title: 13969305 - kim 2 vs wt 2

hyb_protocol: wt 2 Cy5 / kim 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: 13969153 - irx12 1 vs wt 1

status: Public on May 01 2010

type: RNA

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

hyb_protocol: wt 1 Cy5 / irx12 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,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: wt 1

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

growth_protocol: stem - media: in soil hydrometry: 40% temperature: 22°C light: 13h

treatment_protocol: no treatment

tag: strain

value: columbia

tag: genotype variation

value: wild type

tag: harvest date

source_name: irx12 1

growth_protocol: stem - Media: in soil  hydrometry: 40% temperature: 22°C light: 13h


title: 13833003 - wt vs kim

hyb_protocol: kim Cy5 / wt 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: kim

value: kim

source_name: wt


title: 13969318 - lac4g 1 vs wt 1

hyb_protocol: wt 1 Cy5 / lac4g 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac4g 1

extract_protocol: lac4g 1:13ug.


title: 13969155 - lac17 1 vs wt 1

hyb_protocol: wt 1 Cy5 / lac17 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: lac17 1


title: FX-iPS-C

status: Public on May 10 2010

city: Ramat Gan

first: Achia

last: Urbach

address: Bar Ilan

department: Faculty of Life Sciences

country: Israel

institute: Bar Ilan University

description: iPS cells from FX-fibroblasts C

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label: biotin

organism: Homo sapiens

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: cell type

value: iPS cells

tag: sample type

value: iPS cells from FX-fibroblasts C


title: 13969150 - wt 1 vs kim 1

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

source_name: kim 1

extract_protocol: kim 1:15ug.


title: 13833004 - kim vs wt

hyb_protocol: wt Cy5 / kim 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: 13969151 - kim 1 vs wt 1

hyb_protocol: wt 1 Cy5 / kim 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: 13969416 - DRNL::GFP+ repeat1 vs DRNL::GFP- repeat1

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

description: DRN targets

hyb_protocol: DRNL::GFP- repet1 Cy5/DRNL::GFP+ repet1 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: DRNL::GFP- repeat1

growth_protocol: protoplast - Media=Gamborg B5;2% sucrose/4,5µM 2,4-D;PH5,8; Temperature=23°C; Light=long day (16h)

extract_protocol: DRNL::GFP- repet1:100ng.

tag: ecotype

tag: genome/variation

value: mutant (drnl::GFP-)

tag: developmental stage (boyes et al. plant cell 2001)

value: embryonic

source_name: DRNL::GFP+ repeat1

growth_protocol: protoplast - Media=Gamborg B5;2% sucrose/4,5µM 2,4-D;PH5,8 Temperature=23°C; Light=long day (16h)

extract_protocol: DRNL::GFP+ repet1:100ng.

value: mutant (drnl::GFP+)


title: 13969417 - DRNL::GFP- repeat2 vs DRNL::GFP+ repeat2

description: DRN targets

hyb_protocol: DRNL::GFP+ repet2 Cy5/DRNL::GFP- repet2 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: DRNL::GFP+ repeat2

extract_protocol: DRNL::GFP+ repet2:100ng.

source_name: DRNL::GFP- repeat2

extract_protocol: DRNL::GFP- repet2:100ng.


title: 13969418 - DRNL::GFP+ repeat2 vs DRNL::GFP- repeat2

description: DRN targets

hyb_protocol: DRNL::GFP- repet2 Cy5/DRNL::GFP+ repet2 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: 13969156 - wt 1 vs lac4g 1

hyb_protocol: lac4g 1 Cy5 / wt 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: 13969415 - DRNL::GFP- repeat1 vs DRNL::GFP+ repeat1

description: DRN targets

hyb_protocol: DRNL::GFP+ repet1 Cy5/DRNL::GFP- repet1 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: 13968891 - DRN::GFP- repeat2 vs DRN::GFP+ repeat2

description: DRN targets

hyb_protocol: DRN::GFP+ repet2 Cy5/DRN::GFP- repet2 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: DRN::GFP+ repeat2

growth_protocol: protoplast - Media=1/2 MS; 2% sucrose/4,5µM 2,4 D;PH5,8; Temperature=23°C; Light=long day (16h)

extract_protocol: DRN::GFP+ repet2:100ng.

value: landsberg erecta

value: mutant (drn::GFP-)

source_name: DRN::GFP- repeat2

extract_protocol: DRN::GFP- repet2:100ng.


title: 13968887 - DRN::GFP+ repeat1 vs DRN::GFP- repeat1

description: DRN targets

hyb_protocol: DRN::GFP- repet1 Cy5/DRN::GFP+ repet1 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: DRN::GFP- repeat1

extract_protocol: DRN::GFP- repet1:100ng.

source_name: DRN::GFP+ repeat1

extract_protocol: DRN::GFP+ repet1:100ng.

value: mutant (drn::GFP+)


title: 13968889 - DRN::GFP- repeat1 vs DRN::GFP+ repeat1

description: DRN targets

hyb_protocol: DRN::GFP+ repet1 Cy5/DRN::GFP- repet1 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: 13969419 - DRN::GFP(pt/amp1)- repeat1 vs DRN::GFP(pt/amp1)+ repeat1

description: DRN targets

hyb_protocol: DRN::GFP(pt/amp1)+ repet1 Cy5/DRN::GFP(pt/amp1)- repet1 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: DRN::GFP(pt/amp1)+ repeat1

extract_protocol: DRN::GFP(pt/amp1)+ repet1:100ng.

value: mutant (drn::GFP(pt/amp1)+)

source_name: DRN::GFP(pt/amp1)- repeat1

extract_protocol: DRN::GFP(pt/amp1)- repet1:100ng.

value: mutant (drn::GFP(pt/amp1)-)


title: 13968890 - DRN::GFP+ repeat2 vs DRN::GFP- repeat2

description: DRN targets

hyb_protocol: DRN::GFP- repet2 Cy5/DRN::GFP+ repet2 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: T4b (cy5) vs. Control_Cb (cy3)

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: T4b (cy5) vs. Control_Cb (cy3)

hyb_protocol: 750ng of each Cyanine-3 and Cyanine-5 labeled cRNA were combined with 50μl of 10x Blocking agent. The volume is made upto 240 ul using Nuclease free water. 10μl of 25x Fragmentation buffer (Agilent) were added and incubated at 60°C for 30 minutes in dark. The fragmented cRNA were mixed with 250μl of 2x Hybridization Buffer (Agilent). About 490μl of the resulting mixture was applied to the 22k Gene Expression Microarray (Agilent Technologies), and hybridized at 65°C for 17 hours in an Agilent Microarray Hybridization Chamber (SureHyb: G2534A) with Hybridization Oven. After hybridization, slides were washed with Agilent Gene expression Wash Buffer-I for 1 minute at room temperature followed by a 1 min wash with Agilent Gene expression Wash Buffer-II at 37ºC. Slides were finally rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Scanned on an Agilent G2505B US45103024 scanner and Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1)

data_processing: Normalization of the data was done using Per spot per chip intensity dependant lowess normalization. Further quality control of normalized data was done using correlation based condition tree to eliminate bad experiments. One fold and above differentially regulated genes were filtered from the data. Ontology based biological analysis was done using Gene Ontology browser in GeneSpring Gx. Further, pathways that were significantly regulated was done using bio script library in GeneSpring Gx

organism: Rattus norvegicus

source_name: saline, 48h hypoxia

label_protocol: Low RNA Input Linear Amplification Kit (Agilent, Santa Clara, CA) was used for labeling. Briefly, both first and second strand cDNA were synthesized by incubating 500ng of total RNA with 1.2μl of oligo dT-T7 Promoter Primer in nuclease-free water at 65ºC for 10 min followed by incubation with 4.0μl of 5× First strand buffer, 2μl of 0.1M DTT, 1 μl of 10mM dNTP mix, 1μl of 200 U/μl MMLV RT, and 0.5μl of 40U/μl RNaseOUT, at 40ºC for 2 hour. Immediately following cDNA synthesis, the reaction mixture was incubated with 2.4 μl of 10 mM Cyanine-3 CTP or 2.4 μl of 10 mM Cyanine-5 CTP (Perkin-Elmer, Boston, MA), 20μl of 4X Transcription buffer, 8 μl of NTP mixture, 6 μl of 0.1M DTT, 0.5 μl of RNaseOUT, 0.6μl of Inorganic pyrophosphatase, 0.8 μl of T7 RNA polymerase, and 15.3μl of nuclease-free water at 40 ºC for 2 hour. Qiagen’s RNeasy mini spin columns were used for purifying amplified aRNA samples. The quantity and specific activity of cRNA was determined by using NanoDrop ND-1000 UV-VIS Spectrophotometer version3.2.1. Samples with specific activity >8 were used for hybridization.

