title: 13757026 - Col0 T48h Root Rep1 vs dcl234 T48h Root  Rep1

hyb_protocol: dcl234 T48h Root  Rep1  Cy5 / Col0 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.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_70

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: genomic_DNA_Breast_PRIMARY_AJP10_0850_69

description: Primary


title: 13757019 - Col0 T48h Root Rep1 vs Col0 T10d Root Rep1

type: RNA

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: Col0 T10d Root Rep1 Cy5 / Col0 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.

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.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col0 T10d Root 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: 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: Col0 T10d Root Rep1:4.67ug. (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: root

tag: ecotype

tag: age

source_name: Col0 T48h Root Rep1

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


title: 13757020 - Col0 T10d Root Rep1 vs Col0 T48h Root Rep1

hyb_protocol: Col0 T48h 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.


title: 13757018 - dcl1-9 T10d Root Rep1 vs Ler T10d Root Rep1

hyb_protocol: Ler T10d Root Rep1 Cy5 / dcl1-9 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: Ler T10d Root Rep1

extract_protocol: Ler T10d Root Rep1:4.42ug. (Qiagen_RNeasy.pdf)

value: Landsberg erecta

source_name: dcl1-9 T10d Root Rep1

extract_protocol: dcl1-9  T10d Root Rep1:3.08ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_MET_AJP10_0850_68

description: Metastasis

source_name: Breast_Metastasis, ER+


title: 13757016 - dcl1-9 T48h Root Rep1 vs dcl1-9 T0 Root Rep1

hyb_protocol: dcl1-9 T0 Root Rep1 Cy5 / dcl1-9 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: dcl1-9 T0 Root Rep1

extract_protocol: dcl1-9 T0 Root Rep1:15.54ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

source_name: dcl1-9 T48h Root Rep1

extract_protocol: dcl1-9 T48h Root Rep1 :12.63ug. (Qiagen_RNeasy.pdf)


title: 13757017 - Ler T10d Root Rep1 vs dcl1-9 T10d Root Rep1

hyb_protocol: dcl1-9 T10d Root Rep1 Cy5 / Ler 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_67

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_62

description: Primary

source_name: Breast_Primary, ER-

value: ER-


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_60

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_66

description: Primary


title: 13757013 - Ler T48h Root Rep1 vs Ler T10d Root Rep1

hyb_protocol: Ler T10d Root Rep1 Cy5 / Ler 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: Ler T48h Root Rep1

extract_protocol: Ler T48h Root Rep1:14.21ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_59

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_65

description: Primary


title: 13757015 - dcl1-9 T0 Root Rep1 vs dcl1-9 T48h Root Rep1

hyb_protocol: dcl1-9 T48h Root Rep1 Cy5 / dcl1-9 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: 13757014 - Ler T10d Root Rep1 vs Ler T48h Root Rep1

hyb_protocol: Ler T48h Root Rep1 Cy5 / Ler 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_61

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_64

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_58

description: Primary


title: 13757011 - Ler T0 Root Rep1 vs dcl1-9 T0 Root Rep1

hyb_protocol: dcl1-9 T0 Root Rep1 Cy5 / Ler 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: Ler T0 Root Rep1

extract_protocol: Ler T0 Root Rep1:29.38ug. (Qiagen_RNeasy.pdf)


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_56

description: Primary


title: 13757004 - dcl1-9 T0 Leaf Rep1 vs dcl1-9 T48h Leaf Rep1

hyb_protocol: dcl1-9 T48h 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 T48h Leaf Rep1

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

value: leaf

source_name: dcl1-9 T0 Leaf Rep1

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


title: 13757002 - Ler T10d Leaf Rep1 vs Ler T48h Leaf Rep1

hyb_protocol: Ler T48h 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.

source_name: Ler T48h Leaf Rep1

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

source_name: Ler T10d Leaf Rep1

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


title: 13757009 - dcl1-9 T10d Root Rep1 vs dcl1-9 T48h Root Rep1

hyb_protocol: dcl1-9 T48h Root Rep1 Cy5 / dcl1-9 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: 13757000 - Ler T48h Leaf Rep1 vs Ler T10d Leaf Rep1

hyb_protocol: Ler T10d 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: 13688458 - dcl234 T10d Leaf Rep1 vs Col0 T10d Leaf Rep1

hyb_protocol: Col0 T10d Leaf Rep1 Cy5 / dcl234 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: Col0 T10d Leaf Rep1

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

source_name: dcl234 T10d Leaf Rep1

extract_protocol: dcl234  T10d Leaf Rep1:10.42ug. (Qiagen_RNeasy.pdf)


title: 13757012 - dcl1-9 T0 Root Rep1 vs Ler T0 Root Rep1

hyb_protocol: Ler T0 Root Rep1 Cy5 / dcl1-9 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: genomic_DNA_Breast_PRIMARY_AJP10_0850_57

description: Primary

source_name: Breast_Primary, ER+


title: 13688449 - Col0 T10d Leaf Rep1 vs dcl234 T10d Leaf Rep1

hyb_protocol: dcl234 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.


