title: 13832677 - Col0 N3 vs ss4c N3

hyb_protocol: ss4c N3 Cy5 / Col0 N3 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: 13832683 - Col0 N3 vs ss3 N3

status: Public on May 12 2011

type: RNA

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves.

hyb_protocol: ss3 N3 Cy5 / Col0 N3 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 in R version 2.8.1 (2008-12-22) (ISBN 3-900051-07-0). 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: ss3 N3

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: rosette - Media: peat-based compost Hygrometry: approximately 60% during the day Temperature: 22°C during the day/ 17°C during the night Light: 16h light

treatment_protocol: no treatment

tag: ecotype

tag: genotype/variation

value: mutant (ss3-)

tag: age

source_name: Col0 N3

extract_protocol: Col0 N3:18ug.

value: wild type


title: 13832676 - ss4c N2 vs Col0 N2

hyb_protocol: Col0 N2 Cy5 / ss4c N2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 N2

source_name: ss4c N2

extract_protocol: ss4c N2:20ug.

value: mutant (ss4-)


title: 13832690 - Col0 N3 vs ss3-ss4 N3

hyb_protocol: ss3-ss4 N3 Cy5 / Col0 N3 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: ss3-ss4 N3

value: mutant (ss3- ss4-)


title: 13832667 - ss4c D3 vs Col0 D3

hyb_protocol: Col0 D3 Cy5 / ss4c D3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 D3

source_name: ss4c D3


title: 13832673 - Col0 N1 vs ss4c N1

hyb_protocol: ss4c N1 Cy5 / Col0 N1 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: ss4c N1

source_name: Col0 N1

extract_protocol: Col0 N1:11ug.


title: 13832663 - Col0 D3 vs ss3-ss4 D3

hyb_protocol: ss3-ss4 D3 Cy5 / Col0 D3 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: ss3-ss4 D3


title: 13832664 - ss3-ss4 D3 vs Col0 D3

hyb_protocol: Col0 D3 Cy5 / ss3-ss4 D3 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: 13832659 - ss3-ss4 D1 vs Col0 D1

hyb_protocol: Col0 D1 Cy5 / ss3-ss4 D1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 D1

source_name: ss3-ss4 D1


title: 13832670 - ss3-ss4 D2 vs Col0 D2

hyb_protocol: Col0 D2 Cy5 / ss3-ss4 D2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 D2

source_name: ss3-ss4 D2


title: 13832674 - ss4c N1 vs Col0 N1

hyb_protocol: Col0 N1 Cy5 / ss4c N1 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: 13832658 - Col0 D1 vs ss3-ss4 D1

hyb_protocol: ss3-ss4 D1 Cy5 / Col0 D1 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: 13832657 - ss3 D2 vs Col0 D2

hyb_protocol: Col0 D2 Cy5 / ss3 D2 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: ss3 D2


title: 13832675 - Col0 N2 vs ss4c N2

hyb_protocol: ss4c N2 Cy5 / Col0 N2 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: 13832652 - Col0 D1 vs ss3 D1

hyb_protocol: ss3 D1 Cy5 / Col0 D1 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: ss3 D1

extract_protocol: ss3 D1:6ug.


title: 13832656 - Col0 D2 vs ss3 D2

hyb_protocol: ss3 D2 Cy5 / Col0 D2 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: 13832654 - Col0 D2 vs ss4c D2

hyb_protocol: ss4c D2 Cy5 / Col0 D2 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: ss4c D2


title: Double-sided 42 day

city: Nagoya

first: Tatsuhiko

last: Kadowaki

address: Chikusa

country: Japan

institute: Nagoya University

description: no additional information

hyb_protocol: After purification, Cy3-labeled cRNA (2 µg) was fragmented and applied to a pre-hybridized microarray slide, and then hybridized for 17 h at 65°C.  Arrays were sequentially washed with Agilent Gene Expression washing buffer 1 and 2, and then dried.

scan_protocol: They were scanned with an Agilent Technologies Microarray Scanner, and then the intensity of each spot was quantified using a Feature Extraction 9.5.3.1 (Agilent Technologies).

data_processing: Background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA) including a quantile normalization (all arrays are considered to have an equal intensity distribution). Partek Genomic Suite 6.5 software.

organism: Apis mellifera

source_name: Honey bee samples at 42 days after the installation of the double-sided entrance hive into strawberry greenhouse

label_protocol: RNA (0.2 µg) was used for cDNA synthesis followed by cRNA labeling and amplification with a Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Honey bees in hives put into greenhouses

extract_protocol: Total RNA was isolated from 50 honey bees with Trizol reagent.

treatment_protocol: Honey bee samples were immediately frozen with dry ice at collection sites.

