title: 13690386 - Col flag15 set1 vs Col flag22 set1

hyb_protocol: Col flag22 set1 Cy5 / Col flag15 set1 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: 13690377 - dcl2-dcl3-dcl4 flag22 set2 vs dcl2-dcl3-dcl4 flag15 set2

status: Public on Jun 02 2008

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Time course : What are the genes (incuding microRNA precursors) that are differentially regulated upon flg22 treatment? miRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of microRNA mutants? siRNA : What are the genes (including miRNA precursors) that are differentially regulated in a set of siRNA mutants?

hyb_protocol: dcl2-dcl3-dcl4 flag15 set2 Cy5 / dcl2-dcl3-dcl4 flag22 set2 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 6.0, Cy3:pmt voltage 532nm,500V,laser power 30%, Cy5:635nm,pmt voltage 500V,laser power 30%

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: dcl2-dcl3-dcl4 flag15 set2

label_protocol: labeling

growth_protocol: plantlet - Media : 1x MS medium (Duchefa), 1% sucrose and 1% agar. 12-day old seedlings were then transferred to liquid MS medium for 2 days before flg22 treatment (two seedlings per 500 ul of medium in wells of 24-well-plates). Temperature : 22°C Light : continuous light conditions of 60 uE m-2 sec-1 (Biolux lamps)

extract_protocol: dcl2-dcl3-dcl4 flag15 set2:4.64ug.

treatment_protocol: Name:flag 15 dcl234 - biotic stress - compound addition,flg15:time 30min . 14-day old were transferred into MS liquid medium and then supplied with flg15 peptide to a final concentration 100nM.; Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.

tag: Arabidopsis thaliana (columbia)  mutant (dcl2-1 dcl3-1 dcl4-2) - age:14daydev.stage (Boyes et al. Plant Cell 2001):1-5 rosette leaf,10-15 rosette leaf

source_name: dcl2-dcl3-dcl4 flag22 set2

extract_protocol: dcl2-dcl3-dcl4 flag22 set2:5.2ug.

treatment_protocol: Name:flag 22 dcl234 - biotic stress - compound addition,flg22:time 30min . 14-day old were transferred into MS liquid medium and then supplied with flg22 peptide to a final concentration 100nM.; Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.


title: 13690373 - dcl2-dcl3-dcl4 ctrl set2 vs Col ctrl set2

hyb_protocol: Col ctrl set2 Cy5 / dcl2-dcl3-dcl4 ctrl set2 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: Col ctrl set2

extract_protocol: Col ctrl set2:7.3ug.

treatment_protocol: no treatment

tag: Arabidopsis thaliana (columbia)  - age:14daydev.stage (Boyes et al. Plant Cell 2001):1-5 rosette leaf,10-15 rosette leaf

source_name: dcl2-dcl3-dcl4 ctrl set2

extract_protocol: dcl2-dcl3-dcl4 ctrl set2:4.03ug.


title: 13365882 - rdr6-1 flg22 30min vs rdr6-1 flg15 30min

hyb_protocol: rdr6-1 flg15 30min Cy5 / rdr6-1 flg22 30min 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,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

source_name: rdr6-1 flg15 30min

growth_protocol: whole plant - Media: 1x MS medium (Duchefa), 1% sucrose and 1% agar. 12-day old seedlings were then transferred to liquid MS medium for 2 days (two seedlings per 500 ul of medium in wells of 24-well-plates) and then treated. Temperature: 22°C Light: continuous light conditions of 60 uE m-2 sec-1 (Biolux lamps).

extract_protocol: Pool of extract, rdr6-1 flg15 30min set1:0.5ug, rdr6-1 flg15 30min set2:0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (rdr6-1) - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: rdr6-1 flg22 30min

extract_protocol: Pool of extract, rdr6-1 flg22 30min set1:0.5ug, rdr6-1 flg22 30min set2:0.5ug.

treatment_protocol: Name:flg15 10(u)M - compound based treatment - compound addition,flg15:quantity 10000mM time 30min . Add 10uM flagellin in liquid MS medium and harvest samples at 30 minutes. Name: - compound based treatment - compound addition,flg22:quantity 10000mM time 30min . Add 10uM flagellin in liquid MS medium and harvest samples at 30 minutes.


title: 13275764 - dcl1-9 flg22 30min vs dcl1-9 flg15 30min

hyb_protocol: dcl1-9 flg15 30min Cy5 / dcl1-9 flg22 30min 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: dcl1-9 flg15 30min

extract_protocol: Pool of extract, dcl1-9 flg15 30min (1):0.5ug, dcl1-9 flg15 30min (2):0.5ug.

treatment_protocol: Name:flg15 30min - compound based treatment - biotic stress,flg15:quantity 10000mM time 30min . Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg15 peptide to a final concentration of 10 uM. Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.

tag: Arabidopsis thaliana (landsberg erecta)  mutant (dcl1-9) - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

source_name: dcl1-9 flg22 30min

extract_protocol: Pool of extract, dcl1-9 flg22 30min (1):0.5ug, dcl1-9 flg22 30min (2):0.5ug.

treatment_protocol: Name:flg22 30min - compound based treatment - biotic stress,flg22:quantity 10000mM time 30min . Protocol : 12-day old were transferred into MS liquid medium and then supplied with flg22 peptide to a final concentration of 10 uM. Plantlets were collected 30min after treatment, frozen in liquid nitrogen and stored at -80degre Celsius.