title: 13757005 - dcl1-9 T48h Leaf Rep1 vs dcl1-9 T0 Leaf Rep1

hyb_protocol: dcl1-9 T0 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: 13757008 - dcl1-9 T48h Root Rep1 vs dcl1-9 T10d Root Rep1

hyb_protocol: dcl1-9 T10d Root Rep1 Cy5 / dcl1-9 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.


title: genomic_DNA_Breast_MET_AJP10_0850_55

description: Metastasis

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

source_name: Breast_Metastasis, ER-


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_63

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_53

description: Metastasis


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_54

description: Primary


title: 13688315 - Col0 T48h Leaf Rep1 vs Col0 T10d Leaf Rep1

hyb_protocol: Col0 T10d 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.

source_name: Col0 T48h Leaf Rep1

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


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_48

description: Primary


title: 13688316 - Col0 T10d Leaf Rep1 vs Col0 T48h Leaf Rep1

hyb_protocol: Col0 T48h 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.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_47

description: Primary


title: 13688129 - dcl1-9 T10d Leaf Rep1 vs Ler T10d Leaf Rep1

hyb_protocol: Ler T10d 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 T10d Leaf Rep1

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


title: 13688130 - Col0 T0 Leaf Rep1 vs Col0 T48h Leaf Rep1

hyb_protocol: Col0 T48h 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: Col0 T0 Leaf Rep1

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


title: 13688126 - dcl1-9 T48h Leaf Rep1 vs Ler T48h Leaf Rep1

hyb_protocol: Ler T48h 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_45

description: Primary

extract_protocol: Genomic DNA was extracted using standard techniques.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_46

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_52

description: Primary


title: 13688127 - Ler T10d Leaf Rep1 vs dcl1-9 T10d Leaf Rep1

hyb_protocol: dcl1-9 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: 13688133 - Col0 T48h Leaf Rep1 vs Col0 T0 Leaf Rep1

hyb_protocol: Col0 T0 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: 13688124 - dcl1-9 T48h Root Rep1 vs Ler T48h Root Rep1

hyb_protocol: Ler T48h Root Rep1 Cy5 / dcl1-9 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.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_50

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_51

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_49

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_44

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_41

description: Primary


title: 13688125 - Ler T48h Leaf Rep1 vs dcl1-9 T48h Leaf Rep1

hyb_protocol: dcl1-9 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: 13688120 - Ler T48h Root Rep1 vs dcl1-9 T48h Root Rep1

hyb_protocol: dcl1-9 T48h Root Rep1 Cy5 / Ler 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.


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_39

description: Primary


title: 13688117 - Ler T48h Root Rep1 vs Ler T0 Root Rep1

hyb_protocol: Ler T0 Root Rep1 Cy5 / Ler 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.


title: 13688109 - Ler T0 Leaf Rep1 vs Ler T48h Leaf Rep1

hyb_protocol: Ler T48h 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.

source_name: Ler T0 Leaf Rep1

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


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_43

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_42

description: Primary


title: 13688111 - Ler T48h Leaf Rep1 vs Ler T0 Leaf Rep1

hyb_protocol: Ler T0 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_40

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_38

description: Metastasis


title: 13688106 - Col0 T0 Root Rep1 vs Col0 T48h Root Rep1

hyb_protocol: Col0 T48h 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: Col0 T48h Root Rep1

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

source_name: Col0 T0 Root Rep1

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


title: 13688108 - Col0 T48h Root Rep1 vs Col0 T0 Root Rep1

hyb_protocol: Col0 T0 Root Rep1 Cy5 / Col0 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.


title: 13757123 - Col0 T10d  Root vs Col0 T0  Root

hyb_protocol: Col0 T0  Root Cy5 / Col0 T10d  Root 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 T0 Root

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

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

source_name: Col0 T10d Root

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


title: 13757119 - Col0 T0  Root vs Col0 T10d  Root

hyb_protocol: Col0 T10d  Root Cy5 / Col0 T0  Root 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_34

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_37

description: Primary


title: genomic_DNA_Breast_MET_AJP10_0850_33

description: Metastasis

source_name: Breast_Metastasis, ER+


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_36

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_32

description: Terminal ductal-lobular unit (TDLU)

source_name: Breast_Terminal ductal-lobular unit (TDLU)

value: TDLU


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_30

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_35

description: Primary


title: 13757117 - Col0 T0 Leaf vs Col0 T10d  Leaf

hyb_protocol: Col0 T10d  Leaf Cy5 / Col0 T0 Leaf 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 Leaf