tag: tissue

value: whole body

tag: hive

value: double-sided entrance hive

tag: greenhouse

value: strawberry greenhouse

tag: time

value: 42 days


title: 13832665 - ss4c D2 vs Col0 D2

hyb_protocol: Col0 D2 Cy5 / ss4c D2 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: Standard 70 day

description: no additional information

source_name: Honey bee samples at 70 days after the installation of the standard hive into strawberry greenhouse

value: standard hive

value: 70 days


title: 13832653 - ss3 D1 vs Col0 D1

hyb_protocol: Col0 D1 Cy5 / ss3 D1 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: 13832666 - Col0 D3 vs ss4c D3

hyb_protocol: ss4c D3 Cy5 / Col0 D3 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: Double-sided 70 day

description: no additional information

source_name: Honey bee samples at 70 days after the installation of the double-sided entrance hive into strawberry greenhouse


title: 13832651 - ss4c D1 vs Col0 D1

hyb_protocol: Col0 D1 Cy5 / ss4c D1 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: ss4c D1


title: 13832660 - Col0 D2 vs ss3-ss4 D2

hyb_protocol: ss3-ss4 D2 Cy5 / Col0 D2 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: Eggplant #4 70day

description: no additional information

source_name: Honey bee samples at 70 days after the installation of the hive #4 into eggplant greenhouse

value: hive #4

value: eggplant greenhouse


title: Standard 0 day

description: no additional information

source_name: Honey bee samples prior to the installation of the standard hive into strawberry greenhouse

value: prior to installation


title: Double-sided 0 day

description: no additional information

source_name: Honey bee samples prior to the installation of the double-sided entrance hive into strawberry greenhouse


title: Eggplant #4 42 day

description: no additional information

source_name: Honey bee samples at 42 days after the installation of the hive #4 into eggplant greenhouse


title: Standard 42 day

description: no additional information

source_name: Honey bee samples at 42 days after the installation of the standard hive into strawberry greenhouse


title: Eggplant #4 14 day

description: no additional information

source_name: Honey bee samples at 14 days after the installation of the hive #4 into eggplant greenhouse

value: 14 days


title: Eggplant #4 0 day

description: no additional information

source_name: Honey bee samples prior to the installation of the hive #4 into eggplant greenhouse


title: R1881-treated 24h RWPE-1-AR cells, biological rep3

city: OULLINS

first: Virginie

last: Vlaeminck-Guillem

address: Chemin du Grand Revoyet

department: Faculté de Médecine Lyon Sud

institute: Institut de Génomique Fonctionnelle de Lyon

description: Gene expression data from RWPE-1-AR cell line treated wih R1881for 24h

hyb_protocol: 15 ug of cRNA were hybridized according to the Affymetrix protocol (Expression Analysis Technical Manual, 2008, Affymetrix) using the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: 24h 1nM R1881-treated RWPE-1-AR cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: RWPE-1-AR cells were maintained in keratinocyte growth medium (Invitrogen 17005-042) supplemented with rEGF (recombinant epithelial growth factor) and BPE (bovine pituary extract) (Invitrogen 37000015) at 37°C, 5%CO2.

extract_protocol: Total RNA were extracted using Rneasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: RWPE-1-AR cells were stimulated with a non-metabolisable androgen, R1881, in the growth medium deprived of BPE for 48h.

tag: celll line

tag: treatment protocol

value: RWPE-1-AR prostatic cell line was steroid-depleted for 48h and treated with 1nM R1881 for 24h


title: Control RWPE-1-AR cells at 24h, biological rep3

description: Gene expression data from RWPE-1-AR cell line treated wih vehicle for 24h (control).

source_name: Control RWPE-1-AR cells at 24h

value: RWPE-1-AR prostatic cell line was steroid-depleted for 48h and treated with vehicle (ethanol) for 24h


title: R1881-treated 24h RWPE-1-AR cells, biological rep2


title: 13832650 - Col0 D1 vs ss4c D1

hyb_protocol: ss4c D1 Cy5 / Col0 D1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col0 D1


title: R1881-treated 24h RWPE-1-AR cells, biological rep1


title: Control RWPE-1-AR cells at 24h, biological rep1


title: Eggplant #3 0 day

description: no additional information

source_name: Honey bee samples prior to the installation of the hive #3 into eggplant greenhouse

value: hive #3


title: Control RWPE-1-AR cells at 24h, biological rep2


title: Eggplant #3 70day

description: no additional information

source_name: Honey bee samples at 70 days after the installation of the hive #3 into eggplant greenhouse


title: Eggplant #3 42 day

description: no additional information

source_name: Honey bee samples at 42 days after the installation of the hive #3 into eggplant greenhouse


title: Eggplant #3 14 day

description: no additional information

source_name: Honey bee samples at 14 days after the installation of the hive #3 into eggplant greenhouse