title: 13278972 - ler vs dcl1-9

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

growth_protocol: plantlet - Media : 1x MS medium (Duchefa), 1% sucrose and 1% agar. 12-day old seedlings were then transferred to liquid MS medium for 2 days (two seedlings per 500 ul of medium in wells of 24-well-plates) and then harvested Temperature : 22°C Light : continuous light conditions of 60 uE m-2 sec-1 (Biolux lamps)

extract_protocol: Pool of extract, hasty set 1:0.5ug, hasty set 2:0.5ug.

tag: Arabidopsis thaliana (landsberg erecta)  mutant (hasty) - age:14day

source_name: ler

extract_protocol: Pool of extract, ler set 1:0.5ug, ler set 2:0.5ug.

tag: Arabidopsis thaliana (landsberg erecta)  mutant (ler) - age:14day


title: 13366177 - rdr6-1 flg15 30min vs rdr6-1 flg22 30min

hyb_protocol: rdr6-1 flg22 30min Cy5 / rdr6-1 flg15 30min 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.

treatment_protocol: Name:flg15 10(u)M - compound based treatment - compound addition,flg15:quantity 10000mM time 30min . Add 10uM flagellin in liquid MS medium and harvest samples at 30 minutes.


title: 13690376 - dcl2-dcl3-dcl4 flag15 set2 vs dcl2-dcl3-dcl4 flag22 set2

hyb_protocol: dcl2-dcl3-dcl4 flag22 set2 Cy5 / dcl2-dcl3-dcl4 flag15 set2 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: 13281168 - dcl1-9 vs ler

hyb_protocol: ler Cy5 / dcl1-9 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: 13690362 - dcl2-dcl3-dcl4 flag22 set1 vs dcl2-dcl3-dcl4 flag15 set1

hyb_protocol: dcl2-dcl3-dcl4 flag15 set1 Cy5 / dcl2-dcl3-dcl4 flag22 set1 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: dcl2-dcl3-dcl4 flag15 set1

extract_protocol: dcl2-dcl3-dcl4 flag15 set1:4.08ug.

source_name: dcl2-dcl3-dcl4 flag22 set1

extract_protocol: dcl2-dcl3-dcl4 flag22 set1:5.74ug.


title: 13279338 - hasty vs ler

hyb_protocol: ler Cy5 / hasty 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: hasty


title: 13279333 - ler vs hasty

hyb_protocol: hasty Cy5 / ler 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: 13281178 - hen1-1 vs ler

hyb_protocol: ler Cy5 / hen1-1 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: Pool of extract, hen1-1 set 1:0.5ug, hen1-1 set 2:0.5ug.

tag: Arabidopsis thaliana (landsberg erecta)  mutant (hen1-1) - age:14day


title: 13281189 - rdr2-1 vs Col-0

hyb_protocol: Col-0 Cy5 / rdr2-1 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: Pool of extract, Col-0 set 1:0.5ug, Col-0 set 2:0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (Col-0) - age:14day

extract_protocol: Pool of extract, rdr2-1 ser 1:0.5ug, rdr2-1 ser 2:0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (rdr2-1) - age:14day


title: 13275770 - ler vs hen1-1

hyb_protocol: hen1-1 Cy5 / ler 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: 13690743 - Col ctrl set1 vs dcl2-dcl3-dcl4 ctrl set1

hyb_protocol: dcl2-dcl3-dcl4 ctrl set1 Cy5 / Col ctrl set1 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: dcl2-dcl3-dcl4 ctrl set1

extract_protocol: dcl2-dcl3-dcl4 ctrl set1:3.87ug.

source_name: Col ctrl set1

extract_protocol: Col ctrl set1:4.63ug.


title: 13279329 - Col-0 vs dcl4-1

hyb_protocol: dcl4-1 Cy5 / Col-0 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: Pool of extract, dcl4-1 (1):0.5ug, dcl4-1 (2):0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (dcl4-1) - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes

extract_protocol: Pool of extract, Col-0 (1):0.5ug, Col-0 (2):0.5ug.

tag: Arabidopsis thaliana (columbia)  - age:14daydev.stage (Boyes et al. Plant Cell 2001):boyes


title: 13281186 - dcl3-1 vs Col-0

hyb_protocol: Col-0 Cy5 / dcl3-1 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: Pool of extract, dcl3-1set 1:0.5ug, dcl3-1set 2:0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (dcl3-1) - age:14day


title: 13281185 - Col-0 vs dcl3-1

hyb_protocol: dcl3-1 Cy5 / Col-0 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: 13275756 - rdr6-1 vs Col-0

hyb_protocol: Col-0 Cy5 / rdr6-1 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: Pool of extract, rdr6-1 (1):0.5ug, rdr6-1 (2):0.5ug.


title: 13278956 - Tumor vs Calli

hyb_protocol: Calli Cy5 / Tumor 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: Calli

growth_protocol: seed - Media for Calli formation:1x MS medium (Duchefa), 1% sucrose and 1% agar. MS media was supplemented with 1xB5 vitamins, 2,4-dichlorophenoxyacetic acid [2,4-D, 2,26 mM], indole-3-acetic acid [IAA, 11,42 mM], 6-[g,g-dimethylallylamino]-purine riboside [IPAR, 1,49 mM]. Seeds were directly put to germinate on CIM media and the resulting calli were harvested 18 days later. Temperature : 23°C Light : For calli formation, plates were put in growth chamber with a 10h photoperiod. For tumor formation, plants were grown under normal greenhouse conditions.

