title: 13969655 - Col0 T4d 1leaf vs wat1 T4d 1leaf

hyb_protocol: wat1 T4d 1leaf Cy5 / Col0 T4d 1leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1 T4d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T4d 1leaf:26.6ug.

source_name: Col0 T4d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T4d 1leaf:16.4ug.


title: 13969639 - wat1 T6d 1leaf vs Col0 T6d 1leaf

status: Public on Aug 01 2010

type: RNA

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: identification of the role of the plant cell wall in the interactions between plants and pathogenic agents

hyb_protocol: Col0 T6d 1leaf Cy5 / wat1 T6d 1leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col0 T6d 1leaf

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

growth_protocol: leaf - day 16h/22°C night 8h/20°C relative humidity 70%

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6d 1leaf:19.4ug.

treatment_protocol: Name:Ralstonia infection 6d - abiotic stress - abiotic stress,ralstonia solanacearum gmi 1000 strain:time 6day .

tag: ecotype

tag: genotype/variation

value: wild-type

tag: age

tag: time point

tag: agent

value: Ralstonia solanacearum gmi 1000

source_name: wat1 T6d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6d 1leaf:23.4ug.

value: mutant (wat1-)


title: 13969643 - Col0 T1d 2leaf vs wat1 T1d 2leaf

hyb_protocol: wat1 T1d 2leaf Cy5 / Col0 T1d 2leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1 T1d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T1d 2leaf:28.2ug.

treatment_protocol: Name:Ralstonia infection 1d - abiotic stress - abiotic stress,ralstonia solanacearum gmi 1000 strain:time 1day .

source_name: Col0 T1d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T1d 2leaf:21.5ug.


title: 13969635 - wat1 T6d 1root vs Col0 T6d 1root

hyb_protocol: Col0 T6d 1root Cy5 / wat1 T6d 1root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T6d 1root

growth_protocol: root - day 16h/22°C night 8h/20°C relative humidity 70%

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6d 1root:26.6ug.

source_name: wat1 T6d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6d 1root:17.9ug.


title: 13969638 - Col0 T6d 2leaf vs wat1 T6d 2leaf

hyb_protocol: wat1 T6d 2leaf Cy5 / Col0 T6d 2leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1 T6d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6d 2leaf:15.6ug.

source_name: Col0 T6d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6d 2leaf:16.2ug.


title: 13969652 - wat1 T4d 2leaf vs Col0 T4d 2leaf

hyb_protocol: Col0 T4d 2leaf Cy5 / wat1 T4d 2leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T4d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T4d 2leaf:22.7ug.

treatment_protocol: Name:Ralstonia infection 4d - abiotic stress - abiotic stress,ralstonia solanacearum gmi 1000 strain:time 4day .

source_name: wat1 T4d 2leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T4d 2leaf:16.3ug.


title: 13969641 - Col0 T6d 1leaf vs wat1 T6d 1leaf

hyb_protocol: wat1 T6d 1leaf Cy5 / Col0 T6d 1leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969653 - Col0 T4d 2leaf vs wat1 T4d 2leaf

hyb_protocol: wat1 T4d 2leaf Cy5 / Col0 T4d 2leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cafeteria roenbergensis infected with CroV 48 h post infection

status: Public on Jul 18 2010

city: Plymouth

first: Michael

middle: James

last: Allen

address: Prospect Place

country: United Kingdom

institute: Plymouth Marine Laboratory

description: no additional information

hyb_protocol: Cy3-labeled cRNA was hybridised for 18 hours on the microarray slide at 60ºC in 3 x SSC buffer and 0.1% SDS (total volume 45 ul). Slides were washed for 5 mins in washbuffer 1 (1 x SSC, 0.1% SDs), 5 mins in washbuffer 2 (0.1 x SSC, 0.1% SDS) and then repeatedly submersed 12 times in washbuffer 3 (0.1 x SSC).

scan_protocol: Microarrays were scanned scanned on an Affymetrix 418 Array Scanner at at gain setting between 50 and 80, maximum laser power.

data_processing: Images were analysed with ImaGene software (BioDiscovery, UK). Spots were assessed by visual inspection. No normalisation or data processing was necessary.

organism:
Cafeteria roenbergensis
Cafeteria roenbergensis virus BV-PW1

source_name: Infected culture

label_protocol: mRNA was then reverse-transcribed, PCR-amplified, and cRNA generated and Cy3-labeled by in vitro transcription (Microarray Target Kits, Roche).