title: NSCB_CGH_12x135K_369_hFIB2

type: genomic

city: Madison

first: Melodee

last: Patterson

state: WI

address: 510 Charmany Dr Ste 58 & 59

country: USA

institute: WiCell

hyb_protocol: Step 1. Prepare the Samples 1. Set the Hybridization System to 42°C. With the cover closed, allow at least 3 hours for the temperature to stabilize. 2. Resuspend the dried sample pellet in 3.3 ul Sample Tracking Control. Use a unique STC to resuspend each sample to be hybridized. Record which STC is used for each sample. If you are not using Sample Tracking Controls, resuspend the dried sample pellet in the equivalent volume of water. 3. Vortex well and spin to collect contents in bottom of the tube. 4. Using components from a NimbleGen Hybridization Kit, prepare the hybridization solution master mix - 88.5 ul of 2x Hybridization Buffer (vial 1), 35.4 ul of  Hybridization Component A (vial 2), 3.6 ul of Alignment Oligo (vial 3).  The amount listed is sufficient to hybridize all arrays on one slide. To hybridize multiple slides, adjust the amounts accordingly. 5. Add 8.7 ul of hybridization solution to each sample pair. 6. Vortex well (approximately 15 seconds) and spin to collect contents in bottom of the tube. Incubate at 95°C for 5 minutes, protected from light. 7. Place tubes at 42°C (in the Hybridization System sample block or heat block) for at least 5 minutes or until ready for sample loading. Vortex and spin prior to loading. Step 2. Prepare Mixers 1. Locate an HX12 mixer. Remove from its package. For best results, use a compressed gas nozzle to gently blow compressed nitrogen or argon gas across the mixer and slide to remove any dust or debris. The use of canned aerosol compressed air for this purpose is not recommended and could compromise array and data quality. Load samples within 30 minutes of opening the vacuum-packaged mixer to prevent the formation of bubbles during loading and/or hybridization. 2. Position the Precision Mixer Alignment Tool (PMAT) with its hinge on the left. Open the PMAT. 3. Snap the mixer onto the two alignment pins on the lid of the PMAT with the tab end of the mixer toward the inside hinge and the mixer’s adhesive gasket facing outward. 4. While pushing back the plastic spring with a thumb, place the slide in the base of the PMAT so that the barcode is on the right and the corner of the slide sits against the plastic spring. The NimbleGen logo and barcode number should be readable. Remove your thumb and make sure the spring is engaging the corner of the slide and the entire slide is registered to the edge of the PMAT to the rightmost and closest to you. In addition, be sure that the slide is lying flat against the PMAT. Gently blow compressed nitrogen or argon gas across the mixer and slide to remove dust. Take care to align the slide correctly in the PMAT. Incorrectly aligned slides may result in inaccurate attachment of the mixer and may affect the array features, or may not fit well into the Mixer Disassembly Tool used to remove the mixers after hybridization. 5. Using forceps, remove the backing from the adhesive gasket of the mixer and close the lid of the PMAT so that the gasket makes contact with the slide. 6. Lift the lid by grasping the long edges of the PMAT while simultaneously applying pressure with a finger through the window in the lid of the PMAT to free the mixer-slide assembly from the alignment pins. 7. Remove the mixer-slide assembly from the PMAT. 8. Place the mixer-slide assembly on the back of a 42°C heating block for 5 minutes to facilitate adhesion of the mixer to the slide. 9. Rub the Mixer Brayer over the mixer with moderate pressure to adhere the adhesive gasket and remove any bubbles. For HX12 mixers, first use a corner of the Mixer Brayer to rub the borders between the arrays and then rub around the outside of the arrays. The adhesive gasket will become clear when fully adhered to both surfaces. 10. Place the mixer-slide assembly in the slide bay of the Hybridization System. Step 3. Load & Hybridize Samples 1. Keep the following in mind before loading sample: • When pipetting the sample before loading, leave residual volume in the sample tube to avoid introducing bubbles. The volumes listed in the table below allow for this residual volume. • After aspirating the designated sample volume, inspect the pipette tip for air bubbles. Dispense and reload the pipette if bubbles exist. Keep the following in mind when loading sample: • Keep the pipette tip perpendicular to the slide to avoid possible leakage at the fill port. • Apply gentle pressure of the tip into the port to ensure a tight seal while loading the sample. 2. Using the appropriate Gilson Microman pipette, slowly dispense the appropriate sample volume into the fill port. Load samples and seal mixer ports as described below for each array format: •For 12x135K arrays: a. Load 6 ul using a CP10 Pipette tip into a fill port. Due to the close proximity of the fill and vent ports, do not overfill the arrays. Load sample until it enters the vent port channel. Do not allow sample to come to the surface of the HX12 mixer. Dry any overflow from the fill and vent ports with a cotton swab after loading the array. It is not unusual for small bubbles to form in the corners of the mixer-slide assembly during loading. These bubbles will dissipate upon mixing and will not compromise the data. b. Use one mixer port seal to cover both the fill and vent ports on the mixers, filling and sealing one chamber at a time. Press the mixer port seal, using uniform pressure across the seal to adhere. Mixer port seals are now used to seal fill and vent ports on HX12 mixers instead of mixer multi-port seals. c. Use forceps to press the mixer port seal around the fill and vent ports to ensure it is adhered in those areas. 4. Close the bay clamp. 5. Turn on the Mixing Panel on the Hybridization System, set the mix mode to B, and press the mix button to start mixing. Confirm that the Hybridization System recognizes the slide in each occupied bay (its indicator light becomes green). 6. Approximately 10 minutes after starting the Hybridization System: • Ensure the mix mode is set to B. • Ensure a green light is displayed for all occupied stations. 7. Hybridize sample at 42°C to the array(s) for the following incubation times: • For  12x135K arrays: 40 - 72 hours Roche NimbleGen has found that longer hybridization times result in higher signal-to-noise ratios, which may be beneficial for some experiments. 7.11. Array Washing 7.11.1. Turn on GenePix 4000B to warm up lasers prior to beginning wash procedure. 7.11.2. Disassemble and wash arrays according to NimbleGen™ Arrays User Guide (CGHv Analysis v5.0) with the following exceptions: 7.11.2.1. Heat both Wash Buffer I solutions to 42ºC. 7.11.2.2. Agitate array in Wash Buffer I for 3 minutes. 7.11.2.3. Follow 1 minute agitation in Wash Buffer 2 with a 2 minute incubation. 7.11.3. Perform washes protecting arrays from light and ozone. 7.11.4. Place array in corresponding case and wrap case in aluminum foil. 7.11.4.1. Label with CGH number. 7.11.5. Scan arrays immediately after washing (ref: SOP-CH-309). 7.12. Array Storage 7.12.1. Store scanned arrays in the dessicator.