extract_protocol: Pool of extract, Calli 1:0.5ug, Calli 2:0.5ug.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

value: between 6.00 et 6.50

source_name: Tumor

growth_protocol: stem - Media for Calli formation:1x MS medium (Duchefa), 1% sucrose and 1% agar. MS media was supplemented with 1xB5 vitamins, 2,4-dichlorophenoxyacetic acid [2,4-D, 2,26 mM], indole-3-acetic acid [IAA, 11,42 mM], 6-[g,g-dimethylallylamino]-purine riboside [IPAR, 1,49 mM]. Seeds were directly put to germinate on CIM media and the resulting calli were harvested 18 days later. Temperature : 23°C Light : For calli formation, plates were put in growth chamber with a 10h photoperiod. For tumor formation, plants were grown under normal greenhouse conditions.

extract_protocol: Pool of extract, Tumor 1:0.5ug, Tumor 2:0.5ug.

treatment_protocol: Name:Agrobacterium - biotic stress - pathogen infection,agrobacterium:time 18week . Wild-type Agrobacterium were grown on LB Agar (+rifampicin) for 48h. Fresh agrobacterium colonies were coated onto toothpick before stabbing the Arabidopsis stems with it. Tumors were leave to grow for 18 days before harvesting and RNA extraction.


title: 13281048 - Col-0 vs rdr6-1

hyb_protocol: rdr6-1 Cy5 / Col-0 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: 13281188 - Col-0 vs rdr2-1

hyb_protocol: rdr2-1 Cy5 / Col-0 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: 13279308 - dcl4-1 vs Col-0

hyb_protocol: Col-0 Cy5 / dcl4-1 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: 13281180 - Col-0 vs dcl2-1

hyb_protocol: dcl2-1 Cy5 / Col-0 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: Pool of extract, dcl2-1set 2:0.5ug, dcl2-1set 1:0.5ug.

tag: Arabidopsis thaliana (columbia)  mutant (dcl2-1) - age:14day


title: 13281182 - dcl2-1 vs Col-0

hyb_protocol: Col-0 Cy5 / dcl2-1 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: 13281061 - Stem vs Tumor

hyb_protocol: Tumor Cy5 / Stem 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: Stem

extract_protocol: Pool of extract, Stem 1:0.5ug, Stem 2:0.5ug.


title: 13278957 - Calli vs Tumor

hyb_protocol: Tumor Cy5 / Calli 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: Mfav_bleaching_rep3

status: Public on May 31 2008

city: San Francisco

first: Michael

last: DeSalvo

state: CA

department: Department of Anesthesia

country: USA

institute: UC San Francisco

description: A single time point, single genotype thermal stress experiment was performed.  A large colony of Montastraea faveolata was divided into ten coral “plugs” using a 2.5cm diameter punch tool.  The fragments were divided evenly between 2 identical 75-liter aquaria, ca. 25cm deep, and kept at ambient temperature (29.23±0.48oC) for 3 days.  After the acclimation period, 2 200-Watt aquarium heaters were turned on in the experimental aquarium, which subsequently heated to 32.23±0.48oC. The experiment lasted 10 days and 17 hours, after which all fragments were frozen in liquid nitrogen for molecular analysis.

hyb_protocol: Prior to hybridization, microarrays were post-processed by: 1) UV crosslinking at 60 mJ; 2) a “shampoo” treatment (3x SSC, 0.2% SDS at 65oC); 3) blocking with 5.5g succinic anhydride dissolved in 335mL 1-methyl-2-pyrrilidinone and 15mL sodium borate; and 4) drying via centrifugation. Dye-coupled cDNAs were cleaned (Zymo), and appropriate Cy3 and Cy5 labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC.  The hybridization mixtures were boiled for 2min at 99oC then allowed to cool at room temperature for 5min.  The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in Corning hybridization chambers overnight at 63oC.  Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.  Slides were immediately scanned using an Axon 4000B scanner.  Microarray data analysis followed a dye-swap design where each of the 5 control fragments was randomly paired to one of the 5 heat-stressed fragments.  Each hybridization was performed twice with dye swapping between technical replicates, which allows for the measurement of dye labeling bias. http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf

scan_protocol: Scanned using Axon 4100B scanner with GenePix 6.0 software.

data_processing: Data analysis was performed using J/MAANOVA in the R statistical environment. Background-subtracted mean intensity values were log2 transformed and normalized using the spatial-intensity joint lowess algorithm.  A fixed-effect MAANOVA model was fit to the intensity data with array, sample, and dye terms.  Differentially expressed genes were identified by testing the sample term according to the Empirical-Bayes Fs statistic.  P-values for each gene were generated by shuffling the residuals over 500 permutations. FDR adjustments were applied to the p-values using a step-down FDR control method.