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

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

source_name: Col0 T0 Leaf

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


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_29

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_28

description: Primary


title: 13757118 - Col0 T10d  Leaf vs Col0 T0 Leaf

hyb_protocol: Col0 T0 Leaf Cy5 / Col0 T10d  Leaf 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: Basal IFE epidermal stem cells from WT mice 3

city: Barcelona

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

country: Spain

institute: Institute for Research in Biomedicine (IRB, Barcelona)

description: Gene expression data from purified clock positive Basal IFE stem cells

hyb_protocol: Affymetrix GeneChip Human Gene 1.0ST arrays were hybridized with 10 ug of labeled, amplified dsDNA, washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003)

label: Biotin

organism: Mus musculus

source_name: Basal IFE cells isolated from 1 year old WT mice

label_protocol: The indicated starting amount of total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2) and subsequently labeled using GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441), according to manufacturer's instructions.

growth_protocol: Mice were housed under standard SPF conditions and according to the Ethical Committee for Animal Experimentation of the Government of Catalonia.

extract_protocol: Total RNA was isolated from FACS-sorted cells in Trizol by chloroform extraction, followed by the RNA clean-up protocol of RNeasy Micro or Mini Kit (Qiagen)

treatment_protocol: There was no treatment prior to the purification of the cells

tag: cell type

value: Dorsal skin Basal IFE epidermal stem cells

tag: genotype

value: wild type


title: Basal IFE epidermal stem cells from KO mice 1

description: Gene expression data from purified clock negative Basal IFE stem cells

source_name: Basal IFE cells isolated from 1 year old KO mice

value: Bmal1 KO


title: Basal IFE epidermal stem cells from WT mice 1


title: Mdx diaphragm-derived cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Freshly isolated cells from diaphragm of mdx mouse by FACS.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing:
F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.
We used Microsoft Office Excel 2003 for generating our normalized data.

source_name: SC

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Mdx dystrophic mice at 23 to 27 week old were used. Total of 10 mdx mice were used to collect cells.

extract_protocol: Total RNA extracted using Qiagen RNeasy Micro following manufacturer's instructions.

treatment_protocol: Diaphragm of mdx mouse was enzymatically digested to liberate mononucleated cells. Satellite cells and PDGFRa+ cells were directly isolated by FACS. Freshly isolated cells were frozen for RNA extraction immediately after cell sorting. Total of 2.3 x 105 satellite cells and 5 x 105 PDGFRa+ cells were collected.

value: satellite cells

tag: strain

value: Mdx

source_name: Pα

value: PdGFRa+ cells


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_27

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_31

description: Primary

source_name: Breast_Primary, ER+


title: Basal IFE epidermal stem cells from KO mice 2


title: Basal IFE epidermal stem cells from WT mice 2


title: Basal IFE epidermal stem cells from KO mice 3


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_26

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_24

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_23

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_25

description: Primary


title: Clock negative bulge cells 2

description: Gene expression data from purified clock negative bulge stem cells

source_name: Venus GFP negative Bulge cells (alpha6bright/CD34+/Venushigh population) isolated from the dorsal skin of P18-19 mice

value: Dorsal skin bulge epidermal stem cells

tag: cell phenotype


title: Clock positive bulge cells 3

description: Gene expression data from purified clock positive bulge stem cells

source_name: Venus GFP positive Bulge cells (alpha6bright/CD34+/Venushigh population) isolated from the dorsal skin of P18-19 mice


title: HMEC_HighMyc+SUMO depleted_3

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description:
Sample name: 127585
EA10128_127585_HGU133_PLUS_2_TAMDOX3.CEL
rep3 Myc/shSAE2

hyb_protocol: The hybridization cocktail was denatured at 99°C for 5 minutes, incubated at 45°C for 5 minutes and then injected into a GeneChip cartridge which was incubated at 45°C for at least 16 hours in a rotating oven at 60 rpm.  GeneChips were washed and stained using a Fluidics station 450 using protocol: EukGE-WS2v4_450

scan_protocol: GeneChips were scanned using Affymetrix GC3000 scanner with 7G upgrade, Factory PMT settings.

data_processing: data were analyzed in R using the GCRMA R package with defaults

label: biotin

source_name: High Myc+Sumo Depleted in HMEC

label_protocol: 2 ug total RNA using the Single-Round 3’ RNA Amplification and Biotin Labeling (Enzo Life Sciences)

growth_protocol: pINDUCER11-shSAE2 infected Myc-ER human mammary epithelial cells (HMECs) were cultured at 37C with 5% CO2 in mammary epithelial growth medium (MEGM, Lonza)