scan_protocol: NimbleGen scan protocol

data_processing:
1. Image extraction: NimbleScan provided by NimbleGen is used to extract signal data from image files (*.TFF). Signals from the scan for Cy3 (green channel) are saved in a file named as chipID_532.pair while signals from the scan for Cy5 (red channel) are saved in a file named as chipID_635.pair.
2. Normalization: Signals from Cy3/Cy5 channels are transformed by logarithms to base 2 and normalized with loess or qspline (Workman et al., 2002) algorithms by R to resolve the systematic errors and bias introduced by the microarray experimental platform. The log ratios of the signals are obtained by subtracting the log transformed signals from one channel by the corresponding ones from another channel.
3. Data smoothing and break-points identification: Ratios of the normalized data are plotted by the corresponding genome locations. The data are smoothed by an adaptive weights smoothing algorithm (GLAD R-package, Wang et al., 2005), break-points are identified by a binary segmentation algorithm (DNAcopy R-package, Olshen et al., 2004) or by the segmentation algorithm available within Nimbelgen’s Nimblescan software.
4. Data visualization: CGH results can be saved as SignalMap GFF files and can be visualized by SignalMap provided by NimbleGen. CGH results can also be visualized by other software, such as aCGHViewer (Shankar et al., 2006), CHARMView (Myers et al., 2005), etc. However, different software requires different input format.