growth_protocol: Cultures of Cafeteria roenbergensis strain E4-10 were grown in F/2 enriched seawater medium at room temperature in the dark.

extract_protocol: Total RNA was extracted from uninfected and infected host cells using the RNAeasy Protect Midi Kit (Qiagen).

treatment_protocol: Lysis of cultures infected with CroV strain BV-PW1 occurred 4-7 d post infection.

tag: infection

value: CroV

tag: time


title: Cafeteria roenbergensis infected with CroV 72 h post infection

description: no additional information


title: Cafeteria roenbergensis infected with CroV 24 h post infection

description: no additional information


title: 13969634 - Col0 T6d 2root vs wat1 T6d 2root

hyb_protocol: wat1 T6d 2root Cy5 / Col0 T6d 2root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1 T6d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T6d 2root:17.2ug.

source_name: Col0 T6d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T6d 2root:22.7ug.


title: 13969637 - wat1 T6d 2leaf vs Col0 T6d 2leaf

hyb_protocol: Col0 T6d 2leaf Cy5 / wat1 T6d 2leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cafeteria roenbergensis infected with CroV 12 h post infection

description: no additional information


title: 13969654 - wat1 T4d 1leaf vs Col0 T4d 1leaf

hyb_protocol: Col0 T4d 1leaf Cy5 / wat1 T4d 1leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969636 - Col0 T6d 1root vs wat1 T6d 1root

hyb_protocol: wat1 T6d 1root Cy5 / Col0 T6d 1root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13969649 - Col0 T4d 2root vs wat1 T4d 2root

hyb_protocol: wat1 T4d 2root Cy5 / Col0 T4d 2root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1 T4d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T4d 2root:10.3ug.

source_name: Col0 T4d 2root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T4d 2root:13.1ug.


title: 13969651 - Col0 T4d 1root vs wat1 T4d 1root

hyb_protocol: wat1 T4d 1root Cy5 / Col0 T4d 1root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1 T4d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T4d 1root:11ug.

source_name: Col0 T4d 1root

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T4d 1root:22ug.


title: 13969644 - wat1 T1d 1leaf vs Col0 T1d 1leaf

hyb_protocol: Col0 T1d 1leaf Cy5 / wat1 T1d 1leaf Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 T1d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 T1d 1leaf:28.7ug.

source_name: wat1 T1d 1leaf

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1 T1d 1leaf:38.7ug.


title: Cafeteria roenbergensis infected with CroV 3 h post infection

description: no additional information

value: 3 h


title: 13969633 - wat1 T6d 2root vs Col0 T6d 2root

hyb_protocol: Col0 T6d 2root Cy5 / wat1 T6d 2root Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cafeteria roenbergensis infected with CroV 6 h post infection

description: no additional information

value: 6 h


title: Cafeteria roenbergensis infected with CroV 2 h post infection

description: no additional information

value: 2 h


title: Cafeteria roenbergensis infected with CroV 1 h post infection

description: no additional information

value: 1 h


title: Cafeteria roenbergensis infected with CroV 0 h post infection

description: no additional information

value: control

value: 0 h


title: liver at 4 month,treated,biological rep2

status: Public on Jul 01 2010

city: Beijing

first: qiuyue

last: liu

address: Yuanmingyuan, West Road 2, Beijing 100193, China.

department: Biochemistry and Molecular Biology

country: China

institute: China Agricultural University

description: Gene expression data from Chinese miniature hog liver treated with Clenbuterol.

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

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

data_processing: Raw data from the arrays were normalized at probe level using gcRMA algorithm. The normalization target was set to 500. The gcRMA data are attached to the Series record.

label: biotin

organism: Sus scrofa

source_name: pig liver at 4 month treated with Clenbuterol

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

growth_protocol: Chinese mininature pigs were housed in the Nutrition and Metabolism Laboratory at the China Agriculture University. They were firstly maintained at same conditions and fed the same diets until 8 weeks old (average body weight 18 kg).

extract_protocol: QIAGEN mini kit extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Pigs were firstly maintained at same conditions and fed the same diets until 8 weeks old (average body weight 18 kg). Then pigs were broken into 2 groups with each group having two full sib pigs with the same gender. For the following 8 weeks, test pigs were fed 25 mg/kg clenbuterol twice daily in their diets in front 4 weeks and 50 mg/kg clenbuterol for another 4 weeks. The vehicle control pigs were administered in the same manner except that no clenbuterol was added in their diets.