growth_protocol: Animals were maintained at 24oC with food and water adlibitum

extract_protocol: Total RNA extracted using Qiagen RNA isolaation kit following manufacturer's instructions

treatment_protocol: (a) Normal saline pretreatment for 7 days and hypoxia exposure at 30000 ft for 6h (T1b), 12h (T2a), 24h (T3b), 48h (T4b); (b) Cobalt pretreatment (12.5 mg/Kg body weight) for 7 days and hypoxia exposure at 30000 ft for 6h (T5a), 12h (T6a), 24h (T7a), 48h(T8a)

tag: tissue

value: lung

tag: pretreatment

value: Normal saline pretreatment for 7 days

tag: hypoxia exposure

source_name: saline, 0h hypoxia

value: 0h, control


title: T8a (cy3) vs. Control_C2 (cy5)_Dye swap

description: T8a (cy3) vs. Control_C2 (cy5)_Dye swap

source_name: cobalt, 48h hypoxia

value: Cobalt pretreatment (12.5 mg/Kg body weight) for 7 days

source_name: cobalt, 0h hypoxia


title: T6a (cy3) vs. Control_C2 (cy5)_Dye swap

description: T6a (cy3) vs. Control_C2 (cy5)_Dye swap

source_name: cobalt, 12h hypoxia


title: T2a (cy5) vs. Control_Cb (cy3)

description: T2a (cy5) vs. Control_Cb (cy3)

source_name: saline, 12h hypoxia


title: T5a (cy3) vs. Control_C2 (cy5)_Dye swap

description: T5a (cy3) vs. Control_C2 (cy5)_Dye swap

source_name: cobalt, 6h hypoxia

value: 30000 ft for 6h


title: T7a (cy3) vs. Control_C2 (cy5)_Dye swap

description: T7a (cy3) vs. Control_C2 (cy5)_Dye swap

source_name: cobalt, 24h hypoxia


title: T3b (cy5) vs. Control_Cb (cy3)

description: T3b (cy5) vs. Control_Cb (cy3)

source_name: saline, 24h hypoxia


title: T1b (cy5) vs. Control_Cb (cy3)

description: T1b (cy5) vs. Control_Cb (cy3)

source_name: saline, 6h hypoxia


title: mouse embryos at 2-cell stage sample B

city: New York

first: Dieter

middle: M

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

country: USA

institute: Columbia University

description: chip 4068264030 array B

hyb_protocol: Hybridization according to Illumina protocols on Illumina Sentrix Mouse Expression BeadChip RefSeq 8 v1.1 (GPL6103)

scan_protocol: according to Illumina protocols

data_processing: Analysis done using Illumina GenomeStudio program

organism: Mus musculus

source_name: 2-cell stage embryos collected 48-50h post hCG

label_protocol: according to Illumina protocols

growth_protocol: mouse embryos were cultured in KSOM

extract_protocol: PicoPure RNA isolation (Arcturus)

tag: developmental stage

value: 2-cell stage embryos


title: 13969152 - wt 1 vs irx12 1

hyb_protocol: irx12 1 Cy5 / wt 1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: irx12 1

value: columbia

source_name: wt 1

value: wild type


title: interphase nuclear transfer embryo sample A

description: chip 4754483049 array G

source_name: enucleation and transfer of the zygote at interphase, 48-50h post hCG

value: zygotes


title: M phase nuclear transfer embryos sample D

description: chip 4125661075 array F

source_name: mouse nuclear transfer embryos 22-24h post transfer, corresponding to 48-50h post hCG

value: embryo


title: genome less embryos sample B

description: chip 4125661075 array H

source_name: embryo 22-24h after enucleation, without transfer of a genome, corresponding to 48-50h post hCG


title: M phase nuclear transfer embryos sample C

description: chip 4125661075 array E

value: mouse nuclear transfer embryos 22-24h post transfer, corresponding to 48-50h post hCG


title: mouse embryos at 2-cell stage sample A

description: chip 4068264030 array A

value: 2-cell stage embryos collected 48-50h post hCG


title: interphase nuclear transfer embryo sample B

description: chip 4125661075 array G

value: enucleation and transfer of the zygote at interphase, 48-50h post hCG


title: M phase nuclear transfer embryos sample B

description: chip 4754483049 array E


title: drug treatment control sample B

description: chip 4068264030 array G

source_name: mouse embryos collected 48h-50h post hCG, after exposure to nocodazole at mitosis


title: mouse ES cells sample B

description: chip 4125661008 array H

source_name: mouse ES cell culture

value: mouse ES cell culture

value: ES cell


title: drug treatment control sample A

description: chip 4068264018 array F

value: mouse embryos collected 48h-50h post hCG, after exposure to nocodazole at mitosis


title: M phase nuclear transfer embryos sample A

description: chip 4754483049 array D


title: mouse zygote at interphase sample C

description: chip 4125661008 array F

source_name: interphase zygotes collected 24-28h post hCG injection into oocyte donor mouse

value: interphase zygotes


title: drug treatment control sample C

description: chip 4125661075 array B


title: mouse zygote in mitosis sample C

description: chip 4068264030 array H

source_name: zygotes arrested in mitosis by nocodazole 32-34h post hCG

value: zygotes arrested in mitosis


title: mouse zygote in mitosis sample B

description: chip 4068264030 array C

value: zygotes arrested in mitosis by nocodazole 32-34h post hCG


title: mouse zygote at interphase sample A

description: chip 4020498031 array E

value: interphase zygotes collected 24-28h post hCG injection into oocyte donor mouse


title: mouse zygote at interphase sample B

description: chip 4125661008 array E


title: genome less embryos sample A

description: chip 4754483049 array F

value: embryo 22-24h after enucleation, without transfer of a genome, corresponding to 48-50h post hCG


title: 13969420 - DRN::GFP(pt/amp1)+ repeat1 vs DRN::GFP(pt/amp1)- repeat1

description: DRN targets

hyb_protocol: DRN::GFP(pt/amp1)- repet1 Cy5/DRN::GFP(pt/amp1)+ repet1 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: DRN::GFP(pt/amp1)- repeat1

value: landsberg erecta

value: mutant (drn::GFP(pt/amp1)-)

value: embryonic

source_name: DRN::GFP(pt/amp1)+ repeat1

value: mutant (drn::GFP(pt/amp1)+)


title: Poll_v_PollControl_chip5

city: St Lucia

first: Sean

last: McWilliam

state: Queensland

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

hyb_protocol: Hybridized according to Agilent Two-Color Microarray_based Gene Expression Analysis protocol

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Images were quantified using Agilent Feature Extraction software (Version 9.5.1). For each intensity signal we required that the signal to noise ratio s > 1, where s is obtained by dividing the background corrected intensity by the standard deviation of the background pixels. Second, we required that the correlation between the mean and the median signal intensities r > 0.85 where r is obtained by dividing the smaller of the mean or median by the larger. Spots that failed to pass these filtering criteria were assigned a reading of zero. Signals that passed were corrected for background intensity and log2 transformed.