molecule: genomic DNA

source_name: hFIB2-iPS4 p50 DNA579

label_protocol:
7.7. Labeling
7.7.1. Cy3/Cy5 Labeling
7.7.1.1. Verify that the DNA concentration is between 25 and 30ng/ul for all test and reference samples.
7.7.1.2. Thaw the Cy3/Cy5 random nonamers on ice, protected from light.
7.7.1.3. Add 1μg of sonicated test DNA to 40 μl Cy3 dye. Bring to volume in 80 μl VWR water. Repeat for all test samples to be labeled.
7.7.1.4. Add 1 μg of sonicated reference DNA to 40 μl Cy5 dye. Bring to volume in 80 μl VWR water. Repeat for all reference samples to be labeled.
7.7.1.5. Vortex and quickly centrifuge test and reference DNA samples.
7.7.1.6. Incubate samples for 10 minutes at 98ºC protecting from light.
7.7.1.7. Rapidly transfer samples to an ice-water bath for 5 minutes protecting from light.
7.7.1.8. Prepare 20μl of the following aha-dNTP/Klenow Master Mix for each test and reference sample.
7.7.1.8.1. aha-dNTP/Klenow Master Mix per Sample
7.7.1.8.1.1. Thaw all reagents and aha-dNTP/Klenow master mix on ice.
7.7.1.8.1.2. Add 9μl VWR water to 0.2ml PCR tube.
7.7.1.8.1.3. Add 10μl 50X aha-dNTP Mix.
7.7.1.8.1.4. Add 1μl Klenow (50U/μl). DO NOT vortex. Total amount of solution is 20μl.
7.7.1.9. Add 20μl of the aha-dNTP/Klenow Master Mix to each of the cooled samples. Keep on ice.
7.7.1.10. Pipette to mix (15 times). DO NOT vortex.
7.7.1.11. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.12. Incubate the samples for 2 hours 15 minutes at 37°C in thermocycler protected from light.
7.7.1.13. Remove samples from thermocycler, keep at room temperature. Heat thermocycler to 98ºC. Place samples back into thermocycler and incubate for 10 minutes at 98ºC.
7.7.1.14. Rapidly transfer samples to an ice-water bath for 5 minutes protecting samples from light.
7.7.1.15. Add 1 μl of Klenow (50U/μl) to each sample.
7.7.1.16. Pipette to mix (15 times). DO NOT vortex.
7.7.1.17. Briefly centrifuge samples using a tabletop centrifuge.
7.7.1.18. Place samples in thermocycler at 37ºC for overnight amplification.
7.7.2. First DNA Precipitation
7.7.2.1. Set Roche Nimblegen Hybridization System 12 to 48ºC if proceeding to hybridization in the same day to allow for at least 3 hours of stabilization.
7.7.2.2. Cool centrifuge to 4ºC.
7.7.2.3. Add 10μl of 0.5M EDTA to each sample to stop the overnight amplification reaction.
7.7.2.4. Add 11.5 μl of 5M NaCl to each sample, then vortex for 10 seconds.
7.7.2.5. Briefly centrifuge samples using a tabletop centrifuge.
7.7.2.6. Transfer each sample into a 1.5ml tube containing 200 μl of isopropanol.
7.7.2.7. Vortex samples for 20 seconds.
7.7.2.8. Incubate at room temperature for 10 minutes, protected from light.
7.7.2.9. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.2.10. Aspirate supernatant.
7.7.2.11. Rinse pellet with 500μl of 80% ice-cold ethanol. As you rinse, gently wash pellet from tube wall.
7.7.2.12. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.2.13. Aspirate supernatant.
7.7.2.14. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.2.15. Proceed to Alexa Fluor Labeling or store labeled samples at -20°C, protected from light.
7.7.2.15.1. Frozen samples are stable for up to 2 weeks at -20ºC.
7.7.3. Alexa Fluor Labeling
7.7.3.1. Thaw one vial of Alexa Fluor 555 dye per Cy3-labeled test DNA sample on ice. Keep protected from light.
7.7.3.2. Thaw one vial of Alexa Fluor 647 dye per Cy5-labeled reference DNA sample on ice. Keep protected from light.
7.7.3.3. Thaw Alexa Fluor Labeling Buffer on ice.
7.7.3.4. Add 5 μl VWR water to each DNA sample.
7.7.3.5. Place samples in thermocycler at 42ºC for 5 minutes.
7.7.3.6. Add 3 μl Labeling Buffer to each DNA sample.
7.7.3.7. Vortex and quickly centrifuge DNA samples.
7.7.3.8. Add 2 μl DMSO to one of the vials of Alexa Fluor dye (either 555 or 647).
7.7.3.9. Vortex for 10 seconds to dissolve Alexa Fluor dye.
7.7.3.10. Immediately add 8 μl of corresponding DNA to the dissolved dye.
7.7.3.11. Pipette up and down to further dissolve dye pellet, replace lid and vortex briefly to mix.
7.7.3.12. Incubate at room temperature, protected from light for 1 hour.
7.7.3.13. Repeat steps 7.7.3.8.-7.7.3.12 for each Cy-labeled DNA to be labeled with Alexa Fluor dyes.
7.7.4. Second DNA Precipitation
7.7.4.1. Add 100 μl VWR water to each labeled DNA sample.
7.7.4.2. Add 11.5 μl of 5M NaCl to each sample.
7.7.4.3. Vortex for 10 seconds.
7.7.4.4. Briefly centrifuge samples using a tabletop centrifuge.
7.7.4.5. Transfer each sample into 1.5ml tubes containing 200 μl each of isopropanol.
7.7.4.6. Vortex samples for 20 seconds.
7.7.4.7. Incubate at room temperature for 10 minutes, protected from light.
7.7.4.8. Centrifuge at 13,000 rpm 4ºC for 10 minutes.
7.7.4.9. Aspirate supernatant.
7.7.4.10. Add 500μl of 80% ice-cold ethanol to the pellet and gently wash pellet from tube wall by pipetting.
7.7.4.11. Centrifuge at 13,000 rpm 4ºC for 2 minutes.
7.7.4.12. Aspirate supernatant.
7.7.4.13. Dry contents in a SpeedVac with tube lids open on ‘low’ heat until dry (5-15 minutes), protected from light. Close lids when dried.
7.7.4.14. Proceed to ‘Specific Activity Calculation’ or store labeled samples at -20°C, protected from light. Frozen samples are stable for up to 2 weeks at -20ºC.