tag: Strain

value: Chinese mininature pig

tag: Gender

value: female

tag: Age

value: 4 months

tag: Tissue

value: liver


title: Bone marrow_diabetic_PMa08

city: Amsterdam

first: Anton

middle: J

last: Horrevoets

address: van der Boechorststraat 7

department: Molecular Cell Biology

country: Netherlands

institute: VU University Medical Center

description: Biological replicate 4 of 4.

hyb_protocol: Standard Illumina protocol at ServiceXS (Leiden, The Netherlands).

data_processing: Illumina Beadstudio data were Interarray Quantile normalized (Bioconductor).

label: Biotin

organism: Mus musculus

source_name: bone marrow endothelial cells, diabetic mouse

label_protocol: Illumina Total Prep (Ambion)

growth_protocol: Bone marrow cells were cultured for 10 days under endothelial cell growth conditions.

extract_protocol: RNAeasy Microkit (Qiagen)

tag: Cultured after isolation from diabetic mice.


title: triple knockout hepatocellular carcinoma - 4

city: Stanford

first: Julien

last: Sage

state: CA

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

country: USA

institute: Stanford University

description: Mouse HCCs tumors were dissected from TKO mice infected with Ad-Cre 4 months before via intrasplenic injection.

hyb_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix 430-2.0 arrays as recommended by the manufacturer.

scan_protocol: Gene Chip Scanner 3000.

data_processing: RMA normalization was performed using Command Console ver1.

label: streptavidin

source_name: triple Knock out (TKO) mouse

label_protocol: RNA was isolated with Trizol and twice amplified with a RiboAmp RNA amplification kit.

tag: genome/variation

tag: tissue

tag: disease status

value: hepatocellular carcinoma


title: normal liver -1

description: Normal, tumor-free adult mouse liver.

source_name: normal mouse

extract_protocol: RNA was isolated with Trizol and twice amplified with a RiboAmp RNA amplification kit.

value: wild type


title: Bone marrow_healthy_PMa04

description: Biological replicate 4 of 4.

scan_protocol: Standard Illumina protocol at ServiceXS (Leiden, The Netherlands).

source_name: bone marrow endothelial cells, healthy mouse

tag: Cultured after isolation from healthy mice.


title: triple knockout hepatocellular carcinoma - 5

source_name: triple knock out (TKO) mouse


title: normal liver - 4

description: Normal, tumor-free adult mouse liver.


title: normal liver - 2

description: Normal, tumor-free adult mouse liver.


title: liver at 4 month,control,biological rep1

description: Gene expression data from Chinese miniature hog liver treated without Clenbuterol.

source_name: pig liver at 4 month treated without Clenbuterol

tag: hog liver treated without Clenbuterol

value: male

value: 4 month


title: triple knockout hepatocellular carcinoma - 3


title: Bone marrow_healthy_PMa01

description: Biological replicate 1 of 4.


title: 13967986 - Control DMSO 1 vs Control quinolinate 1

description: Study of the impact of an inductible increase in the NAD concentration in arabidopsis

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

source_name: Control quinolinate 1

growth_protocol: leaf - 6 short day weeks and 1 long day week in greenhouse

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Control quinolinate 1:10ug.

treatment_protocol: Name:Quinolinate - abiotic stress - abiotic stress,quinolinate:quantity 10uM time 48hour . Obscurity

value: quinolinate

value: wild-type

source_name: Control DMSO 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Control DMSO 1:10ug.

treatment_protocol: Name:DMSO - compound based treatment - compound addition,dmso:time 3hour . 5ml of 3 days-old suspension cells were incubated with ABA or DGPP 18:1 for 3hours under the conditions of culture. DGPP was emulsified by sonication for 1min 4 times at 4degre Celsius in 1ml of culture medium then added to 4ml of suspension cells, for 3h. Cells were filtrated under vacuum, frozen in liquid nitrogen.

value: DMSO


title: Bone marrow_healthy_PMa02

description: Biological replicate 2 of 4.


title: Bone marrow_diabetic_PMa06

description: Biological replicate 2 of 4.


title: normal liver - 3

description: Normal, tumor-free adult mouse liver.


title: liver at 4 month,treated,biological rep1


title: Bone marrow_healthy_PMa03

description: Biological replicate 3 of 4.