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: pINDUCER11-shSAE2 infected Myc-ER HMECs were treated for three days -/+ 1ug/mL dox and one day -/+ 300nM TAM (all samples done in triplicate)

tag: cell line

value: human mammary epithelial cells (HMECs)

tag: treatment

value: Tamoxifen+shRNA


title: Clock positive bulge cells 1

value: Venus GFP positive Bulge cells (alpha6bright/CD34+/Venushigh population)


title: genomic_DNA_Breast_TDLU_AJP10_0850_21

description: Terminal ductal-lobular unit (TDLU)

value: breast


title: Clock negative bulge cells 3

value: Venus GFP negative Bulge cells (alpha6bright/CD34+/Venushigh population)


title: genomic_DNA_Breast_TDLU_AJP10_0850_22

description: Terminal ductal-lobular unit (TDLU)


title: Mouse 597 duodenum

city: Gothenburg

first: Erik

last: Larsson

address: Bruna stråket 16

department: Wallenberg Laboratory

country: Sweden

institute: University of Gothenburg

description: RMA expression value derived from Expression Console software; gene level analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the Uppsala Array Platform microarray core facility (Sweden).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression Console software (Affymetrix) for background correction and normalization. Downstream data analysis and statistical evaluations were performed using customized matlab scripts.

source_name: Healthy male, autoclaved chow diet

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: RNA was isolated using the RNeasy mini kit or the RNeasy Lipid tissue mini kit (QIAGEN), according to the manufacturer's instructions.

value: duodenum

value: GF


title: Mouse 587 duodenum

value: CONV-R


title: Clock negative bulge cells 1


title: Mouse 591 duodenum

value: WT


title: Mouse 592 duodenum


title: Clock positive bulge cells 2


title: Mouse 596 duodenum


title: Mouse 602 duodenum


title: HMEC_Control_3

description:
Sample name: 127582
EA10128_127582_HGU133_PLUS_2_03.CEL
rep3 Control

source_name: normal HMEC

value: Control


title: Mouse 598 duodenum


title: Mouse 595 duodenum


title: Mouse 590 duodenum


title: HMEC_SUMO depleted_3

description:
Sample name: 127584
EA10128_127584_HGU133_PLUS_2_DOX3.CEL
rep3 shSAE2

source_name: SUMO depleted in HMEC

value: shRNA SAE2


title: HMEC_HighMyc_2

description:
Sample name: 127579
EA10128_127579_HGU133_PLUS_2_TAM2.CEL
rep2 Myc

source_name: High Myc in HMEC

value: Tamoxifen induced


title: 13688114 - Ler T0 Root Rep1 vs Ler T48h Root Rep1

hyb_protocol: Ler T48h Root Rep1 Cy5 / Ler 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: Ler T48h Root Rep1

extract_protocol: Ler T48h Root Rep1:14.21ug. (Qiagen_RNeasy.pdf)

value: root

value: Landsberg erecta

source_name: Ler T0 Root Rep1

extract_protocol: Ler T0 Root Rep1:29.38ug. (Qiagen_RNeasy.pdf)


title: Mouse 588 duodenum


title: Mouse 593 duodenum


title: HMEC_HighMyc+SUMO depleted_2

description:
Sample name: 127581
EA10128_127581_HGU133_PLUS_2_TAMDOX2.CEL
rep2 Myc/shSAE2


title: HMEC_HighMyc_3

description:
Sample name: 127583
EA10128_127583_HGU133_PLUS_2_TAM3.CEL
rep3 Myc


title: Mouse 600 duodenum


title: Mouse 594 duodenum


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_20

description: Primary

value: ER+


title: HMEC_SUMO depleted_2

description:
Sample name: 127580
EA10128_127580_HGU133_PLUS_2_DOX2.CEL
rep2 shSAE2


title: genomic_DNA_Breast_TDLU_AJP10_0850_19

description: Terminal ductal-lobular unit (TDLU)

source_name: Breast_Terminal ductal-lobular unit (TDLU)

value: TDLU


title: Mouse 589 duodenum


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_18

description: Primary


title: genomic_DNA_Breast_TDLU_AJP10_0850_17

description: Terminal ductal-lobular unit (TDLU)


title: Mouse 586 duodenum


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_16

description: Primary


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_14

description: Primary


title: HMEC_Control_2

description:
Sample name: 127578
EA10128_127578_HGU133_PLUS_2_02.CEL
rep2 Control


title: Mouse 600 jejunum

value: jejunum


title: HDMVEC_Basal Growth_Rep1

city: Baltimore

first: Marc

middle: K

last: Halushka

address: 720 Rutland Avenue / Ross Rm 632B

department: Pathology

institute: Johns Hopkins University SOM

hyb_protocol: The Cy3-labled RNA was dried for 1-2h at 55°C. then assembled the hybridization mixture and hybridize for 20h at 55°C. Finally the hybridized slides were washed for scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides [Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% (XDR Hi) and 5%(XDR Lo)].