extract_protocol:
1. Cells arrived pelleted and frozen in 1.5mL microcentrifuge tubes, which were stored at -80C until extraction.
2. Thaw samples in 37C waterbath for ~5 min. until completely thawed.
3. Resuspend pellet in PBS
4. Add cell solution to 5mL PBS in 15mL centrifuge tube and resuspend to wash cells
5. Centrifuge the tube for 5 minutes at 1000 RPM.
6. RNA Digestion
A) Aspirate the supernatant and gently flick the tube until the pellet is resuspended.
B) Slowly add 200μl PBS to the cells while tapping gently on the tube to ensure good mixing.
C) Add 4μl RNase A (100mg/ml) and incubate at room temperature (RT) for 2 minutes.
7. Protein Digestion
A) Add 20μl Proteinase K and 200μl Buffer AL to the sample, mixing thoroughly by vortexing. It is important that the solution is immediately and thoroughly mixed by vortexing and pipetting to yield a homogenous solution.
NOTE: Do not add proteinase K directly to buffer AL.
B) Incubate the cell solution in a 70°C waterbath for 10 minutes.
8. DNA Precipitation and Separation of Cellular Components
A) Add 200μl ethanol (96-100%) to the sample, and mix thoroughly by vortexing.
B) A white precipitate may form on addition of ethanol. This precipitate does not interfere with the DNeasy procedure.
C) Pipet the mixture (including all of the precipitate) into the DNeasy Mini spin column placed in a 2ml collection tube. Centrifuge at ≥6000 x g (8000 rpm) for 1 minute. Discard flowthrough and collection tube.
NOTE: In order to obtain optimum DNA yield and quality, it is important not to overload the spin column. The maximum number of hES cells that should be used in a DNA extraction is 5x106 (normally, 2 wells of a 6-well plate). For larger amounts of starting material use multiple spin columns.
9. Wash the DNA
A) Place the DNeasy spin column in a new collection tube and add 500μl of Buffer AW1.
B) Centrifuge at ≥6000 x g (8000rpm) for 1 minute. Discard flow-through and collection tube.
C) Place the DNeasy spin column in a new collection tube and add 500μl of buffer AW2.
D) Centrifuge at 20,000 x g (14,000 rpm) for 3 minutes to dry the DNeasy membrane. Discard flow-through and collection tube.
NOTE: It is important to dry the membrane of the DNeasy Mini spin column, since residual ethanol may interfere with subsequent reactions. This centrifugation step ensures that no residual ethanol will be carried over during the following elution.
E) Following the centrifugation step, remove the DNeasy Mini spin column carefully so the column does not come into contact with the flow-through, since this will result in carryover of ethanol. If carryover of ethanol occurs, place the spin column in a new collection tube and centrifuge again for 1 minute at 20,000 x g (14,000 rpm). Again discard the flow-through and collection tube.
10. Elution
A) Place the DNeasy Mini spin column in a clean 1.5ml or 2ml microcentrifuge tube and pipet 50-200μl Buffer AE directly onto the DNeasy membrane. Incubate the column at room temperature for 1 minute and then centrifuge for 1 minute at ≥6000 x g (8000rpm) to elute.
NOTE: Elution with less than 200μl of Buffer AE increases the final DNA concentration in the elute, but also decreases the overall DNA yield.
B) Repeat elution step as described in 7 A).
NOTE: A new microcentrifuge tube can be used for the second elution step to prevent dilution of the first elute. Alternatively, to combine the two elutes, the microcentrifuge tube from step 4.7.1 can be reused for the second elution step.
NOTE: More than 200μl should not be eluted into a 1.5 ml microcentrifuge tube because the DNeasy spin column will come into contact with the elute.