title: Col-7_flower_33d_rep4

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128, Section 2, Academia Road, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

hyb_protocol: Standard hybridization protocol of Affymetrix expression array

scan_protocol: Standard scanning protocol of Affymetrix expression array

source_name: Col-7, 33-day-old, excised flower

label_protocol: Standard labeling protocol of Affymetrix expression array

growth_protocol: Soil-grown plants

extract_protocol: QIAGEN RNease Plant Kit

tag: genotype

tag: developmental stage

value: 33 days old

value: flower


title: 13967985 - Mutant quinolinate 1 vs Control quinolinate 1

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

tag: genotype/variation

tag: age

source_name: Mutant quinolinate 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Mutant quinolinate 1:10ug.

value: mutant (qprtase overexpressor)


title: liver at 4 month,control,biological rep2


title: 13967984 - Control quinolinate 1 vs Mutant quinolinate 1

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

tag: agent


title: Bone marrow_diabetic_PMa07

description: Biological replicate 3 of 4.


title: 13967987 - Control quinolinate 1 vs Control DMSO 1

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


title: triple knockout hepatocellular carcinoma - 2

label_protocol: As recommended by the manufacturer (Affymetrix, Santa Clara).


title: 13912844 - Control DMSO 2 vs Control quinolinate 2

hyb_protocol: Control quinolinate 2 Cy5 / Control DMSO 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Control quinolinate 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Control quinolinate 2:10ug.

source_name: Control DMSO 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Control DMSO 2:10ug.


title: 13912845 - Control quinolinate 2 vs Control DMSO 2

hyb_protocol: Control DMSO 2 Cy5 / Control quinolinate 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: triple knockout hepatocellular carcinoma - 1


title: Bone marrow_diabetic_PMa05

description: Biological replicate 1 of 4.


title: 13912847 - Mutant quinolinate 1 vs Mutant DMSO 1

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

source_name: Mutant DMSO 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Mutant DMSO 1:10ug.


title: 13912846 - Mutant DMSO 1 vs Mutant quinolinate 1

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


title: 13912843 - Mutant quinolinate 2 vs Control quinolinate 2

hyb_protocol: Control quinolinate 2 Cy5 / Mutant quinolinate 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Mutant quinolinate 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Mutant quinolinate 2:10ug.


title: 13968010 - Col0 root 3 vs wat1.1 root 3

hyb_protocol: wat1.1 root 3 Cy5 / Col0 root 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1.1 root 3

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1.1 root 3:12.6ug.

treatment_protocol: no treatment

value: mutant (wat1-)

tag: ecotype

source_name: Col0 root 3

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 root 3:12.55ug.


title: 13968009 - wat1.1 leaf 3 vs Col0 leaf 3

hyb_protocol: Col0 leaf 3 Cy5 / wat1.1 leaf 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 leaf 3

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 leaf 3:34.1ug.

source_name: wat1.1 leaf 3

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1.1 leaf 3:29.55ug.


title: 13968521 - wat1.1 root 2 vs Col0 root 2

hyb_protocol: Col0 root 2 Cy5 / wat1.1 root 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 root 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 root 2:14ug.

source_name: wat1.1 root 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1.1 root 2:11.65ug.


title: 13912839 - Mutant DMSO 2 vs Mutant quinolinate 2

hyb_protocol: Mutant quinolinate 2 Cy5 / Mutant DMSO 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Mutant DMSO 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Mutant DMSO 2:10ug.


title: 13912842 - Control quinolinate 2 vs Mutant quinolinate 2

hyb_protocol: Mutant quinolinate 2 Cy5 / Control quinolinate 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13912841 - Mutant quinolinate 2 vs Mutant DMSO 2

hyb_protocol: Mutant DMSO 2 Cy5 / Mutant quinolinate 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: DMSO 2


title: 13968008 - Col0 root 2 vs wat1.1 root 2

hyb_protocol: wat1.1 root 2 Cy5 / Col0 root 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13968006 - wat1.1 leaf 1 vs Col0 leaf 1

hyb_protocol: Col0 leaf 1 Cy5 / wat1.1 leaf 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 leaf 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 leaf 1:27.5ug.

source_name: wat1.1 leaf 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1.1 leaf 1:41.45ug.


title: 13968003 - Col0 leaf 2 vs wat1.1 leaf 2

hyb_protocol: wat1.1 leaf 2 Cy5 / Col0 leaf 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1.1 leaf 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1.1 leaf 2:19.6ug.