organism: Orbicella faveolata

source_name: bleached fragment 4

label_protocol:
Labeled using Amersham CyDye Post-labeling kit.
http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf
Specifically, 1ug of total RNA was amplified using the MessageAmp II aRNA kit (Ambion), and 3ug of aRNA per sample were primed with 5ug/uL random nonamer for 10min at 70oC.   Reverse transcription (RT) lasted for 2hr at 42oC using a master mix containing a 3:2 ratio of aminoallyl-dUTP to TTP.  Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10uL 0.5M EDTA and 10uL 1M NaOH for 15min at 65oC.  After hydrolysis, RT reactions were cleaned using Zymo Clean and Concentrator columns.  Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 17uL DMSO, and the coupling reactions lasted for 2hr at room temperature in the dark.

extract_protocol:
Qiazol used to extract total RNA.
RNeasy Mini kit used to clean RNA.
Details: Total RNA from all frozen coral fragments was isolated using Qiazol lysis reagent (QIAGEN).  Live tissue was chiseled off each coral fragment and homogenized using a pre-chilled mortar and pestle embedded in dry ice.  Frozen coral powder was transferred directly to Qiazol.  Two chloroform extractions were performed, followed by isopropanol precipitation and 2 washes in 80% ethanol.  RNA pellets were re-dissolved in nuclease-free water and cleaned further over RNeasy Mini columns (QIAGEN).  RNA quality and quantity were assessed with a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Microarray protocols followed those established by the Center for Advanced Technology at the University of California, San Francisco (http://cat.ucsf.edu/).

tag: fragment thermal stressed for 11 days

source_name: control fragment 2

label_protocol:
Labeled using Amersham CyDye Post-labeling kit.
http://cat.ucsf.edu/pdfs/hybCourseProtocols_v2.7.pdf
Details same as for channel 1

extract_protocol:
Qiazol used to extract total RNA.
RNeasy Mini kit used to clean RNA.
Details same as for channel 1

tag: fragment kept at control temperature for 11 days


title: 13278961 - Tumor vs Stem

hyb_protocol: Stem Cy5 / Tumor 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: Mfav_bleaching_rep5

source_name: bleached fragment 1

source_name: control fragment 3


title: Mfav_bleaching_rep2

source_name: bleached fragment 5

source_name: control fragment 5


title: Mfav_bleaching_rep4

source_name: bleached fragment 2

source_name: control fragment 4


title: Mfav_bleaching_rep1

source_name: bleached fragment 3

tag: fragment exposed to thermal stress for 11 days

source_name: control fragment 1


title: 13420210 - 35S-ABA4#7b vs WT set1

status: Public on May 20 2008

description: Identification of genes deregulated in aba4 mutant or overexpressers.

hyb_protocol: WT set1 Cy5 / 35S-ABA4#7b 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: WT set1

growth_protocol: aerial - Media=soil hygrometry=70 Temperature=21/18 Light=16h

extract_protocol: WT set1:13.6ug.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10

tag: Arabidopsis thaliana (columbia)  mutant (35S-ABA4#7b) - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10


title: 13420444 - aba4-3 set2 vs WT set2

hyb_protocol: WT set2 Cy5 / aba4-3 set2 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: WT set2

extract_protocol: WT set2:2.07ug.

source_name: aba4-3 set2

tag: Arabidopsis thaliana (columbia)  mutant (aba4-3) - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10


title: 13420204 - WT set1 vs 35S-ABA4#16i

hyb_protocol: 35S-ABA4#16i Cy5 / WT set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (35S-ABA4#16i) - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10


title: 13420201 - 35S-NCED6#27.10 vs WT set1

hyb_protocol: WT set1 Cy5 / 35S-NCED6#27.10 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (35S-NCED6#27.10) - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10


title: 13420202 - WT set1 vs 35S-NCED6#22.4

hyb_protocol: 35S-NCED6#22.4 Cy5 / WT set1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  mutant (35S-NCED6#22.4) - dev.stage (Boyes et al. Plant Cell 2001):boyes = 1.10


title: 13420211 - WT set2 vs aba4-3 set2

hyb_protocol: aba4-3 set2 Cy5 / WT set2 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: 13420208 - WT set1 vs 35S-ABA4#7b

hyb_protocol: 35S-ABA4#7b Cy5 / WT set1 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: 13420205 - 35S-ABA4#16i vs WT set1

hyb_protocol: WT set1 Cy5 / 35S-ABA4#16i 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: 13420203 - 35S-NCED6#22.4 vs WT set1

hyb_protocol: WT set1 Cy5 / 35S-NCED6#22.4 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: 13420199 - aba4-3 set1 vs WT set1

hyb_protocol: WT set1 Cy5 / aba4-3 set1 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: aba4-3 set1


title: 13420198 - WT set1 vs aba4-3 set1

hyb_protocol: aba4-3 set1 Cy5 / WT set1 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: PBMCs enriched for CD8+ cells from normal control subject K (KCD8)

status: Public on May 01 2008

city: Washington, DC

first: Norman

middle: H

last: Lee

state: DC

address: 2300  I Street, N.W.

department: Pharmacology & Physiology

institute: The George Washington University Medical Center

description: Gene expression data from PBMC of normal control subject K enriched for CD8+ T cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45C on the GeneChip Human Genome U133 Array Set HG-U133A. GeneChips were washed and stained on the Affymetrix Fluidics Station 450 using Fluidics Script EukGE-WS2v5

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with the Affymetrix GeneChip Operating Software 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling to a target intensity value of 500.

label: Biotin

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA was generated according to the standard Affymetrix protocol from 5 ug of total RNA (GeneChip Expression Analysis Technical Manual; Affymetrix).