organism: Bos taurus

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol:
Biopsies (average weight 63 mg) that included epidermis, dermis and dermal connective tissue were obtained from the horn-forming region of the skull. Control samples taken from skull away from horn site.
Total RNA extracted using RiboPure (Applied Biosystems) following manufacturer's instructions

value: Skin

tag: horn type

value: cPoll

tag: gender

value: Female

value: Poll


title: mouse zygote in mitosis sample A

description: chip 4068264018 array H


title: Horn_v_Scur_chip4

value: Scur

value: Male

value: Horn


title: ScurControl_v_Scur_chip5_dyeswap

value: cScur


title: PollControl_v_Poll_chip5_dyeswap


title: Poll_v_Horn_chip4


title: Horn_v_Poll_chip4_dyeswap


title: Scur_v_Poll_chip4


title: Scur_v_ScurControl_chip5


title: Poll_v_Horn_chip3


title: rdp1 YPD 1st

city: Seoul

first: Yong-Sun

last: Bahn

address: 134 Shinchon-dong Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

description: CTR vs rdp1 YPD

hyb_protocol: Microarray Hybridization and Washing. C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (110g, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by coverslide 22X22.  The Cy3/Cy5-labeled cDNA samples were applied in between coverslide and slides.  To prevent slides from drying, 10 µl of 3x SSC buffer was applied into the chamber hole, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed, including one-dye swap experiment.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100B scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 6.0) and gal file (http://genomeold.wustl.edu/activity/ma/cneoformans/).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity by employing LOWESS M normalization, reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans H99

source_name: rdp1 YPD 1st

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.5 µl RNasin (Promega), 0.6 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM)), 1.5 µl AffinityScript reverse transcriptase (Stratagene), 3 µl AffinityScript buffer, 7 µl water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPE-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr.  For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1.25 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy3 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy5.  For a dye-swap experiment, control and test RNAs were labeled oppositely.  Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: To obtain total RNA for DNA microarray analysis of the serotype A wild-type H99 strain and ago1(YSB299) and rdp1(YSB467) mutant strains, cells were grown in 50 ml YPD medium at 30°C for 16 h. Then 5 ml of the overnight culture was inoculated into 100 ml of fresh YPD medium and further incubated for 4 h at 30°C to an optical density at 600 nm (OD600 =1.0). Then the culture was frozen in liquid nitrogen and lyophilized overnight. Three independent cultures for each strain were prepared for total RNA isolation as biological replicates.

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 15 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT, hog1, ssk1, and skn7 mutant cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: For zero-time samples, 50 ml of culture was sampled and rapidly frozen in liquid nitrogen.

tag: genotype/variation

tag: growth condition

value: innoculate 1/20 volume of overnight culture into YPD media and incubate 4hrs until OD600nm reach to 0.1

source_name: pooled total RNA from all strain all time point all stress

tag: reference


title: rdp1 MAT a 3rd

description: rdp1 MATa/WT MAT a

hyb_protocol: Microarray Hybridization and Washing. C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (110g, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by coverslide 22X22.  The Cy3/Cy5-labeled cDNA samples were applied in between coverslide and slides.  To prevent slides from drying, 10 µl of 3x SSC buffer was applied into the chamber hole, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100B scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genomeold.wustl.edu/activity/ma/cneoformans/).

data_processing: The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity by employing LOWESS M normalization, reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus deneoformans JEC21

source_name: rdp1 MATa

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.5 µl RNasin (Promega), 0.6 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM)), 1.5 µl AffinityScript reverse transcriptase (Stratagene), 3 µl AffinityScript buffer, 7 µl water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPE-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr.  For Cy3 and Cy5 labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1.25 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from backcorssed WT RNAs were mixed with Cy3 as a control and the cDNAs prepared from each rdp1 mutant RNAs (each experimental condition) were mixed with Cy5.  Each mixture was further incubated at room temperature for 1 hr in the dark and purified by PCR purification kit.

growth_protocol: To obtain total RNA for DNA microarray analysis of the serotype D wild-type (NE519 MAT alpha, NE520 MAT a) strain and rdp1 mutant strains (NE517 MAT alpha, NE518 MAT a), cells were grown in YPD liquid culture to a density of 5 x 107 cells/ml. RNA was extracted with TRIZOL Reagent (Invitrogen) following the manufacturer’s instructions. Total RNA of the wild-type and the rdp1 mutant strains of each mating type were used for Cy3 and Cy5 labeling, respectively.

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 15 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.

value: NE518 rdp1 MATa

source_name: WT MATa

value: NE520 WT MATa


title: Horn_v_Poll_chip2_dyeswap


title: rdp1 MAT a 2nd

description: rdp1 MATa/WT MAT a


title: rdp1 MAT alpha 3rd

description: rdp1 MATalpha/WT MATalpha

source_name: rdp1 MATalpha

value: NE517 rdp1 MATalpha

source_name: WT MATalpha

value: NE519 WT MATalpha


title: rdp1 MAT a 1st

description: rdp1 MATa/WT MAT a


title: rdp1 MAT alpha 1st

description: rdp1 MATalpha/WT MATalpha


title: Scur_v_Poll_chip2


title: Scur_v_Poll_chip3


title: rdp1 YPD 2nd

description: CTR vs rdp1 YPD

source_name: rdp1 YPD 2nd

value: pooled total RNA from all strain all time point all stress


title: rdp1 YPD 3rd

description: CTR vs rdp1 YPD

source_name: rdp1 YPD 3rd


title: rdp1 MAT alpha 2nd

description: rdp1 MATalpha/WT MATalpha


title: Poll_v_Horn_chip2


title: Scur_v_Poll_chip1


title: Horn_v_Poll_chip3_dyeswap


title: rdp1 YP 2nd

description: CTR vs rdp1 YP

source_name: rdp1 YP 2nd

value: innoculate 1/20 volume of overnight culture into YP media and incubate 4hrs until OD600nm reach to 0.1


title: Horn_v_Scur_chip2


title: rdp1 YP 3rd

description: CTR vs rdp1 YP

source_name: rdp1 YP 3rd


title: ago1 YPD 3rd

description: CTR vs ago1 YPD

source_name: ago1 YPD 3rd


title: Horn_v_Poll_chip1_dyeswap


title: Horn_v_Scur_chip3


title: rdp1 YP 1st

description: CTR vs rdp1 YP

source_name: rdp1 YP 1st


title: ago1 YPD 1st

description: CTR vs ago1 YPD

source_name: ago1 YPD 1st


title: ago1 YP 3rd

description: CTR vs ago1 YP

source_name: ago1 YP 3rd


title: Poll_v_Horn_chip1


title: H99 YPD 1st

description: CTR vs WT YPD

source_name: H99 YPD 1st

value: wild type


title: H99 YPD 2nd

description: CTR vs WT YPD

source_name: H99 YPD 2nd


title: ago1 YP 1st

description: CTR vs ago1 YP

source_name: ago1 YP 1st


title: H99 YP 3rd

description: CTR vs WT YP

source_name: H99 YP 3rd


title: Cardiac left ventricle_sham operated_42days_ rep6

city: Umea

first: Urban

last: Hellman

address: Nus 6M

department: Public health and clinical medicine

country: Sweden

institute: Umea University

hyb_protocol: Performed according to Illumina protocol

scan_protocol: Illumina Beadstation 500GX according to Illumina protocol

data_processing: Cubic spline normalization, subtracted background, False Discovery Rate using Illumina Beadstudio 3.3 with gene expression module 3.4.0 (GenomeStudio).

source_name: Cardiac left ventricle_42days

label_protocol: Illumina TotalPrep RNA Amplification Kit was used

extract_protocol: Cardiac tissue was put in RNAlater and extracted using

treatment_protocol: Abdominal aorta was ligated to induce cardiac hypertrophy

tag: strain

value: Wistar

tag: sex

value: male

value: cardiac left ventricle

tag: treatment

value: sham operated


title: Cardiac left ventricle_sham operated_42days_ rep5

extract_protocol: Cardiac tissue was put in RNAlater and extracted using Qiagen RNeasy Fibrous Tissue Mini Kit for total RNA.