tag: cell line

value: hFIB2-iPS4 p50 DNA579

tag: sample type

value: human induced pluripotent stem (hiPSC) cell line CTR#3678, CGH#369

extract_protocol:
7.5. Dispase the Cells
7.5.1. Heat the Circulating Waterbath to 70C
7.5.2. Warm buffer AW2 for at least 10 minutes in the 37C waterbath.
7.5.3. Aspirate the media from each well to be extracted.
7.5.4. Add 1ml of Accumax to each well of four 6-well plates at a time.
7.5.4.1.This may be staggered according to number of people performing the extraction.
7.5.5. Return the plate to the 37C incubator for 9-11 minutes.
7.5.6. Remove the plate from the incubator and observe cell detachment with an inverted phase contrast microscope. Proceed to next step when colony edges begin to lift off the plate.
7.5.7. Gently wash the cells from the surface of the well with a serological pipette, using the previously added 1ml of dispase.
7.5.8. Transfer the dispased cells from two 6-well plates to a 50ml centrifuge tube containing 25ml of PBS. Repeat as needed for additional plates.
7.5.9. Gently resuspend cells in PBS using a serological pipette.
7.5.10. Wash well(s) with 1-2ml of the resuspended cell solution to ensure complete cell removal.
7.5.11. Gently pipette solution up and down to mix thoroughly.
7.5.12. Centrifuge the tube for 5 minutes at 1000 RPM.
7.5.13. Aspirate the supernatant.
7.5.14. Add 30 ml of PBS and resuspend the cell pellet gently to wash.
7.5.15. Centrifuge the tube for 5 minutes at 1000 RPM.
7.5.16. Aspirate the supernatant.
7.5.17. Add 2 ml of PBS to each cell pellet and gently resuspend, using a serological pipette.
7.5.18. Keep tubes on ice until all plates are extracted and resuspended..
7.6. Digest Protein and RNA
7.6.1. Vortex Qiagen protease .
7.6.2. Prepare one 15 ml centrifuge tube for each 50 ml conical tube.
7.6.3. Add 200μl Qiagen protease to each 15 ml centrifuge tube.
7.6.4. Transfer 2ml of cells in PBS from one 50 ml conical tube to one 15 ml centrifuge tube containing Qiagen protease and pipette to resuspend.
7.6.4.1. Repeat for additional 50 ml conical tubes.
7.6.5. Add 20μl RNase A to each tube and vortex.
7.6.6. Incubate at room temperature for 3 minutes.
7.6.7. Add 2.4 ml Buffer AL, and mix thoroughly by inverting the tubes 15 times, followed by additional vigorous shaking for at least 1 minute.
7.6.7.1. Do not add Qiagen protease directly to buffer AL
7.6.7.2. Buffer AL may form a precipitate upon storage. If a precipitate has formed,
incubate the buffer at 55C until the precipitate has fully dissolved.
7.6.8. Close caps and incubate in a 70C waterbath for 10 minutes.
7.6.8.1. Monitor the waterbath rack during incubation to insure samples remain above the water level.
7.7. Precipitate DNA and Separate Cellular Components
7.7.1. Add 2 ml ethanol (200 proof) to each tube, and mix by inverting tubes 10 times, followed by additional vigorous shaking for 1 minute.
7.7.2. Carefully transfer one half (approx. 3.5 ml) of the solution onto the labeled QIAamp Midi columns placed into 15 ml centrifuge tubes.
7.7.3. Close the caps and centrifuge at 3000 rpm for 3 minutes.
7.7.4. Remove the columns, discard the filtrate, and place the columns back into the 15 ml centrifuge tubes.
7.7.4.1. Wipe off any spillage from the thread of the tubes before re-inserting the
columns.
7.7.5. Load the remainder of the solution onto the columns.
7.7.6. Close the caps and centrifuge again at 3000 rpm for 3 minutes.
7.8. Wash the DNA
7.8.1. Remove the columns, discard the filtrate, and place the columns back into the 15 ml centrifuge tubes.
7.8.1.1. Wipe off any spillage from the thread of the tubes before re-inserting the
columns.
7.8.2. Add 2 ml of Buffer AW1 to the columns, without moistening the rim.
7.8.3. Close the caps and centrifuge at 5000 rpm for 1 minute.
7.8.3.1. Do not discard the flow-through at this stage.
7.8.4. Add 2 ml of warm Buffer AW2 to the columns, without moistening the rim.
7.8.5. Centrifuge at 5000 rpm for 15 minutes.
7.8.5.1. If the centrifugal force is below 5000 rpm, incubating the column for 10 minutes in an incubator or waterbath to evaporate residual ethanol is recommended.
7.8.6. Remove the columns, discard the filtrate, and place the columns back into 15ml centrifuge tubes.
7.8.6.1. Wipe off any spillage from the thread of the tube before re-inserting the column.
7.8.7. Remove caps and place tubes in the 70ºC waterbath for 10 minutes.
7.9. Elute the DNA
7.9.1. Place the columns in clean, labeled 15ml centrifuge tubes (provided in kit) and discard the collection tube.
7.9.2. Pipette 300μl Buffer AE directly onto the membrane of the columns, close the caps and incubate at room temperature for 5 minutes.
7.9.3. Centrifuge at 5000 rpm for 2 minutes to elute.
7.9.4. Transfer eluate to labeled 1.5ml microcentrifuge tubes and proceed to spectrophotometry.
7.9.5. Store columns/15 ml elution tubes at 4ºC until spectrophotometric results are obtained.
7.9.5.1. Additional AE buffer may be added to columns pending spectrophotometric
results.
7.10. Perform UV Spectrophotometry
7.10.1. Choose the ND-1000 icon from the desktop of the lab computer and select “Nucleic
Acid”.
7.10.2. Wipe the bottom and top pedestal vigorously with a Kimwipe.
7.10.3. Use a p2 micropipetter and carefully load 1.5μl of nuclease-free water into the bottom pedestal of the NanoDrop and gently lower the top pedestal. Click “OK”.
7.10.4. Wipe the bottom and top pedestal vigorously with a Kimwipe.
7.10.5. Load 1.5μl of AE Buffer onto the bottom pedestal, close the top, and click “Blank”.
7.10.6. Wipe the bottom and top pedestal vigorously with a Kimwipe.
7.10.7. Enter the DNA # (DNAXXX), tube#, and elution description of the sample you are
quantifying into the Sample ID box.
7.10.8. Vortex and quick spin the sample and load 1.5μl onto the bottom pedestal of the NanoDrop.
7.10.9. Close the top and click “Measure”.
7.10.10. Verify that the DNA absorbance ratios meet the requirements: 260/280 ≥ 1.75, 260/230 ≥
1.85 (as seen in SOP-CH-014).
7.10.10.1. If the ratios are do not meet the requirements, add 300ul fresh AE buffer to columns/15ml elution tubes and incubate at room temperature for 5 minutes.
7.10.10.2. Centrifuge at 5000 rpm for 2 minutes to elute.
7.10.10.3. Transfer eluate to new, labeled 1.5 ml microcentrifuge tubes and proceed to spectrophotometry.
7.10.10.4. If the ratios are still do not meet requirements, add the original eluate to a new column/15 ml elution tube. If necessary, dilute with additional AE buffer and
incubate at room temperature for 5 minutes.
7.10.10.5. Centrifuge at 5000 rpm for 2 minutes to elute.
7.10.11. Verify that the DNA concentration is between 250-1000ng/ul.
7.10.12. Discard samples that do not meet required ratios.
7.10.13. Click “Show Report” and check that all samples are recorded.
7.10.13.1. Use the “Data” tab to delete or rename samples.
7.10.14. Click “Reports”  “Save Reports”  “Full Report” and save the report with the naming convention Date, DNA#(s) (Ex:052207.DNA145.146.147) under In-House CGH/CGH Reference Standard.
7.11. Perform Agarose Gel Electrophoresis and Imaging
7.11.1. Prepare and run samples for DNA Gel Electrophoresis and Imaging (ref SOP-CH-007).
7.11.2. Analyze gel image to verify that there is no RNA contamination or degradation of DNA.
7.11.3. DO NOT use samples that have RNA contamination or degradation of DNA.
7.12. Aliquot and Store Samples
7.12.1. In ND-1000 software, load the previous report containing uncombined samples.
7.12.2. Combine all samples with acceptable ratios and dilute with AE buffer until a
concentration of 200-250 μg/ml is achieved.
7.12.3. Print report by clicking “Load Report Format”, choose “notebook.ndf”. Click “Reports” “Print Report”.
7.12.4. Tape the printout into the lab notebook.
7.12.5. Enter the absorbance ratios (260/280 and 260/230) and the concentration into the DNA Extraction Log form under the appropriate DNA# previously entered. Save the DNA Extraction Log.
7.12.6. If DNA does NOT meet the above acceptable ratio requirements and/or does not yield a minimum of 450ug, it must be re-extracted.
7.12.7. La