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent G4450AA) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human Dermal (neonatal) Microvascular Endothelial Cells (HDMVECs) Basal Growth

label_protocol: The microRNAs were labled by Cy3 using Agilent’s miRNA Complete Labeling and Hyb Kit.

growth_protocol: Grown on a 2% gelatin matrix with ECM media and 5% FBS. Grown to 75% confluence, media changed and RNA harvested the following day at ~95% confluence

extract_protocol: miRNeasy kit (Qiagen)

tag: source

value: Cascade Biologics, Invitrogen cell culture


title: HMEC_HighMyc+SUMO depleted_1

description:
Sample name: 127577
EA10128_127577_HGU133_PLUS_2_TAMDOX1.CEL
rep1 Myc/shSAE2

value: human mammary epithelial cells (HMECs)

value: Tamoxifen+shRNA


title: Mouse 585 duodenum


title: Mouse 584 duodenum


title: HMEC_SUMO depleted_1

description:
Sample name: 127576
EA10128_127576_HGU133_PLUS_2_DOX1.CEL
rep1 shSAE2


title: Mouse 583 duodenum


title: Mouse 601 jejunum


title: Mouse 598 jejunum


title: Mouse 599 jejunum


title: HAEC_Basal Growth_Ref2

source_name: Human Aortic Endothelial Cell (HAEC) Basal Growth

treatment_protocol: Grown on a 2% gelatin matrix with ECM media and 5% FBS.

value: heart transplantation, 7 year old girl


title: HCEC_Basal Growth_Rep1

source_name: Human Coronary Endothelial Cells (HCECs) Basal Growth

value: Heart Transplanation of a 7 year old girl


title: Mouse 597 jejunum


title: Mouse 602 jejunum


title: genomic_DNA_Breast_TDLU_AJP10_0850_15

description: Terminal ductal-lobular unit (TDLU)

value: breast


title: HMEC_HighMyc_1

description:
Sample name: 127575
EA10128_127575_HGU133_PLUS_2_TAM1.CEL
rep1 Myc


title: Mouse 596 jejunum

value: GF


title: Replicate 4 3151T4 LM

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Following fragmentation, 4 ug of cDNA was hybridized for 16 hr at 45C on Mouse 430A_2 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix 3000 7G scanner.

data_processing: R version 2.11.0 (x86_64-pc-linux-gnu), affyPLM_1.24.0, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.0, Biobase_2.8.0

source_name: mSCLC cell line derived from tumor 3151T4 stably expressing Mycl1

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using Nugen Ovation RNA amplification system V2 according to the manufacturers instructions.

growth_protocol: To dissociate tumors for cell lines, minced tumors were digested in HBSS (without calcium and magnesium), 1 mg/mL Collagenase IV (Worthington Biochemicals), and 0.025% trypsin-EDTA (Gibco) at 37C for 30 minutes. Following dissociation, samples were quenched in PBS with 10% FBS, incubated in 25 µg/mL DNase I (Sigma), centrifuged, filtered, and plated in standard tissue culture media (DME, 10% FBS, 1% L-glutamine and 50 units/mL Penicillin, 50 µg/mL Streptomycin).

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

treatment_protocol: Nfib and L-myc were stably expressed in mouse cell lines using MSCV-Nfib-PGK-Neo and MSCV-L-myc-PGK-Puro, and selected with G418 (Invitrogen) or Puromycin (Sigma), respectively. The mouse Nfib cDNA was FLAG tagged, and a Kozak sequence was added before the ATG in both the L-myc and Nfib expression vectors.

tag: transfection

value: MSCV-L-myc-PGK-Puro


title: Mouse 594 jejunum


title: Mouse 595 jejunum


title: Replicate 4 3151T4 LM, N45

source_name: mSCLC cell line derived from tumor 3151T4 stably expressing Nfib and Mycl1

value: MSCV-Nfib-PGK-Neo,MSCV-L-myc-PGK-Puro


title: Mouse 593 jejunum


title: Replicate 4 3151T4 N45

source_name: mSCLC cell line derived from tumor 3151T4 stably expressing Nfib

value: MSCV-Nfib-PGK-Neo


title: genomic_DNA_Breast_TDLU_AJP10_0850_13

description: Terminal ductal-lobular unit (TDLU)


title: HPMVEC_Basal Growth_Rep1_1%O2

source_name: Human Pulmonary Microvascular Endothelial Cells (HPMVECs) Basal Growth

treatment_protocol: Grown on a 2% gelatin matrix with ECM media and 5% FBS.  Grown in a hypoxic chamber at 1% O2 for 48 hours prior to harvesting.