title: Cardiac left ventricle_aorta ligated_42days_ rep5

value: aorta ligated


title: H99 YPD 3rd

description: CTR vs WT YPD

source_name: H99 YPD 3rd

source_name: pooled total RNA from all strain all time point all stress


title: ago1 YP 2nd

description: CTR vs ago1 YP

source_name: ago1 YP 2nd


title: Cardiac left ventricle_sham operated_42days_ rep3


title: H99 YP 1st

description: CTR vs WT YP

source_name: H99 YP 1st


title: Cardiac left ventricle_sham operated_42days_ rep1


title: Cardiac left ventricle_sham operated_42days_ rep2


title: Cardiac left ventricle_aorta ligated_42days_ rep4


title: Cardiac left ventricle_aorta ligated_42days_ rep6


title: Cardiac left ventricle_aorta ligated_42days_ rep1


title: Cardiac left ventricle_aorta ligated_42days_ rep3


title: Cardiac left ventricle_aorta ligated_42days_ rep2


title: Cardiac left ventricle_sham operated_42days_ rep4


title: SCO_13_bc

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

country: Germany

institute: University Hospital Hamburg-Eppendorf

description: Patient with Sertoli-cell only syndrome and AZFb+c deletion #1

hyb_protocol: Hybridization was conducted for 20h at 37°C and arrays washed in 1x TNT (10 min, RT) and 1x TNT (60 min, 46°C). Staining with Cy5-Streptavidin was done for 30 min at RT. Then, arrays were washed 2 times with 1x TNT for 10 min and 0.2x SSPE for 30s. They were spin-dried in a centrifuge at 2000 rpm for 2 min.

scan_protocol: Scanning was done on an Affymetrix 428 Scanner (Affymetrix, USA) at PMT 70 settings using the Jaguar 2.0 software for image acquisition.

data_processing: Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA) and these normalized by quantile normalization using the Bioconducter package 'affy'.

source_name: testicular biopsy

label_protocol: total RNA was amplified with the MessageAmp III Kit (Ambion, USA) and Biotin-UTP incorporated as a label.

extract_protocol: Biopsies were homogeneized in RNApure (Peqlab, Germany) with an Ultra-Thurrax and total RNA repurified on RNeasy columns (Qiagen, Germany). Quality control was done with a Bioanalyzer (Agilent, USA).

treatment_protocol: Testicular biopsies were obtained from open surgery and classified based on homogeneous histology with no discrepancy to paralle biopsies and test-TESE.

tag: deletion

value: AZFb+c

tag: histology

value: SCO


title: SCO_10_c

description: Patient with Sertoli-cell only syndrome and AZFc deletion #3

value: AZFc


title: Cardiac left ventricle_sham operated_6days_ rep6

source_name: Cardiac left ventricle_6days


title: Cardiac left ventricle_sham operated_6days_ rep3


title: Horn_v_Scur_chip1

value: Skin

value: Scur

value: Male

value: Horn


title: SCO_12_c

description: Patient with Sertoli-cell only syndrome and AZFc deletion #5


title: SCO_9_c

description: Patient with Sertoli-cell only syndrome and AZFc deletion #2


title: SCO_4

description: Patient with Sertoli-cell only syndrome #4

value: control


title: Cardiac left ventricle_sham operated_6days_ rep5


title: SCO_3

description: Patient with Sertoli-cell only syndrome #3


title: Cardiac left ventricle_sham operated_6days_ rep2


title: SCO_7

description: Patient with Sertoli-cell only syndrome #7


title: Cardiac left ventricle_sham operated_6days_ rep1


title: SCO_6

description: Patient with Sertoli-cell only syndrome #6


title: SCO_8_c

description: Patient with Sertoli-cell only syndrome and AZFc deletion #1


title: SCO_5

description: Patient with Sertoli-cell only syndrome #5


title: Cardiac left ventricle_sham operated_6days_ rep4


title: Cardiac left ventricle_aorta ligated_6days_ rep5


title: Cardiac left ventricle_aorta ligated_6days_ rep1


title: Cardiac left ventricle_sham operated_1day_ rep4

source_name: Cardiac left ventricle_1day


title: Cardiac left ventricle_aorta ligated_6days_ rep4


title: Cardiac left ventricle_aorta ligated_6days_ rep2


title: Cardiac left ventricle_aorta ligated_6days_ rep3


title: Cardiac left ventricle_sham operated_1day_ rep6


title: Cardiac left ventricle_sham operated_1day_ rep3


title: SCO_2

description: Patient with Sertoli-cell only syndrome #2


title: MA_10

description: Patient with meiotic arrest #10

value: MA


title: MA_14_bc

description: Patient with meiotic arrest and AZFb+c deletion #1


title: MA_13_c

description: Patient with meiotic arrest and AZFc deletion #3


title: MA_11_c

description: Patient with meiotic arrest and AZFc deletion #1


title: Cardiac left ventricle_sham operated_1day_ rep1


title: Cardiac left ventricle_sham operated_1day_ rep2


title: MA_12_c

description: Patient with meiotic arrest and AZFc deletion #2


title: MA_6

description: Patient with meiotic arrest #6


title: MA_4

description: Patient with meiotic arrest #4


title: MA_3

description: Patient with meiotic arrest #3


title: Cardiac left ventricle_aorta ligated_1day_ rep6


title: MA_5

description: Patient with meiotic arrest #5


title: Cardiac left ventricle_aorta ligated_1day_ rep5


title: MA_7

description: Patient with meiotic arrest #7


title: Cardiac left ventricle_aorta ligated_1day_ rep2


title: MA_8

description: Patient with meiotic arrest #8


title: Cardiac left ventricle_aorta ligated_1day_ rep3


title: HYS_5_c

description: Patient with hypospermatogenesis and AZFc deletion #1

value: HYS


title: HYS_7_c

description: Patient with hypospermatogenesis and AZFc deletion #3


title: Cardiac left ventricle_aorta ligated_1day_ rep4


title: HYS_6_c

description: Patient with hypospermatogenesis and AZFc deletion #2


title: MA_2

description: Patient with meiotic arrest #2


title: MA_9

description: Patient with meiotic arrest #9


title: MA_1

description: Patient with meiotic arrest #1


title: SCO_1

description: Patient with Sertoli-cell only syndrome #1


title: GSK-3 inhibitor effect on MLL leukemia cells - 2

city: Stanford

first: Michael

middle: L

last: Cleary

state: CA

address: Room L232, Stanford Medical Center

department: Pathology

web_link: http://    http://med.stanford.edu/profiles/pathology/researcher/Michael_Cleary/  At Stanford

institute: Stanford University

description: Study the effect of GSK-3 inhibition on MLL leukemia cells

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit

scan_protocol: GeneChip® Scanner 3000 7G

data_processing:
Expression Console (Affymetrix)
affymetrix-algorithm-name = rma-gene-default.

label: Biotin

source_name: Human Leukemia cell line RS4.11

label_protocol: GeneChip® WT Terminal Labeling Kit(Affymetrix)

extract_protocol: Trizol

tag: treatment protocol

value: GSK-3 inhibitor (SB216763) treated for 20 hours


title: HYS_3

description: Patient with hypospermatogenesis #3


title: HYS_4

description: Patient with hypospermatogenesis #4


title: Cardiac left ventricle_sham operated_1day_ rep5


title: HYS_2

description: Patient with hypospermatogenesis #2


title: HYS_1

description: Patient with hypospermatogenesis #1


title: GSK-3 inhibitor effect on MLL leukemia cells - 1


title: GSK-3 inhibitor effect on MLL leukemia cells - 3


title: control-2


title: Parenteral feeding 72hr 8307

status: Public on Apr 29 2010

city: New Brunswick

first: Stephen

middle: F

last: Lowry

state: NJ

address: 125 Paterson St

department: Surgery

institute: UMDNJ

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Focus Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring GX11.0.1 - RMA - baseline transformation, log

source_name: Healthy Volunteer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell type

value: Monocytes

tag: protocol

value: Parenteral feeding 72hr


title: control-1


title: Enteral feeding 72hr 8311

value: Enteral feeding 72hr


title: Parenteral - with lipid feeding 72hr 8303

value: Parenteral - with lipid feeding 72hr


title: Pre-feeding 8310

value: Pre-feeding


title: Enteral feeding 72hr 8310


title: Pre-feeding 8311


title: Pre-feeding 8305


title: Pre-feeding 8301


title: Pre-feeding 8304


title: Pre-feeding 8306


title: Parenteral - with lipid feeding 72hr 8309


title: Pre-feeding 8309


title: Parenteral - with lipid feeding 72hr 8306


title: Enteral feeding 72hr 8302


title: Parenteral feeding 72hr 8305


title: Cardiac left ventricle_aorta ligated_1day_ rep1

value: Wistar

value: male

tag: tissue

value: cardiac left ventricle

value: aorta ligated


title: excess_prolif_ya_rep2

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description: RNA was amplified

