T48h Root Rep1 Cy5 / dcl234 T48h Root  Rep1  Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T48h Root Rep1

extract_protocol: Col0 T48h Root Rep1:26.23ug. (Qiagen_RNeasy.pdf)

source_name: dcl234 T48h Root Rep1

extract_protocol: dcl234 T48h Root Rep1:15.81ug. (Qiagen_RNeasy.pdf)


title: 13757007 - dcl234 T0 Leaf Rep1 vs Col0 T0 Leaf Rep1

hyb_protocol: Col0 T0 Leaf Rep1 Cy5 / dcl234 T0 Leaf Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13757021 - Col0 T10d Root Rep1 vs dcl234 T10d Root Rep1

hyb_protocol: dcl234 T10d Root Rep1 Cy5 / Col0 T10d Root Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl234 T10d Root Rep1

extract_protocol: dcl234  T10d Root Rep1:2.28ug. (Qiagen_RNeasy.pdf)

source_name: Col0 T10d Root Rep1

extract_protocol: Col0 T10d Root Rep1:4.67ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_76

description: Primary

source_name: Breast_Primary, ER+


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_78

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_77

description: Primary


title: 13757122 - dcl234 T10d Root Rep1 vs Col0 T10d Root Rep1

hyb_protocol: Col0 T10d Root Rep1 Cy5 / dcl234 T10d Root Rep1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_71

description: Primary