value: ScienCell Research Laboratories


title: HMEC_Control_1

description:
Sample name: 127574
EA10128_127574_HGU133_PLUS_2_01.CEL
rep1 Control

value: Control


title: HUVEC_Basal Growth_Rep1

source_name: Human Umbilical Vein Endothelial Cells (HUVEC) Basal Growth


title: genomic_DNA_Breast_MET_AJP10_0850_9

description: Metastasis

source_name: Breast_Metastasis, ER+


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_8

description: Primary


title: HPMVEC_Basal Growth_Rep2_RA

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent G4450AA) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human Pulmonary Microvascular Endothelial Cell (HPMVEC) Basal Growth


title: HBMVEC_Basal Growth_Rep2

source_name: Human Brain Microvascular Endothelial Cells (HBMVECs) Basal Growth


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_10

description: Primary

source_name: Breast_Primary, ER+


title: HPAEC_Basal Growth_Rep1

source_name: Human Pulmonary Artery Endothelial Cells (HPAECs) Basal Growth


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_11

description: Primary


title: Mouse 591 jejunum

source_name: Healthy male, autoclaved chow diet

value: CONV-R

value: WT


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_6

description: Primary

value: ER+


title: HAEC_Basal Growth_Rep1

value: Human Aortic Endothelial Cell (HAEC) Basal Growth

value: Heart Transplantation from 7 year old girl


title: genomic_DNA_Breast_MET_AJP10_0850_7

description: Metastasis


title: HUVEC_Basal Growth_Rep2

source_name: Human Umbilical Vein Endothelial Cell (HUVEC) Basal Growth


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_5

description: Primary


title: Replicate 3 3151T4 N45


title: Mouse 589 jejunum

value: jejunum


title: Replicate 3 3151T4 LM, N45


title: Mouse 587 jejunum


title: Replicate 4 3151T4 control

source_name: mSCLC cell line derived from tumor 3151T4


title: Mouse 590 jejunum


title: Replicate 3 3151T4 LM


title: HCEC_Basal Growth_Rep2

source_name: Human Coronary Endothelial Cell (HCEC) Basal Growth

value: Heart Transplant of a 7 year old girl


title: Mouse 588 jejunum


title: HDMVEC_Basal Growth_Rep2

source_name: Human Dermal (neonatal) Microvascular Endothelial Cells Basal Growth

value: Cascade Biologics


title: Mouse 586 jejunum


title: genomic_DNA_Breast_MET_AJP10_0850_4

description: Metastasis


title: Replicate 3 3151T4 control


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_3

description: Primary


title: Replicate 2 3583T3 LM

source_name: mSCLC cell line derived from tumor 3583T3 stably expressing Mycl1


title: Replicate 2 3583T3 LM, N45

source_name: mSCLC cell line derived from tumor 3583T3 stably expressing Nfib and Mycl1


title: genomic_DNA_Breast_MET_AJP10_0850_2

description: Metastasis


title: Mouse 585 jejunum


title: HPMVEC_Basal Growth_Rep2

value: Human Pulmonary Microvascular Endothelial Cells (HPMVECs) Basal Growth

value: Purchased from ScienCell Research Laboratories


title: Mouse 584 jejunum


title: HBMVEC_Basal Growth_Rep1

value: Human Brain Microvascular Endothelial Cells (HBMVECs) Basal Growth


title: HPAEC_Basal Growth_Rep2

source_name: Human Pulmonary Artery Cells (HPAECs) Basal Growth


title: genomic_DNA_Breast_PRIMARY_AJP10_0850_1

description: Primary

value: breast


title: Mouse 583 jejunum


title: HPMVEC_Basal Growth_Rep1_4%O2

growth_protocol: Grown on a 2% gelatin matrix with ECM media and 5% FBS.  Grown to 75% confluence, media changed and RNA harvested the following day at ~95% confluence

treatment_protocol: Grown on a 2% gelatin matrix with ECM media and 5% FBS.  Grown in a hypoxia chamber maintaining O2 levels at 4% for 48 hours prior to processing.


title: Replicate 1 3583T3 LM, N45


title: Replicate 1 3583T3 LM

value: MSCV-L-myc-PGK-Puro


title: Mouse 602 ileum

value: ileum

value: GF


title: Replicate 2 3583T3 control

source_name: mSCLC cell line derived from tumor 3583T3


title: Replicate 2 3583T3 N45

source_name: mSCLC cell line derived from tumor 3583T3 stably expressing Nfib

value: MSCV-Nfib-PGK-Neo


title: Mouse 599 ileum


title: Replicate 1 3583T3 N45


title: Mouse 598 ileum


title: BMDC control

city: Shanghai

first: Yuan

last: Zhang

address: Yueyang St. 320#

country: China

institute: Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

hyb_protocol: Following fragmentation, 12.5ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse 430_2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.Eukaryotic Target Hybridization,Lot no.900720, is used for the experiment.

scan_protocol: the chips were scanned withthe affymetrix genechip 7G plus, and GCOS v1.0 is used for the image processing.

data_processing: genespring 10.0, is used for automatic normalizing the chip data and analysis the fold change.