source_name: Col0 leaf 2

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 leaf 2:9.1ug.


title: 13968007 - wat1.1 leaf 2 vs Col0 leaf 2

hyb_protocol: Col0 leaf 2 Cy5 / wat1.1 leaf 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13968522 - wat1.1 root 3 vs Col0 root 3

hyb_protocol: Col0 root 3 Cy5 / wat1.1 root 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MS patient 14 relapse

status: Public on Jun 30 2010

city: Houston

first: John

middle: William

last: Lindsey

state: TX

address: 6431 Fannin, Suite 7.044

department: Neurology

institute: University of Texas Health Science Center at Houston

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: background subtracted, normalized to quantiles in BeadStudio, paired comparison of normalized data in BRB

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: RNA expression was profiled on Illumina (San Diego, CA) beadchip humanRef-8 v3.0 microarrays at the UTHSC-H Quantitative Genomics Core Laboratory.  Two hundred ng of total RNA were amplified and purified using Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX) following kit instructions.  Amplified cRNA was subsequently purified and concentration was measured by NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE). An aliquot of 750 ng was loaded onto the microarray, hybridized at 58°C in an Illumina Hybridization Oven for 17 hours, washed and incubated with streptavidin-Cy3 to detect the biotin-labeled cRNA.  Arrays were dried and scanned with the Illumina BeadArray Reader. Each chip contains 8 separate microarrays, and the samples were run on 5 separate chips in 4 different experiments with the stable and relapse specimen for each patient on the same chip.  Data were extracted, background subtracted, and normalized by quantiles using Illumina BeadStudio 3.2, and then exported to a worksheet.  These files for all experiments were combined in a single worksheet, and data for non-expressed transcripts were removed.  The edited worksheet was then analyzed using BRB-ArrayTools 3.8.0 and Ingenuity (version 7).

extract_protocol: Trizol followed by Qiagen Rneasy columns

treatment_protocol: heparinized blood samples, peripheral blood mononuclear cells isolated with Ficoll density gradients, cells lysed in Trizol and stored at -80

tag: clinical state

value: relapse

tag: gender

tag: treatment

value: interferon

tag: ethnicity

value: african-american

tag: disease

value: multiple sclerosis

tag: experiment number

tag: cell type

value: peripheral blood mononuclear cells


title: 13968005 - Col0 leaf 3 vs wat1.1 leaf 3

hyb_protocol: wat1.1 leaf 3 Cy5 / Col0 leaf 3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13968004 - Col0 root 1 vs wat1.1 root 1

hyb_protocol: wat1.1 root 1 Cy5 / Col0 root 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: wat1.1 root 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), wat1.1 root 1:6.25ug.

source_name: Col0 root 1

extract_protocol: According to Qiagen RNeasy Mini protocol (June 2001), Col0 root 1:9.95ug.


title: MS patient 11 stable

value: stable

value: indian


title: MS patient 13 stable

value: female

value: glatiramer

value: white


title: MS patient 12 stable


title: MS patient 14 stable

value: male


title: MS patient 12 relapse


title: 13968520 - wat1.1 root 1 vs Col0 root 1

hyb_protocol: Col0 root 1 Cy5 / wat1.1 root 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: wild-type


title: MS patient 9 stable


title: MS patient 9 relapse


title: MS patient 10 stable


title: MS patient 11 relapse


title: 13968002 - Col0 leaf 1 vs wat1.1 leaf 1

hyb_protocol: wat1.1 leaf 1 Cy5 / Col0 leaf 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MS patient 8 relapse


title: MS patient 8 stable


title: MS patient 7 relapse


title: MS patient 5 relapse


title: MS patient 7 stable


title: MS patient 4 stable


title: MS patient 6 stable


title: MS patient 3 stable


title: MS patient 2 stable


title: SCR5.5-NRSF5.5

status: Public on Jun 06 2010

city: PARIS

first: Gilles

last: Maussion

address: 16 rue Henri Huchard

institute: INSERM U675

description: Murine neuroblastoma cell line N18 transfected with Nrsf siRNA or with a Scrambled siRNA (control condition).

hyb_protocol: After checking the labeling efficiency and the product integrity, 750 ng Cy3- and 750 ng Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven, using an Agilent in situ hybridization kit. The slides were washed and then any traces of water were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Slides were scanned using a GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) at 5-μm resolution. The photo multiplier tube (PMT) levels of the two channels at 635 nm (for Cy5) and 532 nm (for Cy3) were balanced to limit the number of saturated pixels (less than 0.005%) for generating gray scale 16-bit TIFF image files.