hyb_protocol: Hybing protocol followed that of Chi and Reinke, 2006

scan_protocol: Scanning was performed on Axon Genepix 4.0

data_processing: Lowess normalization was performed

organism: Caenorhabditis elegans

source_name: unc-32 glp-1, excess proliferation

label_protocol: Labeling protocol followed that of Chi and Reinke, 2006

growth_protocol: animals were grown under standard conditions on growth plates at 15deg C, staged as embryos by bleach and L1 starve, and then shifted to 25deg C for growth to young adult

extract_protocol: RNA was extracted from worm pellets using Trizol, and then amplified using the protocol described in Chi and Reinke, 2006

tag: stage

value: young adult

value: hermaphrodite

tag: genotype

value: unc-32 glp-1, excess proliferation

source_name: unc-32, normal proliferation control

value: unc-32, normal proliferation control


title: BPA-to-Ctrl_#3 [mRNA]

city: Columbus

first: Pei-Yin

last: Hsu

state: OH

address: BRT836, 460W 12th Ave

institute: OSU

description:
Gene expression data from rat with BPA exposure
Gene expression data from rat with sesame oil exposure

hyb_protocol: Eight picograms of Cy3 and Cy5 from labeled control probe and labeled BPA group probe respectively, were used to hybridize an Agilent 60-mer oligo-microarrays slide containing 22 000 features. Slides were hybridized at 60 8C for 18 h in SureHyb chambers (Agilent Technologies)

scan_protocol: The images obtained were analyzed with Feature extraction software (Agilent Technologies) to verify the quality of the hybridization by the report of the outlier data. The intensity of the spots was measured using ImaGene 5.6 software (BioDiscovery Inc., El Segundo, CA, USA)

data_processing: The data from each microarray was adjusted for background noise using the normexp procedure, and normalized by fitting the lowess curve to the of log-ratios of Cy5 to Cy3 channel and the average log-intensities of the two as implemented in the limma package

source_name: BPA-exposed rat_#3

label_protocol: Fluorescent cRNA probes were prepared using Agilent Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies) in the presence of Cy3-dCTP or Cy5-dCTP (Perkin–Elmer, Wellesley, MA, USA), and then purified using RNeasy Mini Kit (Qiagen Inc)

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

value: Female

value: Sprague Dawley CD

tag: agent

value: BPA

value: the fourth abdominal mammary glands

tag: age

source_name: Seasame oil-exposed rat_#3

value: sesame oil (control)


title: excess_prolif_ya_rep4

description: RNA was amplified


title: excess_prolif_ya_rep1

description: RNA was amplified


title: adipose tissue postpartum cow 386 +14 d 011708

city: Pullman

first: John

middle: P

last: McNamara

state: WA

address: 233 Clark Hall

department: Animal Sciences

institute: Washington State University

hyb_protocol: Samples were analyzed with an Affymetrix GeneChip® Bovine Genome Array (Santa Clara, CA).  Total RNA was subjected to single cycle amplification, according to manufacturer’s suggestion.  First RNA was copied to cDNA using a one-cycle cDNA synthesis. RNA,

scan_protocol: according to manufacturers instructions

data_processing: MAS 5.0 signal, mean signal of 125

source_name: SC WAT, dorsal, in periischeum region

label_protocol: no label was used other than the above description of the affymetrix array methodology.  This was performed by Mr. Derek Pouchnik in the Bioinformatics Core Laboratory of Washington State University.

growth_protocol: Animals were from 24 to 28 months of age, raised on a diet formulated to meet requirements and bred at signs of first estrus (approximately 13 MOA). They calved from 24 to 28 months of age, within 60 calendar days of each ot

extract_protocol: samples were placed immediately into Trizol reagent, homogenized, and kept on ice until RNA was extracted, within 2 hours.  Total RNA was extracted with the RNeasy® Lipid Tissue Midi Kit  (Qiagen 75842, Maryland  20874).  RNA sample were resuspended in di

treatment_protocol: Animals were fed ad libitum prepartum diets that were 44 % alfalfa haylage, 44 % orchardgrass hay, and 12 % concentrate mix (80.3 % ground corn; 11.9 % SBM, 5 % molasses, and 2.8 % vitamin and mineral mixes) on a DM basis.  Postpartum, animals were fed (D

value: subcutaneous white adipose tissue, dorsal, in periischeum region

tag: parturition period

value: postpartum

tag: breed

value: Holstein


title: adipose tissue postpartum cow 382 +14 d 011708


title: adipose tissue prepartum cow 382 -30 d 011708

value: prepartum


title: BPA-to-Ctrl_#4 [mRNA]

source_name: BPA-exposed rat_#4

tag: gender

source_name: Seasame oil-exposed rat_#4


title: adipose tissue prepartum cow 387 -30 d 011708


title: SCO_11_c

description: Patient with Sertoli-cell only syndrome and AZFc deletion #4

value: AZFc

value: SCO


title: adipose tissue postpartum cow 346 +14 d 011708


title: adipose tissue postpartum cow 387 +14 d 011708


title: adipose tissue postpartum cow 360 +14 d 082407


title: BPA-to-Ctrl_#2 [mRNA]

source_name: BPA-exposed rat_#2

source_name: Seasame oil-exposed rat_#2


title: excess_prolif_ya_rep3

description: RNA was amplified


title: adipose tissue prepartum cow 384 -30 d 011708


title: adipose tissue postpartum cow 341 +14 d 082407


title: adipose tissue prepartum cow 346 -30 d 011708


title: adipose tissue prepartum cow 330 -30 d 011708


title: adipose tissue prepartum cow 347 -30 d 082407


title: BPA-to-Ctrl_#1 [mRNA]

source_name: BPA-exposed rat_#1

source_name: Seasame oil-exposed rat_#1


title: adipose tissue postpartum cow 330 +14 d 011708


title: adipose tissue prepartum cow 386 -30 d 011708


title: adipose tissue prepartum cow 360 -30 d 082407


title: adipose tissue prepartum cow 341 -30 d 082407


title: adipose tissue postpartum cow 338 +14 d 082407


title: adipose tissue postpartum cow 331 +14 d 082407


title: adipose tissue prepartum cow 338 -30 d 082407


title: adipose tissue postpartum cow 347 +14 d 082407


title: adipose tissue postpartum cow 384 +14 d 011708


title: adipose tissue prepartum cow 331 -30 d 082407


title: Caco2_NPIP_24hr40mM_rep1

city: Maastricht

first: Dennie

last: Hebels

address: Universiteitssingel 50

department: Health Risk Analysis and Toxicology

country: Netherlands

institute: Maastricht University

description: Biological replicate 1

hyb_protocol: Hybridization according to Agilent instructions.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 and Cy5 were excited at wavelengths of 532 and 635 nm, respectively. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 587 (Cy3) and 705 (Cy5) for replicates 1 and 2, and 628 (Cy3) and 560 (Cy5) for replicates 3 and 4, based on automatic establishment of ideal scan settings. The images obtained (resolution 5 micron, 16 bit tiff image) were processed with Imagene 8.0.1 software (Biodiscovery, El Segundo, USA) to measure mean signal intensities for spots and local backgrounds followed by a quality control in Microsoft Excel.

data_processing: Data preparations were performed in GenePix Pro software (version 6.0, Molecular Devices) and included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), and flagging of spots (control spots and bad spots). One raw data file was created by GenePix Pro (a GPR file) containing data from both channels (Cy3 and Cy5). LOWESS normalization, log (base=2) transformations and calculation of difference of test compound versus respective vehicle control (log2 ratios) were calculated in ArrayTrack (version 3.4).

source_name: Control for NPIP 40mM 24h

label_protocol: The Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, The Netherlands) was used to generate Cyanine (Cy) labelled cRNA according to the manufacturer’s protocol.

growth_protocol: Caco-2 cell cultures were transferred weekly by trypsinization and incubated at 37 ºC in a humidified incubator containing 5% CO2

extract_protocol: RNA was isolated from TRIzol® suspended cells according to the manufacturer’s protocol with minor modifications, followed by a clean up, using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) with DNase treatment.