extract_protocol: Tissue was processed and extracted using TRIzol reagent (Invitrogen) and total RNA was purified using RNeasy columns (Qiagen) according to manufacturer's protocols.


title: Phytohemagglutinin-activated PBMCs from normal control subject J (JAcPBMC)

description: Gene expression data from PBMC of normal control subject J followig PHA+IL2 activation for 10 days

tag: phytohemagglutinin-activated PBMCs from normal control subject J


title: Phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject J (JAcCD8)

description: Gene expression data from PBMC of normal control subject J followig PHA+IL2 activation for 10 days followed by CD8+ enrichment

tag: phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject J


title: 13420200 - WT set1 vs 35S-NCED6#27.10

hyb_protocol: 35S-NCED6#27.10 Cy5 / WT set1 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: PBMCs enriched for CD8+ cells from normal control subject J (JCD8)

description: Gene expression data from PBMC of normal control subject J enriched for CD8+ T cells


title: PBMCs from normal control subject C (CPBMC)

description: Gene expression data from PBMC of normal control subject C

tag: PBMCs from normal control subject C


title: PBMC from T cell LGL leukemia patient #1375 (TLGL1375)

description: Gene expression data from PBMC of a T-LGL patient

tag: PBMC from T cell Large granular lymphocyte leukemia patient#1375


title: PBMC from T cell LGL leukemia patient #1352 (TLGL1352)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#1352


title: Phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject C (CAcCD8)

description: Gene expression data from PBMC of normal control subject C followig PHA+IL2 activation for 10 days followed by CD8+ enrichment

tag: phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject C


title: Pooled PBMC sample enriched for CD8+ cells from normal control subjects (140CD8)

description: Gene expression data from pooled PBMC of normal control subjects enriched for CD8+ T cells


title: PBMCs from normal control subject J (JPBMC)

description: Gene expression data from PBMC of normal control subject J

tag: PBMCs from normal control subject J


title: PBMCs from normal control subject K (KPBMC)

description: Gene expression data from PBMC of normal control subject K

tag: PBMCs from normal control subject K


title: Phytohemagglutinin-activated PBMCs from normal control subject C (CAcPBMC)

description: Gene expression data from PBMC of normal control subject C followig PHA+IL2 activation for 10 days

tag: phytohemagglutinin-activated PBMCs from normal control subject C


title: Phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject K (KAcCD8)

description: Gene expression data from PBMC of normal control subject K followig PHA+IL2 activation for 10 days followed by CD8+ enrichment

tag: phytohemagglutinin-activated PBMCs enriched for CD8+ cells from normal control subject K


title: PBMCs enriched for CD8+ cells from normal control subject C (CCD8)

description: Gene expression data from PBMC of normal control subject C enriched for CD8+ T cells


title: Phytohemagglutinin-activated PBMCs from normal control subject K (KAcPBMC)

description: Gene expression data from PBMC of normal control subject K followig PHA+IL2 activation for 10 days

tag: phytohemagglutinin-activated PBMCs from normal control subject K


title: PBMC from T cell LGL leukemia patient #133 (TLGL133)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#133


title: PBMC from T cell LGL leukemia patient #129 (TLGL129)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#129


title: PBMC from T cell LGL leukemia patient #130 (TLGL130)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#130


title: PBMC from T cell LGL leukemia patient #128 (TLGL128)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#128


title: PBMC from T cell LGL leukemia patient #1233 (TLGL1233)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#1233


title: PBMC from T cell LGL leukemia patient #136 (TLGL136)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#136


title: PBMC from T cell LGL leukemia patient #131 (TLGL131)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#131


title: PBMC from T cell LGL leukemia patient #132 (TLGL132)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#132


title: PBMC from T cell LGL leukemia patient #123 (TLGL123)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#123


title: PBMC from T cell LGL leukemia patient #124 (TLGL124)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#124


title: PBMC from T cell LGL leukemia patient #121 (TLGL121)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#121


title: PBMC from T cell LGL leukemia patient #113 (TLGL113)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#113


title: PBMC from T cell LGL leukemia patient #120 (TLGL120)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#120


title: PBMC from T cell LGL leukemia patient #111 (TLGL111)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#111


title: PBMC from T cell LGL leukemia patient #114 (TLGL114)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#114


title: PBMC from T cell LGL leukemia patient #115 (TLGL115)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#115


title: PBMC from T cell LGL leukemia patient #106 (TLGL106)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#106


title: PBMC from T cell LGL leukemia patient #108 (TLGL108)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#108


title: PBMC from T cell LGL leukemia patient #112 (TLGL112)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#112


title: PBMC from T cell LGL leukemia patient #116 (TLGL116)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#116


title: PBMC from T cell LGL leukemia patient #110 (TLGL110)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#110


title: PBMC from T cell LGL leukemia patient #104 (TLGL104)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#104


title: PBMC from T cell LGL leukemia patient #122 (TLGL122)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#122


title: PBMC from T cell LGL leukemia patient #107 (TLGL107)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#107


title: CRU957Cy5_CRU957CCy3

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

description: alveolar macrophages from 6 subjects were treated in vitro with PM2.5 particles or vehicle control for 4 hrs

hyb_protocol: standard Agilent hybridization

scan_protocol: Axon 4000B scanner

data_processing: Feature extraction done in TIGR Spotfinder and lowess normalization done in TIGR MIDAS.