data_processing:
The resulting images were processed using the GenePix Pro (v6.0.1.26) image analysis software. This included defining the spots, measuring the intensities, flagging the spots having inadequate quality control parameters and evaluating local background
The pre-processing of the data and its quality assessment were done using the MANGO (MicroArray Normalization tool of GODMAP) tools suit (version 1.0, CNRS BioInfome Team [http://bioinfome.cgm.cnrs-gif.fr/]), an R script that allows integrated analysis of two-color microarrays. The background level was calculated using morphological operators (a short closing followed by a large opening) and subtracted. Raw data were normalized using the print-tip lowess method, i.e. local regression normalization within an artificial print-tip block.

label: Cy5-CTP Agilent

source_name: Murine neuroblastoma cell line N18 transfected with a Scrambled siRNA (control condition)

label_protocol: Briefly, 1-μg aliquots of total RNA were labeled using the Agilent Linear Amplification/Labeling kit (Agilent Technologies).

extract_protocol: Trizol (InVitrogen)

tag: Cells transfected with a Scrambled siRNA (control condition)

label: Cy3-CTP Agilent

tag: Cells transfected with Nrsf siRNA


title: SCR6.6-NRSF6.6

source_name: Murine neuroblastoma cell line N18 transfected with Nrsf siRNA


title: MS patient 10 relapse


title: MS patient 6 relapse


title: MS patient 1 relapse


title: MS patient 3 relapse


title: MS patient 1 stable


title: MS patient 5 stable


title: 13833022 - L H2O 24h 2 vs L DFO 24h 2

status: Public on Jun 01 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

description: What are the effects of the siderophore deferoxamine on Arabidopsis leaves and roots?

hyb_protocol: L DFO 24h 2 Cy5 / L H2O 24h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: L DFO 24h

growth_protocol: leaf - Media=hydropony (Segond et al. 2009 10.1111/j.1365-313X.2008.03775.x )	 hygrometry=70%	 Temperature=21°C (day)/19°C (night)	 Light=8h

extract_protocol: L DFO 24h 2:10ug.

treatment_protocol: Name:DFO 24h - compound based treatment - compound addition,dfo:quantity 1mM time 24hour . Leaves or roots of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves or roots were harvested 7 and 24 h.p.i.

tag: tissue

value: leaves

value: Columbia

tag: harvest date

source_name: L H2O 24h

treatment_protocol: Name:H2O 24h - control buffer - control,h2o:time 24hour . Leaves or roots of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves or roots were harvested 7 and 24 h.p.i.


title: SCR4.4-NRSF4.4


title: 13833023 - L DFO 24h 2 vs L H2O 24h 2

hyb_protocol: L H2O 24h 2 Cy5 / L DFO 24h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: NRSF3.3-SCR3.3


title: 13833019 - L DFO 7h 2 vs L H2O 7h 2

hyb_protocol: L H2O 7h 2 Cy5 / L DFO 7h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: L H2O 7h

treatment_protocol: Name:H2O 7h - control buffer - control,h2o:time 7hour . Leaves or roots of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves or roots were harvested 7 and 24 h.p.i.

source_name: L DFO 7h

extract_protocol: L DFO 7h 2:10ug.

treatment_protocol: Name:DFO 7h - compound based treatment - compound addition,dfo:quantity 1mM time 7hour . Leaves or roots of six week old hydroponically grown A. thaliana Col0 plants were infiltrated with 1mM deferoxamine or sterile distilled water. Leaves or roots were harvested 7 and 24 h.p.i.


title: NRSF1.1-SCR1.1


title: MS patient 13 relapse


title: MS patient 2 relapse


title: 13833018 - L H2O 7h 2 vs L DFO 7h 2

hyb_protocol: L DFO 7h 2 Cy5 / L H2O 7h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13833020 - L H2O 24h 1 vs L DFO 24h 1

hyb_protocol: L DFO 24h 1 Cy5 / L H2O 24h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: L DFO 24h 1:10ug.


title: NRSF2.2-SCR2.2


title: 13833017 - L DFO 7h 1 vs L H2O 7h 1

hyb_protocol: L H2O 7h 1 Cy5 / L DFO 7h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: L DFO 7h 1:10ug.