treatment_protocol: Caco-2 cells were treated for 1, 6 or 24 hours with one of the following six NOC: MNNG (1μM), MNU (1mM), NDEA (50mM), NDMA (100mM), NPIP (40mM) and NPYR (100mM)

value: Human colonic adenocarcinoma cells

tag: cell line

source_name: NPIP 40mM 24h


title: Caco2_NPIP_24hr40mM_rep2

description: Biological replicate 2


title: Caco2_NPYR_24hr100mM_rep1

description: Biological replicate 1

source_name: Control for NPYR 100mM 24h

source_name: NPYR 100mM 24h


title: Caco2_NDEA_24hr50mM_rep2

description: Biological replicate 2

source_name: NDEA 50mM 24h

source_name: Control for NDEA 50mM 24h


title: Caco2_MNU_24hr1mM_rep2

description: Biological replicate 2

source_name: MNU 1mM 24h

source_name: Control for MNU 1mM 24h


title: Caco2_NDMA_24hr100mM_rep1

description: Biological replicate 1

source_name: Control for NDMA 100mM 24h

source_name: NDMA 100mM 24h


title: Caco2_NPYR_6hr100mM_rep1

description: Biological replicate 1

source_name: Control for NPYR 100mM 6h

source_name: NPYR 100mM 6h


title: Caco2_NDEA_24hr50mM_rep1

description: Biological replicate 1


title: Caco2_NPYR_24hr100mM_rep2

description: Biological replicate 2


title: Caco2_NDMA_6hr100mM_rep2

description: Biological replicate 2

source_name: NDMA 100mM 6h

source_name: Control for NDMA 100mM 6h


title: Caco2_NDEA_6hr50mM_rep2

description: Biological replicate 2

source_name: NDEA 50mM 6h

source_name: Control for NDEA 50mM 6h


title: Caco2_NDMA_6hr100mM_rep1

description: Biological replicate 1


title: Caco2_MNNG_24hr1μM_rep2

description: Biological replicate 2

source_name: MNNG 1μM 24h

source_name: Control for MNNG 1μM 24h


title: Caco2_NDMA_24hr100mM_rep2

description: Biological replicate 2


title: Caco2_MNU_6hr1mM_rep2

description: Biological replicate 2

source_name: MNU 1mM 6h

source_name: Control for MNU 1mM 6h


title: Caco2_NPIP_6hr40mM_rep2

description: Biological replicate 2

source_name: NPIP 40mM 6h

source_name: Control for NPIP 40mM 6h


title: Caco2_NDEA_6hr50mM_rep1

description: Biological replicate 1


title: Caco2_MNNG_6hr1μM_rep2

description: Biological replicate 2

source_name: MNNG 1μM 6h

source_name: Control for MNNG 1μM 6h


title: Caco2_MNNG_24hr1μM_rep1

description: Biological replicate 1


title: Caco2_MNU_6hr1mM_rep1

description: Biological replicate 1


title: Caco2_MNNG_6hr1μM_rep1

description: Biological replicate 1


title: Caco2_NPIP_6hr40mM_rep1

description: Biological replicate 1


title: wild-type Nalm6 cells vs OGFOD1 knockout Nalm6 cells

city: Okinawa

first: Masayuki

last: Matsushita

address: 207 Uehara, Nishihara

department: Molecular and Cellular Physiology

country: Japan

institute: University of Ryukyus School of Medicine

hyb_protocol: Oligo DNA and hybridization buffer (TOYOBO) were added, and the labeled aRNA hybridyzed oligo DNA microarray contining human 25K transcripts for 16 h at 37°C.(TORAY co. ltd. manufacturer's instructions)

scan_protocol: ScanArray Lite (Perkin Elmer)

data_processing: global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: Nalm6 cells, wild-type

label_protocol: Total RNA (1 microgram) was synthesized into aRNA with the amino allyl aRNA kit (Ambion). The aRNA was labeled with Cy3 monofunctional reactive dye or Cy5 monofunctional reactive dye (GE health care).

growth_protocol: Nalm6 cells were maintained in RPMI1640 medium supplemented with 10% FBS, 55 mM b-ME and 1% penicillin/streptomycine. Cells were seeded at a density of 2 x 10^6 cells / ml in 100-mm dishes.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Cells were cultured for 24h at 37°C with 5% CO2 .

tag: genotype/variation

value: wild-type

value: human lymphoblastic leukemia

source_name: Nalm6 cells, OGFOD1 KO

value: OGFOD1 knockout


title: BPDE

type: genomic

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: BPDE-MIRA vs BPDE-Input

hyb_protocol: According to standard NimbleGen Protocol

data_processing: Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean.

molecule: genomic DNA

source_name: BPDE, MIRA-enriched

growth_protocol: Early passage normal human fibroblasts, prepared from neonatal foreskin, were grown as monolayer at ~25% confluence in Dulbecco’s Modified Eagle’s Medium (DMEM) (Irvine Scientific, Santa Ana, CA) supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Genomic DNA was purified from B[a]PDE-treated versus control normal human fibroblasts using the DNeasy purification kit (Qiagen, Valencia, CA).

treatment_protocol: The culture dishes were filled with serum free DMEM, and subsequently freshly prepared B[a]PDE (1 µM) (Midwest Research Institute, Kansas City, MO) or control solvent [dimethylsulfoxide (DMSO)] were added to the media, and incubation was performed at 37°C for 20 minutes in the dark. Immediately after treatment, the cells were washed with PBS, fed with complete growth medium (DMEM plus 10% FBS), and cultivated for 3 days, after which an ensuing round of chemical treatment was carried out, as described above. When reaching approximately 90% confluency, all cultures underwent passaging (1 to 3 split) either 24- or 48 hours post chemical treatment. Three days after the 10th round of B[a]PDE treatment, the cells were harvested by trypsinization, and subjected to genomic DNA isolation using the DNeasy purification kit (Qiagen, Valencia, CA).

tag: fraction

value: methylated DNA-enriched

value: normal fibroblasts

value: BPDE

source_name: BPDE, Input

value: input


title: Caco2_MNU_24hr1mM_rep1

description: Biological replicate 1

source_name: Control for MNU 1mM 24h

source_name: MNU 1mM 24h


title: Caco2_NPYR_1hr100mM_rep2

description: Biological replicate 2

source_name: NPYR 100mM 1h

source_name: Control for NPYR 100mM 1h


title: BPDEvsControl

description: BPDE-MIRA vs Control-MIRA

scan_protocol: According to standard NimbleGen Protocol

source_name: Control, MIRA-enriched

treatment_protocol: No treatment

value: DMSO (control)


title: Control

description: Control-MIRA vs Control-Input

label_protocol: According to standard NimbleGen Protocol

source_name: Control, Input


title: Parenteral feeding 72hr 8301

source_name: Healthy Volunteer

value: Monocytes

value: Parenteral feeding 72hr


title: Caco2_NDMA_1hr100mM_rep2

description: Biological replicate 2

source_name: NDMA 100mM 1h

source_name: Control for NDMA 100mM 1h


title: Caco2_NDEA_1hr50mM_rep1

description: Biological replicate 1

source_name: Control for NDEA 50mM 1h

source_name: NDEA 50mM 1h


title: Caco2_NPIP_1hr40mM_rep1

description: Biological replicate 1

source_name: Control for NPIP 40mM 1h

source_name: NPIP 40mM 1h


title: Caco2_MNU_1hr1mM_rep1

description: Biological replicate 1

source_name: Control for MNU 1mM 1h

source_name: MNU 1mM 1h


title: Panc-1 Cells that Remained in the Cluster

city: grand rapids

first: brian

last: haab

state: MI

address: 333 bostwick avenue NE

department: lab of cancer immunodiagnostics

institute: van andel institute

hyb_protocol: Approximately 800 ng of both Cy5-labeled experimental cRNA and Cy3-labeled universal reference RNA were hybridized to each microarray (adjusting for labeling efficiency). Whole human genome 4 x 44K microarrays (Agilent) were hybridized and washed following manufacturer’s protocol.

scan_protocol: Images were captured using an Agilent DNA microarray scanner set at default settings for gene expression.

data_processing: Scanned images were processed using Feature Extractor v. 10.5.1.1. By applying a LOWESS (locally weighted linear regression) correction for dye-bias, background noise was subtracted from spot intensities. To filter the preprocessed data, genes with a background signal higher than feature signal were removed.