label_protocol: Low Input Linear Amplification Kit (Agilent)

extract_protocol: Trizol

tag: Alveolar macrophages from subject CRU957 treated with vehicle control.

tag: Alveolar macrophages from subject CRU957 treated with 1 ug/mL Chapel Hill PM2.5 particles for 4 hrs.


title: PBMC from T cell LGL leukemia patient #117 (TLGL117)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#117


title: CRU957Cy5_RefCy3

source_name: Pooled reference

tag: Alveolar macrophages from 6 subjects included in the study.  Macrophages were treated with vehicle control.


title: CRU957Cy3_CRU957CCy5


title: CRU951Cy5_CRU951CCy3

tag: Alveolar macrophages from subject CRU951 treated with vehicle control.

tag: Alveolar macrophages from subject CRU951 treated with 1 ug/mL Chapel Hill PM2.5 particles for 4 hrs.


title: CRU951Cy3_RefCy5


title: Pooled PBMC sample from normal control subjects (139PBMC)

description: Gene expression data from PBMC of pooled normal control subjects


title: PBMC from T cell LGL leukemia patient #102 (TLGL102)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#102


title: CRU951Cy5_RefCy3


title: CRU951Cy3_CRU951CCy5


title: CRU957Cy3_RefCy5


title: PBMC from T cell LGL leukemia patient #101 (TLGL101)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#101


title: PBMC from T cell LGL leukemia patient #100 (TLGL100)

tag: PBMC from T cell Large granular lymphocyte leukemia patient#100


title: CRU950Cy5_RefCy3

source_name: Reference pool

tag: Alveolar macrophages from subject CRU950 treated with 1 ug/mL Chapel Hill PM2.5 particles for 4 hrs.


title: CRU950Cy3_RefCy5


title: 13688396 - Col NaCl 1 vs Control 1

status: Public on Apr 07 2008

description: Small RNAs induced under salt stress.

hyb_protocol: Control 1 Cy5 / Col NaCl 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.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,680V,laser power 33%, Cy5:635nm,pmt voltage 680V,laser power 33%

source_name: Control 1

label_protocol: labelling Cy3 and Cy5 indirect, amplification=yes, DNA 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: whole plant - MS medium in a growth chamber at 20 C with 16h light/8 h dark cycles.

extract_protocol: Control 1:10.5ug.

tag: Arabidopsis thaliana (columbia)  - age:3week

source_name: Col NaCl 1

extract_protocol: Col NaCl 1:19.65ug.

treatment_protocol: Name:NaCl - abiotic stress - abiotic stress,sodium chloride:quantity 200mM time 3hour . 12-day-old seedlings were removed from 0.5 x MS agar plates and transferred onto 0.5xMS liquid medium containing 200 mM NaCl. After 3 h treatment at 22degre Celsius, seedlings were collected and frozen immediately.


title: CRU950Cy3_CRU950CCy5

tag: Alveolar macrophages from subject CRU950 treated with vehicle control.


title: 13688397 - Control 2 vs Col NaCl 2

description: Small RNAs induced under salt stress.

hyb_protocol: Col NaCl 2 Cy5 / Control 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: Col NaCl 2

extract_protocol: Col NaCl 2:3.3ug.

source_name: Control 2

extract_protocol: Control 2:19.65ug.


title: CRU947Cy3_RefCy5

tag: Alveolar macrophages from subject CRU947 treated with 1 ug/mL Chapel Hill PM2.5 particles for 4 hrs.


title: CRU949Cy5_RefCy3

tag: Alveolar macrophages from subject CRU949 treated with 1 ug/mL Chapel Hill PM2.5 particles for 4 hrs.


title: 13688398 - Col NaCl 2 vs Control 2

description: Small RNAs induced under salt stress.

hyb_protocol: Control 2 Cy5 / Col NaCl 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: CRU946Cy5_RefCy3

scan_protocol: Axon4000B scanner

data_processing: Feature extraction doen in TIGR Spotfinder and lowess normalization done in TIGR MIDAS.

tag: RNA from alveolar macrophages from 6 subjects included in the study.  Macrophages were treated with vehicle control.

tag: Alveolar macrophages from subject CRU946 treated with 1 ug/mL Chapel Hill PM2.5 particles for 4 hrs.


title: 13688394 - Control 1 vs Col NaCl 1

description: Small RNAs induced under salt stress.

hyb_protocol: Col NaCl 1 Cy5 / Control 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: HCT116_mock

status: Public on Apr 30 2008

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: Human colorectal cancer cell line treated with mock (PBS)

hyb_protocol: Agilent protocol

scan_protocol: Agilent scanner and Agilent scan control software

data_processing: Feature Extraction ver 9.5

source_name: Human colorectal cancer cell line HCT116

label_protocol: Agilent protocol

extract_protocol: Trizol and RNeasy Mini Elute Cleanup kit

treatment_protocol: Cells were treated with mock (PBS) for 72 h.

tag: HCT116 treated with mock (PBS)


title: CRU950Cy5_CRU950CCy3


title: 13688318 - Col NaCl 3 vs Control 3

description: Small RNAs induced under salt stress.

hyb_protocol: Control 3 Cy5 / Col NaCl 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: Control 3

extract_protocol: Control 3:5.7ug.

source_name: Col NaCl 3

extract_protocol: Col NaCl 3:15.45ug.


title: 13688317 - Control 3 vs Col NaCl 3

description: Small RNAs induced under salt stress.

hyb_protocol: Col NaCl 3 Cy5 / Control 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: Pseudomonas aeruginosa_Ortho-Phenylphenol_60min_replicate2

status: Public on Apr 01 2008

city: ft. meade

first: Hyeung-Jin

last: Jang

state: MD

address: 701 Mapes Road

department: OPP/BEAD

institute: USEPA

description: No treatment

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (target signal value was 500)

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.2

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa_no treatment

label_protocol: Approximately 12 µg of total RNA was processed to produce biotinylated cDNA targets.