title: MS patient 4 relapse


title: 13832794 - R DFO 24h 2 vs R H2O 24h 2

hyb_protocol: R H2O 24h 2 Cy5 / R DFO 24h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: R H2O 24h

growth_protocol: root - Media=hydropony (Segond et al. 2009 10.1111/j.1365-313X.2008.03775.x )	 hygrometry=70%	 Temperature=21°C (day)/19°C (night)	 Light=8h

value: roots

source_name: R DFO 24h

extract_protocol: R DFO 24h 2:10ug.


title: 13833016 - L H2O 7h 1 vs L DFO 7h 1

hyb_protocol: L DFO 7h 1 Cy5 / L H2O 7h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832793 - R H2O 24h 2 vs R DFO 24h 2

hyb_protocol: R DFO 24h 2 Cy5 / R H2O 24h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832788 - R H2O 24h 1 vs R DFO 24h 1

hyb_protocol: R DFO 24h 1 Cy5 / R H2O 24h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: R DFO 24h 1:10ug.


title: 13832790 - R H2O 7h 2 vs R DFO 7h 2

hyb_protocol: R DFO 7h 2 Cy5 / R H2O 7h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: R DFO 7h

extract_protocol: R DFO 7h 2:10ug.

source_name: R H2O 7h


title: 13832792 - R DFO 7h 2 vs R H2O 7h 2

hyb_protocol: R H2O 7h 2 Cy5 / R DFO 7h 2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13833021 - L DFO 24h 1 vs L H2O 24h 1

hyb_protocol: L H2O 24h 1 Cy5 / L DFO 24h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832789 - R DFO 24h 1 vs R H2O 24h 1

hyb_protocol: R H2O 24h 1 Cy5 / R DFO 24h 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: AGA2 lung_rep6

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.1: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: mouse ID: L3

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

tag: female, age

value: 11 days

source_name: Wt RNA pool lung

tag: RNA pool; female, age


title: AGA2 lung_rep9

source_name: mouse ID: L5

value: 10 days


title: BYU_Adams_H_bacteriophora_OHB4

city: Provo

first: Chin-Yo

last: Lin

state: UT

address: 753 WIDB

department: Microbiology and Molecular Biology

institute: Brigham Young University

description:
Genome not available
This sample is the second of four biological replicates of the OHB parental strain of H. bacteriophora.

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: Heterorhabditis bacteriophora

source_name: Heterorhabditis bacteriophora OHB

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

growth_protocol:
An isolate of Heterorhabditis bacteriophora was created by sub-culturing different experimental lines of nematode-bacterium complex over 20 passages in Galleria mellonella . The original parental strain (OHB) was maintained in ringer's solution without sub-culturing while the inbred line (L5M) was continuously cultured in G. mellonella.
Both OHB and L5M were cultured in G. mellonella larvae and emerging infective juveniles (IJs) were collected using white traps. The IJs were stored in ringer's solution at 16ºC until used for experiments.

extract_protocol: Total RNA was isolated from four biological replicates of IJs of each strain. The IJs (~8-10,000) were transferred to 10 volumes of Trizol Reagent (Molecular Research Center Inc., Cincinnati, OH) and RNA extracted according to manufacturer's protocol.

tag: genotype

value: Parental strain OHB

tag: phenotype

value: normal


title: BYU_Adams_H_bacteriophora_L5M6

description:
Genome not available
This sample is the fourth of four biological replicates of the L5M in-bred strain of H. bacteriophora.

source_name: Heterorhabditis bacteriophora LM5

value: In-bred laboratory strain L5M

value: entamopathogenic traits deteriorated


title: AGA2 lung_rep5


title: BYU_Adams_H_bacteriophora_OHB6

description:
Genome not available
This sample is the fourth of four biological replicates of the OHB parental strain of H. bacteriophora.


title: BYU_Adams_H_bacteriophora_L5M2

description:
Genome not available
This sample is the first of four biological replicates of the L5M in-bred strain of H. bacteriophora.


title: AGA2 lung_rep8

source_name: mouse ID: L4


title: BYU_Adams_H_bacteriophora_OHB3

description:
Genome not available
This sample is the first of four biological replicates of the OHB parental strain of H. bacteriophora.


title: AGA2 lung_rep10


title: AGA2 lung_rep3

source_name: mouse ID: L2


title: BYU_Adams_H_bacteriophora_L5M5

description:
Genome not available
This sample is the third of four biological replicates of the L5M in-bred strain of H. bacteriophora.