source_name: Pancreatic cancer cells

label_protocol: Agilent quick-amplification kit was used to amplify and label 200 ng target mRNA species to complementary RNA (cRNA) for oligo microarrays according to the manufacturer’s protocol. For each array, experimental samples (rim or core) and commercial universal reference RNA (Stratagene, La Jolla, CA) were labeled with cyanine 5-CTP and cyanine-3-CTP (Perkin Elmer, Boston, MA), respectively. The cRNA concentration and labeling efficiency was measured spectrophotometrically.

growth_protocol: To simulate a migratory front (rim) and proliferating core, five thousand pancreatic cells were seeded on a confluent circular monolayer using cell sedimentation manifolds (CSM, Inc., Phoenix, AZ) on Collagen IV coated 10-well slides. Migration was initiated by removing the manifolds 16 hours after seeding then radically dispersed for 24 hours.

extract_protocol: Stationary (core and migratory (rim), cells were harvested under and inverse microscope (Axiovert 100, Zeiss, NY) using a P20 pipette in four independent biological replicates. Forty individual dispersion assays (four 10-well slides) were collected and immediately isolated for RNA according to manufacturer’s protocol (Mirvana Total RNA Kit, Ambion, Austin, TX). Core and rim cells were separately lysed with Lysis Binding Buffer . Total RNA quantity was assessed using a NanoDrop 2000c (Thermo Scientific, Wilmington, DE), and quality was assessed by Bioanalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies, Palo Alto, CA).

value: Pancreatic cancer cells

tag: cell migration

value: Remained in the Cluster


title: Panc-1 Cells that Migrated Away from the Cluster

value: Migrated Away from the Cluster

source_name: commercial universal reference RNA (Stratagene, La Jolla, CA)


title: Caco2_NDEA_1hr50mM_rep2

description: Biological replicate 2


title: Caco2_NPYR_1hr100mM_rep1

description: Biological replicate 1


title: Strain LR157 (two biological replicates)

city: Seattle

first: Lakshmi

last: Rajagopal

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

description: 071112 Sagal A909 EXP X4, 1978 genes, 18 probes/target, 4 X 72000 probes, 2 replicates, NC_007432

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

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

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

organism: Streptococcus agalactiae

source_name: A909 DrgfC/A

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol using Cy3. See www.nimblegen.com.

growth_protocol: Total prokaryotic RNA was extracted from exponential phase (O.D 600nm=0.6) cultures of Streptococcus agalactiae WT A909 or the isogenic mutant that were grown in Tryptic Soy Broth at 37C. Two biological replicates of each strain were used on two four plex chips, with average values reported here.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at both Seattle Childrens Research Institute and Nimblegen.

tag: strain

value: rgfC/A deletion mutant


title: Caco2_NPIP_1hr40mM_rep2

description: Biological replicate 2


title: Strain LR154 (two biological replicates)

source_name: A909 Dstp1

value: stp1 deletion mutant


title: Caco2_NDMA_1hr100mM_rep1

description: Biological replicate 1


title: Caco2_MNNG_1hr1μM_rep2

description: Biological replicate 2

source_name: MNNG 1μM 1h

source_name: Control for MNNG 1μM 1h


title: MiaPaCa-2 Cells that Migrated Away from the Cluster

value: commercial universal reference RNA (Stratagene, La Jolla, CA)


title: Caco2_MNNG_1hr1μM_rep1

description: Biological replicate 1

value: Human colonic adenocarcinoma cells


title: MiaPaCa-2 Cells that Remained in the Cluster


title: Strain WT A909 (two biological replicates)

source_name: A909 WT

value: wild type


title: Caco2_MNU_1hr1mM_rep2

description: Biological replicate 2


title: 982_Synovial biopsy_before infliximab treatment

status: Public on Apr 28 2010

city: Stockholm

first: Johan

last: Lindberg

address: Roslagstullsbacken 21, Floor 3

institute: Royal Institute of Technology

hyb_protocol: The slides were prehybridized for 30 minutes at 42°C in pre-hybridization buffer consisting of 1% BSA (Sigma-Aldrich), 5× SSC and 0.1% SDS. Fragmentation was performed after labeling of the aRNA with RNA fragmentation reagents AM870 (Applied Biosystems) yielding aRNA fragment sizes of 60 – 200 nucleotides. The cy5 and cy3 labeled aRNA were then pooled in equivalent amounts and mixed with the hybridization buffer consisting of 5x SSC, 25% formamide (Sigma-Aldrich, St. Louis, MO) 0.1% SDS, 25% Kreablock (Kreatech Diagnostics), 10 ug herring sperm DNA (Invitrogen, Carlsbad, CA) and 10 ug yeast tRNA (Invitrogen). The hybridization mixture was then heat denatured in 70°C for 3 minutes and subsequently put on ice until injection in a MAUI hybridization mixer (Biomicro, Salt Lake City, UT). The hybridization was performed over night in the MAUI hybridization station (Biomicro) in which the hybridization mixture is stirred to increase sensitivity and specificity. After hybridization the slides were washed once for 5 minutes at 42°C in wash buffer 1 (2 × SSC, 0.1% SDS), once for 5 minutes in wash buffer 2 (0.1 × SSC, 0.1% SDS) and five times, for 1 minute each, in wash buffer 3 (0.1 × SSC).

scan_protocol: The microarrays were scanned using the Agilent G2565BA scanner (Agilent Technologies, Palo Alto, CA) with scanner resolution set at 10 µm and the feature intensities were extracted using the GenePix 5.1.0.0 software (Axon Instruments, Sunnyvale, CA).

data_processing: After the result files (gpr) produced by GenePix had been imported into R, unreliable spots with abnormal physical properties were removed with four filters: 1. filterFlags, which removes spots flagged as not found or absent in GenePix. 2. filterSaturated, which removes spots saturated in both cy5 and cy3. 3. filterB2SD, which removes spots in which 70% of the pixels have below background intensity + 2 standard deviations. 4. filterSize, which removes spots that are enlarged due to spotting artefacts. After filtering, the slides were normalized with print-tip loess (local regression) normalization. SAM (Significance Analysis of Microarrays), available as the samr package in R, was applied to identify differentially expressed (DE) genes. Since SAM does not allow for blocking, the LIMMA (Linear Models for Microarray Data) package, present in Bioconductor, was applied to control for the effect of ectopic lymphocyte aggregates when comparing responders. Hierarchical clusters were performed using 1 – the Pearson correlation as the distance measure. Enrichment analysis was carried out to identify biological themes in groups of relevant genes using the the Gene Ontology and KEGG databases. PAGE (Parametric Analysis of Gene set Enrichment) was also used to test for significant pathways/categories between response groups in the above-mentioned databases. FDR was used to correct for multiple testing in all enrichment/pathway analyses. In all tests using the FDR, a q-value (the FDR analog of a p-value) < 0.05 was used as a cut-off for statistical significance. A two-sided binomial exact test was used to test for overrepresentation of lymphoid aggregates within response groups assuming a 0.5 chance of having an aggregate or not.

source_name: Synovium_before infliximab treatment

label_protocol: Labeling was performed with the ULS aRNA Fluorescent Labeling Kit (Kreatech Diagnostics, the Netherlands) that allows for labeling of unmodified aRNA. 2 ug was used as input in the labeling reaction.

extract_protocol: All patients underwent synovial tissue sampling at the Academical Medical Center/University of Amsterdam by needle arthroscopy of an actively inflamed joint (knee, ankle or wrist), performed under local anesthesia. Biopsy specimens were obtained with a 2-mm grasping forceps (Storz, Tuttlingen, Germany) from 6 or more sites within the joint to minimize sampling error. The biopsy specimens (15-50 mg) were snap frozen in liquid nitrogen and homogenised in 1 ml RNA-STAT 60TM reagent (Tel-Test, Friendswood, TX). RNA was extracted with TRIzol reagent and the FAST TRACK 2.0 kit (Invitrogen, Carlsbad, CA). The quality was assured by measuring the OD260/280 ratio using a Thermo Scientific NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE). Samples with a ratio >1.8 were used. A separate block of at least 6 synovial tissue samples from the same patients was snap frozen and assessed for the presence of lymphocyte aggregates. The RNA was amplified with the RiboAmp II kit (Applied Biosystems, Foster City, CA). 500 ng of total RNA was used as input for the amplification for all except 7 patients. For these patients 300 - 500 ng was used due to low yield in the RNA extraction step. RNA from 18 good responding, 30 moderate responding and 14 non-responding patients was successfully amplified and subsequently labeled for hybridization.