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.

extract_protocol: Total RNA was isolated at 0 min after OD600 reached 0.8 using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: Ortho-Phenylphenol (0.82 mM)

tag: PAO1 Wild type


title: HCT116_miR34c

description: Human colorectal cancer cell line with pre-miR34c

treatment_protocol: HCT116 cells were transfected with 100 pmol of Pre-miR miRNA34c Precursor Molecules (Ambion) using a Cell Line Nucleofector kit V (Amaxa) with a Nucleofector I electroporation device (Amaxa) according to the manufacturer’s instructions.  Total RNA was extracted 48 h after transfection.

tag: HCT116 transfected with pre-miR34c


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_60min_replicate1

description: No treatment


title: CRU949Cy3_RefCy5


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_20min_replicate2

description: No treatment


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_20min_replicate1

description: No treatment


title: CRU946Cy3_RefCy5

source_name: Reference Pool


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_60min_replicate3

description: No treatment


title: Pseudomonas aeruginosa_no treatment_0min_replicate4

description: No treatment

treatment_protocol: No treatment


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_20min_replicate4

description: No treatment


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_60min_replicate4

description: No treatment


title: CRU947Cy5_RefCy3


title: Pseudomonas aeruginosa_Ortho-Phenylphenol_20min_replicate3

description: No treatment


title: Pseudomonas aeruginosa_no treatment_0min_replicate3

description: No treatment


title: HCT116_miR34b

description: Human colorectal cancer cell line with pre-miR34b

treatment_protocol: HCT116 cells were transfected with 100 pmol of Pre-miR miRNA34b Precursor Molecules (Ambion) using a Cell Line Nucleofector kit V (Amaxa) with a Nucleofector I electroporation device (Amaxa) according to the manufacturer’s instructions.  Total RNA was extracted 48 h after transfection.

tag: HCT116 transfected with pre-miR34b


title: Pseudomonas aeruginosa_no treatment_0min_replicate2

description: No treatment


title: Staphylococcus aureus_Ortho-Phenylphenol_60min_replicate5

description: Triclosan treatment

organism: Staphylococcus aureus

source_name: Staphylococcus aureus_Triclosan

growth_protocol: (i) we initiated S. aureus cultures at 37°C with shaking at 250 rpm using sterilized Luria-Bertani (LB) broth, (ii) after 17 hours, we diluted the overnight cultures 1:100 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm until OD600 reached the early logarithmic phase (~ 0.8), and (iii) we re-diluted the cells 1:10 in pre-warmed LB broth and incubated at 37°C with shaking at 250 rpm.  Then, we added 0.045 mM triclosan immediately after OD600 reached 0.8.

extract_protocol: Total RNA was isolated after 60 min incubation with triclosan using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.

tag: NCTC 8325 Wild type


title: Staphylococcus aureus_Ortho-Phenylphenol_60min_replicate2

description: Triclosan treatment


title: Staphylococcus aureus_Ortho-Phenylphenol_60min_replicate3

description: Triclosan treatment


title: Staphylococcus aureus_Ortho-Phenylphenol_60min_replicate1

description: Triclosan treatment


title: HCT116_DAC

description: Human colorectal cancer cell line treated with DAC

treatment_protocol: HCT116 cells were treated with 2 uM 5-aza-2’-deoxycytidine (DAC) for 72 h, replacing the drug and medium every 24 h.

tag: HCT116 treated with DAC


title: Staphylococcus aureus_control_0min_replicate5

description: No treatment

source_name: Staphylococcus aureus_no treatment


title: Staphylococcus aureus_control_0min_replicate4

description: No treatment


title: Staphylococcus aureus_Ortho-Phenylphenol_20min_replicate2

description: Triclosan treatment

extract_protocol: Total RNA was isolated after 10 min incubation with triclosan using the RiboPure – Bacteria kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol.


title: Pseudomonas aeruginosa_no treatment_0min_replicate1

description: No treatment


title: Staphylococcus aureus_control_0min_replicate1

description: No treatment


title: SolexaBPmapping_case1

type: genomic

city: Berlin

first: Reinhard

last: Ullmann

department: Human Molecular Genetics

country: Germany

institute: MPIMG

description: Array CGH analysis of a male patient with delayed psychomotor development and congenital bilateral cateracts; severe visual defects and mild mental retardation. Karyotype: 46, XY, t(7;9)(q36;q13)

hyb_protocol: Hybridization was done overnight at 42?C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

scan_protocol: Slides were scanned using an Agilent scanner .