source_name: BMDC cells not infected with Sendai Virus

label_protocol: start with 3μg total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, One-Cycle Eukaryotic Target Labeling Assay(Lot no. 900493) is used in the experiment.

value: BMDC


title: 7H_seedling_rep3

city: Yokohama

first: Jianwei

last: Tang

address: 641-12 Maioka-cho, Totsuka-ku

department: Kihara Institute for Biological Research

institute: Yokohama City University

description: Hordeum vulgare cv. Betzes chromosome 7 addition line of Triticum aestivum cv. Chinese Spring, replicate 3

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is XDR Hi 100% and XDR Li 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent Agilent Technologies) using default parameters(protocol GE1-v5_95) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: Barley chromosome addition line of common wheat

label_protocol: A Cy3 labeled cRNA probe were prepared using a Low RNA Input Linear Amp Kit (Agilent Technologies), and microarray hybridization was performed following the recommended protocol.

growth_protocol: Seeds were germinated and grown on soil at 22 ºC under 16 hr light and 8 hr dark conditions for 2 weeks.

extract_protocol: Total RNA was extracted using an RNeasy Plant Mini kit (Qiagen). Total RNA quality was checked with an Agilent 2100 Bioanalyzer.

tag: line

value: Leaf


title: CS_seedling_rep3

description: Triticum aestivum cv. Chinese Spring, replicate 3

source_name: Common wheat

value: Triticum aestivum cv. Chinese Spring


title: Mouse 601 ileum

value: WT


title: BMDC SV

source_name: BMDC cells infected with Sendai Virus


title: Mouse 600 ileum


title: Ex Vivo Cellulate 2 days 2.5 uM BIO 7 days neurogenic media

city: Gwangju

first: Darren

middle: Reece

last: Williams

address: 1 Oryong-dong

department: School of Life Sciences

country: South Korea

institute: Gwangju Institute of Science and Technology

description: Gene expression of cellulate after 2days 2.5 uM BIO treatmnet and 7days neurogenic media incubation.

hyb_protocol: After labeled aRNAs were placed on Agilent SurePrint G3 Human GE 8x60K array(Agilent technologies, CA) and covered by a Gasket 8-plex slide (Agilent technologies, CA). The slides were hybridized for 17hr at 65 ℃ oven. The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The arrays were analyzed using an Agilent scanner with associated software. Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA) Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm.

data_processing: The data were processed based on quantile normalization method using the GeneSpring GX 11.5.1(Agilent technologies, CA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 11.5.1 (Agilent technologies, CA). Fold change filters included the requirement that the genes be present in at least 200% of controls for up-regulated genes and lower than 50% of controls for down-regulated genes.

label_protocol: Each total RNA sample (200ng) was labeled and amplified using Low Input Quick Amp labeling kit (Agilent technologies, CA). The Cy3-labeled aRNAs were resuspended in 50㎕ of hybridization solution (Agilent technologies, CA).

growth_protocol: 1% antibiotics (penicillin and streptomycin) and 2% horse serum in DMEM is used for myotube formation and drug treatment.

extract_protocol: RNA was prepared using the triazole solution. Extraction is followed isopropanol precipitation protocol:     1. wash with cold PBS.    2. Treat 1 mL trizaole/10 cm culture dish and stand 3min in room temperature.    3. Transfer reagent into a microtube.    4. Add chloroform (1/5 triazole solution), shake several times, and stand 15 min in room temperature.    5. centrifuge 12000 g for 10 min at 4℃     6. Take transparent supernatent into a new microtube, add same volume of isopropanol and stand 5 min in room temperature.    7. Centrifuge 12000 g for 10 min at 4℃.     8. Remove supernatant and dry the RNA pellet.     8. Dissolve pellet with distilled water.

treatment_protocol: In BIO treated cellulate; 30 uM myoseverine, 10 uM AraC and 10 uM BIO were treated in DMEM media containing 1% antibiotics (penicillin and streptomycin), 2% horse serum. In BIO+Neu treated cellulate; Cellulate was seeded in laminin-coated cultures dishes at a density of dishes at a density of 1.5x106 cells/9.6 cm². After small molecule treatment, the cells were incubated with 250 nM reversine for 48 h, and neural induction media (DMEM/F12 supplemented with N2 (Invitrogen)) and 1.5  uM all-trans retinoic acid for 7 days.


title: genomic_DNA_Breast_TDLU_AJP10_0850_12

description: Terminal ductal-lobular unit (TDLU)

source_name: Breast_Terminal ductal-lobular unit (TDLU)

extract_protocol: Genomic DNA was extracted using standard techniques.

value: TDLU


title: Replicate 1 3583T3 control


title: retina TAA day 30 bio rep3

city: Davis

first: Zeljka

last: Smit-McBride

state: CA

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

description:
Gene expression data at day 30 from the eyes intravitreally injected with TAA at day 0
TAA-24 Ret