treatment_protocol: Patients were treated with infliximab. Infliximab was given in a dosage of 3 mg/kg intravenously at baseline, week 2, 6, and subsequently every 8 weeks. The DAS28 was assessed at baseline, week 4, 8, 12, and 16 by skilled research nurses. Clinical response was evaluated according to the EULAR (European League Against Rheumatism) response criteria at week 16 after initiation of infliximab treatment.

value: Synovial tissue

tag: disease status

value: rheumatoid arthritis (RA)

tag: eular response criteria, assessed at week 16 after treatment (no response = 0, moderate response = 1, good response = 2).

tag: presence of large lymphocyte aggregates (0 = negative, 1 = positive, na = not evaluated for this individual)

tag: presence of small lymphocyte aggregates (0 = negative, 1 = positive, na = not evaluated for this individual)

source_name: Stratagene Universal reference

value: A mixture of various cell lines from various tissues from Homo sapiens


title: 984_Synovial biopsy_before infliximab treatment

tag: tissue


title: 957_Synovial biopsy_before infliximab treatment


title: 772_Synovial biopsy_before infliximab treatment


title: 688_Synovial biopsy_before infliximab treatment


title: 597_Synovial biopsy_before infliximab treatment


title: 581_Synovial biopsy_before infliximab treatment


title: 677_Synovial biopsy_before infliximab treatment


title: 632_Synovial biopsy_before infliximab treatment


title: 985_Synovial biopsy_before infliximab treatment


title: 397_Synovial biopsy_before infliximab treatment


title: 578_Synovial biopsy_before infliximab treatment


title: 596_Synovial biopsy_before infliximab treatment


title: 618_Synovial biopsy_before infliximab treatment


title: 576_Synovial biopsy_before infliximab treatment


title: 638_Synovial biopsy_before infliximab treatment


title: 660_Synovial biopsy_before infliximab treatment


title: 637_Synovial biopsy_before infliximab treatment


title: 653_Synovial biopsy_before infliximab treatment


title: 689_Synovial biopsy_before infliximab treatment


title: 664_Synovial biopsy_before infliximab treatment


title: 964_Synovial biopsy_before infliximab treatment


title: 391_Synovial biopsy_before infliximab treatment


title: 631_Synovial biopsy_before infliximab treatment


title: 580_Synovial biopsy_before infliximab treatment


title: MCF-7_1 [MeDIP-chip]

description: meDIP-chip MCF-7 cells with 5-methyl cytidine antibodies

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.  The intensity ratio of the mDIP-chip sample to total DNA was plotted genomic position to identify regions of enrichment.  P-values files were generated from the scaled log2-ratio data to test positive enrichement of DNA methylation for each probe against all probes on the array.  Peak files identifying regions of DNA methylation were generated from the P-value files and the enriched peaks were then mapped to the transcription start site of each gene.

source_name: methylated ChIP DNA from MCF-7 cells

label_protocol: Every sample was hybridized with MeDIP sample (Cyanine-5 dye) and sonicated genomic DNA (Cyanine-3 dye).

extract_protocol: Methylated DNA from MCF7 cells was prepared according to the protocol published by Schubeler and coworkers (Weber et al. 2005). Briefly, high-quality genomic DNA was sheared to 300 bp (fragment size ranging from 200-600 bp) using Bioruptor. Fragmented DNA was heat denatured to produce single-stranded DNA to enhance the immunoselection step. Antibodies against 5-methyl cytidine (MAb-335MEC-500; Monoclonal Methyl DNA IP-grade; 1 μg/μl; Diagenode) were complexed to the magnetic beads (pan-mouse IgG Dynal Beads, Invitrogen). The immunoprecipitated methylated DNA fragments were processed by the NimbleGen Methylation Microarray Service (NimbleGen Systems, Inc. Madison, WI). Methylation analysis was performed on the NimbleGen Two-Array HG18 Promoter Set.

value: MCF-7 breast cancer cell line

tag: antibody

value: anti-5-methyl cytidine (MAb-335MEC-500; Monoclonal Methyl DNA IP-grade; 1 μg/μl; Diagenode)

source_name: input DNA from MCF-7 cells


title: 568_Synovial biopsy_before infliximab treatment


title: 348_Synovial biopsy_before infliximab treatment


title: 374_Synovial biopsy_before infliximab treatment


title: 377_Synovial biopsy_before infliximab treatment


title: 335_Synovial biopsy_before infliximab treatment


title: Caco2_NPYR_6hr100mM_rep2

description: Biological replicate 2

source_name: NPYR 100mM 6h

tag: cell type

source_name: Control for NPYR 100mM 6h


title: 380_Synovial biopsy_before infliximab treatment


title: 338_Synovial biopsy_before infliximab treatment


title: 315_Synovial biopsy_before infliximab treatment


title: 369_Synovial biopsy_before infliximab treatment


title: 316_Synovial biopsy_before infliximab treatment


title: 299_Synovial biopsy_before infliximab treatment


title: 303_Synovial biopsy_before infliximab treatment


title: 310_Synovial biopsy_before infliximab treatment


title: 343_Synovial biopsy_before infliximab treatment


title: 311_Synovial biopsy_before infliximab treatment


title: 333_Synovial biopsy_before infliximab treatment


title: 319_Synovial biopsy_before infliximab treatment


title: 300_Synovial biopsy_before infliximab treatment


title: 332_Synovial biopsy_before infliximab treatment


title: 305_Synovial biopsy_before infliximab treatment


title: 334_Synovial biopsy_before infliximab treatment


title: 313_Synovial biopsy_before infliximab treatment


title: 301_Synovial biopsy_before infliximab treatment


title: 324_Synovial biopsy_before infliximab treatment


title: 320_Synovial biopsy_before infliximab treatment


title: 302_Synovial biopsy_before infliximab treatment


title: 291_Synovial biopsy_before infliximab treatment


title: 292_Synovial biopsy_before infliximab treatment


title: MCF-7_2 [MeDIP-chip]


title: 283_Synovial biopsy_before infliximab treatment


title: 260_Synovial biopsy_before infliximab treatment


title: 254_Synovial biopsy_before infliximab treatment


title: 569_Synovial biopsy_before infliximab treatment


title: 253_Synovial biopsy_before infliximab treatment


title: 237_Synovial biopsy_before infliximab treatment


title: 248_Synovial biopsy_before infliximab treatment


title: 247_Synovial biopsy_before infliximab treatment


title: 146_Synovial biopsy_before infliximab treatment


title: NT-7

status: Public on Apr 27 2010

city: Boston

first: Matthias

last: Stadtfeld

state: MA

address: 185 Cambridge Street

institute: MGH

hyb_protocol: Biotinylated cRNA was cleaned up, fragmented and hybridized to GeneChip HT Array Plates (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip H Scanner (Affymetrix).

data_processing: Normalization of the array data was done using the "mean normalize" function in GeneSifter.

source_name: NT-ESC from iPSC-7, subclone 1

label_protocol: Biotinylated cRNA was prepared from total RNA using the GeneChip HT IVT Labeling Kit (Affymetrix).

growth_protocol: All cells were cultured in standard ESC media (15% FBS, LIF) on irradiated MEFs.

extract_protocol: Total RNA was extracted using the QIAGEN miRNeasy kit.

treatment_protocol: Cells were trypsinized and preplated for 45 minutes to remove MEFs.

tag: origin

value: cloned blastocyst

value: embryonic stem cell


title: Adeno-2

source_name: Adeno-iPSC, clone 2

value: fetal liver

value: induced pluripotent stem cell


title: NT-8

source_name: NT-ESC from iPSC-15, subclone 1


title: NT-4

source_name: NT-ESC from Adeno-2, subclone 1


title: NT-9

source_name: NT-ESC from iPSC-15, subclone 2


title: iPSC-49

source_name: iPSC, clone 49

value: TTFs, chimera 2