data_processing: TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants  (version Dec 2005)

molecule: genomic DNA

source_name: DNA isolated from lymphoblastoid cell lines

label_protocol: Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)

extract_protocol: DNA was extracted  by  a salting out procedure

tag: DNA isolated from a lymphoblastoid cell established from a Male patient with delayed psychomotor development and congenital bilateral cateracts; severe visual defects and mild mental retardation. Karyotype

source_name: Reference DNA isolated from blood

tag: DNA isolated from blood of a healthy male donor


title: Staphylococcus aureus_Ortho-Phenylphenol_20min_replicate5

description: Triclosan treatment


title: Staphylococcus aureus_Ortho-Phenylphenol_20min_replicate3

description: Triclosan treatment


title: Staphylococcus aureus_control_0min_replicate2

description: No treatment


title: Staphylococcus aureus_control_0min_replicate3

description: No treatment


title: SolexaBPmapping_case3

description: Array CGH analysis of a female patient with psychomotor developmental delay; at the age of 17 months she was not able to walk and talk;  frontotemporal atrophy and delayed myelinisation. Karyotype: 46, XX, t(2;12)(q31;q22)

source_name: DNA isolated from a lymphoblastoid cell line

tag: DNA isolated from a lymphoblastoid cell established from a Female patient with psychomotor developmental delay; at the age of 17 months she was not able to walk and talk;  frontotemporal atrophy and delayed myelinisation. Karyotype

extract_protocol: DNA was extracted by a salting out procedure

tag: DNA isolated from blood of a healthy female donor


title: SolexaBPmapping_case2

description: Array CGH analysis of a male patient with delayed psychomotor development; severe mental retardation; not able to talk; walking problems; horizontal nystagmus; Karyotype: 46, XY, t(4;5)(q21.1;p15.33)

tag: DNA isolated from a lymphoblastoid cell established from a Male patient with delayed psychomotor development; severe mental retardation; not able to talk; walking problems; horizontal nystagmus; Karyotype


title: Staphylococcus aureus_Ortho-Phenylphenol_20min_replicate1

description: Triclosan treatment


title: RIP140 knockout 2

status: Public on Mar 31 2008

city: Heidelberg

first: Inka

last: Zschiedrich

address: Im NeuenheimerFeld 280

department: Molecular Metabolic Control

institute: German Cancer Research Center Heidelberg

description: RIP140 knockout  bone marrow macrophages

hyb_protocol: Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2007)

scan_protocol: Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2007)

data_processing: Result files containing all relevant raw data were processed using the statistical Software SAS JMP7 Genomics3 (http://http://www.jmp.com/software/genomics/index.shtml). Raw fluorescence intensity values were normalized applying Mixed Model Normalization (Chu et al., 2002).

label: biotin

organism: Mus musculus

source_name: bone marrow macrophages

label_protocol: Labeling was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2007)

extract_protocol: (Qiagen, Venlo, the Netherlands). Contaminating genomic DNA was removed with the RNase-free DNase set (Qiagen, Venlo, the Netherlands) according the manufactures instructions.

tag: RIP140 knockout  bone marrow macrophages


title: RIP140 knockout 1


title: wildtype 1

tag: wildtype bone marrow macrophages


title: Staphylococcus aureus_Ortho-Phenylphenol_60min_replicate4

description: Triclosan treatment


title: C2C12 Neo cell-4 RNA

status: Public on Mar 25 2008

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: All microarray procedures performed by Duke University Microarray Core Facility.

hyb_protocol: Hybridization of a Cy labeled cDNA probe (mix of Cy3 and Cy5) onto coated slide spotted with oligonucleotides (70mers) was performed as described in detail at http://mgm.duke.edu/genome/dna_micro/core/protocols/SOP_hyb.doc.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a Axon GenePix Pro 4000A scanner and image intensity data were extracted and analyzed with Microarray Analysis Suite (MAS) 5.0 software.

data_processing: VALUE column is the log2 ratio of normalized Cy5:Cy3 signal after Intensity-Dependent normalization.

source_name: C2C12 C3H mouse myoblast cells RNA, control (Neo)

label_protocol: The RNA from cells was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.

growth_protocol: Sample is C2C12 cells stably selected with a Neo encoding retrovirus that were grown to 90% confluence and starved with 2% horse serum for 4 days.

extract_protocol: RNA isolation was accomplished by extracting RNA using TriReagent (Molecular Research Center, Inc.). The RNA (10 µg) was DNase treated using a DNA-free kit (Ambion) and assessed for quality with an Agilent Lab-on-a-Chip 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

source_name: Murine Reference RNA

label_protocol: The RNA from murine liver was directly labeled with Cy dyes using oligo dT primers, for complete details see http://mgm.duke.edu/genome/dna_micro/core/protocols/ for detailed labeling and hybridization protocols.

tag: Murine Universal RNA (Stratagene, La Jolla, CA) which is a mixture of RNA from 10 control cell lines approximating the expression profile of the majority of murine genes was used.


title: wildtype 3


title: C2C12 HDAC4 cell-4 RNA

source_name: C2C12 C3H mouse myoblast cells RNA, HDAC4

growth_protocol: Sample is C2C12 cells stably selected with a HDAC4-Neo encoding retrovirus that were grown to 90% confluence and starved with 2% horse serum for 4 days.


title: Staphylococcus aureus_Ortho-Phenylphenol_20min_replicate4

description: Triclosan treatment