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring GX 11 using RMA algorhitm as analysis and normalization method.

source_name: retina TAA treatment day 30

label_protocol: Biotinylated cRNA were prepared according to the two-cycle Affymetrix protocol from 0.100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were 2 months old, kept at normal 12/12 light/dark conditions, feed ad libitum

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

treatment_protocol: Animals were sacrificed within CO2 chamber, eyes were enucleated, disected, retinal tissue was removed and quicky immersed into 300ul RNALater. Samples were stored in RNALater at -20C till the total RNA isolation step.

tag: gender

value: males

tag: organ

value: eye

value: retina


title: T. reesei sporulation 6 h

city: Vienna

first: Christian

middle: P.

last: Kubicek

address: Getreidemarkt 9

country: Austria

institute: TU Vienna

description: from T. reesei QM 9414

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

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Trichoderma reesei

source_name: Trichoderma reesei QM 9414

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

growth_protocol: T. reesei QM9414 (ATCC 26921), an early cellulase producing mutant was used throughout this work and kept on potato dextrose agar. To induce conidiation in T. reesei, the fungus was grown on malt extract (MEX) agar plates (11 cm diameter) on a layer of cellophane to facilitate removal of mycelia. The formation of conidia was followed microscopically and by measuring a marker enzyme, the D-mannitol dehydrogenase LXR1. Samples of at least two biological replicas were taken at appropriate time points (see results).

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Sporulating mycelia were scraped off the cellophane, washed with distilled cold water, frozen and ground under liquid nitrogen.

tag: phenotype

value: low cellulase producing mutant

tag: time

value: 6 h


title: T. reesei sporulation 9 h

description: from T. reesei QM 9414

value: 9 h


title: Mouse 596 ileum

source_name: Healthy male, autoclaved chow diet

tag: tissue


title: 5H_seedling_rep3

description: Hordeum vulgare cv. Betzes chromosome 5 addition line of Triticum aestivum cv. Chinese Spring, replicate 3


title: retina TAA day 30 bio rep2

description:
Gene expression data at day 30 from the eyes intravitreally injected with TAA at day 0
TAA-23 Ret


title: Mouse 597 ileum

description: RMA expression value derived from Expression Console software; gene level analysis


title: Mouse 594 ileum


title: Mouse 595 ileum


title: retina TAA day 30 bio rep1

description:
Gene expression data at day 30 from the eyes intravitreally injected with TAA at day 0
TAA-21 Ret


title: retina DEX day 30 bio rep3

description:
Gene expression data at day 30 from the eyes intravitreally injected with DEX at day 0
Dex-20 Ret

source_name: retina DEX treatment day 30


title: Ex Vivo C2C12 myoblast

description: Gene expression of C2C12 mouse myoblast cell line

source_name: C2C12 mouse myoblast cell line

value: untreated


title: 4H_seedling_rep3

description: Hordeum vulgare cv. Betzes chromosome 4 addition line of Triticum aestivum cv. Chinese Spring, replicate 3


title: 6H_seedling_rep3

description: Hordeum vulgare cv. Betzes chromosome 6 addition line of Triticum aestivum cv. Chinese Spring, replicate 3


title: 3H_seedling_rep3

description: Hordeum vulgare cv. Betzes chromosome 3 addition line of Triticum aestivum cv. Chinese Spring, replicate 3


title: T. reesei mycelium

description: from T. reesei QM 9414

value: 0 h


title: T. reesei sporulation 3 h

description: from T. reesei QM 9414

value: 3 h


title: Mouse 593 ileum

value: ileum


title: retina DEX day 30 bio rep1

description:
Gene expression data at day 30 from the eyes intravitreally injected with DEX at day 0
Dex-17 Ret


title: retina BSS day 30 bio rep3

description:
Gene expression data at day 30 from the eyes intravitreally injected with BSS at day 0
Con-16 Ret

source_name: retina BSS control day 30


title: CS_seedling_rep2

description: Triticum aestivum cv. Chinese Spring, replicate 2


title: 2H_seedling_rep3

description: Hordeum vulgare cv. Betzes chromosome 2 addition line of Triticum aestivum cv. Chinese Spring, replicate 3


title: Ex Vivo Cellulate 2 days 2.5 uM BIO

description: Gene expression of cellulate after 2days 2.5 uM BIO treatment

source_name: Cellulate 2 days 2.5 uM BIO

value: 2 days 2.5 uM BIO


title: Mouse 590 ileum

value: CONV-R


title: retina BSS day 30 bio rep2

description:
Gene expression data at day 30 from the eyes intravitreally injected with BSS at day 0
Con-14 Ret


title: retina DEX day 30 bio rep2

description:
Gene expression data at day 30 from the eyes intravitreally injected with DEX at day 0
Dex-18 Ret