value: human embryonic stem (hES) cell line WA09 [reference]


title: R1881-treated 3h RWPE-1-AR cells, biological rep3

description: Gene expression data from RWPE-1-AR cell line treated wih R1881for 3h

source_name: 3h 1nM R1881-treated RWPE-1-AR cells

value: RWPE-1-AR prostatic cell line was steroid-depleted for 48h and treated with 1nM R1881 for 3h


title: NSCB_CGH_12x135K_366_ICF

source_name: ICF-TK10 p16 DNA576

value: ICF-TK10 p16 DNA576

value: human induced pluripotent stem (hiPSC) cell line CTR#3673, CGH#366

value: human embryonic stem (hES) cell line WA01 [reference]


title: NSCB_CGH_12x135K_367_IMR90

source_name: IMR90-TZ1 p14 DNA 577

value: IMR90-TZ1 p14 DNA 577

value: human induced pluripotent stem (hiPSC) cell line CTR#3674, CGH#367


title: Strawberry #2 70day

description: no additional information

source_name: Honey bee samples at 70 days after the installation of the hive #2 into strawberry greenhouse

value: whole body

value: hive #2

value: strawberry greenhouse

value: 70 days


title: NSCB_CGH_12x135K_360_HDFa

source_name: HDFa-TK4 p35 DNA562A

value: HDFa-TK4 p35 DNA562A

value: human induced pluripotent stem (hiPSC) cell line CTR#3490, CGH#360


title: NSCB_CGH_12x135K_365_ICF

source_name: ICF-TK1 p17 DNA575

value: ICF-TK1 p17 DNA575

value: human induced pluripotent stem (hiPSC) cell line CTR#3672, CGH#365


title: NSCB_CGH_12x135K_361_HDFa

source_name: HDFa-TK7 p34 DNA564

value: HDFa-TK7 p34 DNA564

value: human induced pluripotent stem (hiPSC) cell line CTR#3492, CGH#361


title: R1881-treated 3h RWPE-1-AR cells, biological rep1


title: 13912488 - ss4-phs1 D2 vs WS D2

hyb_protocol: WS D2 Cy5 / ss4-phs1 D2 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: WS D2

value: wassilewskija

value: wild type

source_name: ss4-phs1 D2

value: mutant (ss4- phs1-)


title: NSCB_CGH_12x135K_370_HDFa

source_name: HDFa-YK26 p56 DNA580

value: HDFa-YK26 p56 DNA580

value: human induced pluripotent stem (hiPSC) cell line CTR#3679, CGH#370


title: NSCB_CGH_12x135K_368_hFIB2

source_name: hFIB2-iPS4 p6 DNA578

value: hFIB2-iPS4 p6 DNA578

value: human induced pluripotent stem (hiPSC) cell line CTR#3677, CGH#368

value: human embryonic stem (hES) cell line WA09 [reference]


title: R1881-treated 3h RWPE-1-AR cells, biological rep2

value: RWPE-1-AR prostatic cell line was steroid-depleted for 48h and treated with 1nM R1881 for 3h


title: NSCB_CGH_12x135K_363_HDFa

source_name: HDFa-TK8 p18 DNA573

value: HDFa-TK8 p18 DNA573

value: human induced pluripotent stem (hiPSC) cell line CTR#3669, CGH#363

value: human embryonic stem (hES) cell line WA01 [reference]


title: NSCB_CGH_12x135K_371_ICF

source_name: ICF-TK7 p8 DNA581

value: ICF-TK7 p8 DNA581

value: human induced pluripotent stem (hiPSC) cell line CTR#3680, CGH#371


title: NSCB_CGH_12x135K_364_HDFa

source_name: HDFa-YK26 p6 DNA574

value: HDFa-YK26 p6 DNA574

value: human induced pluripotent stem (hiPSC) cell line CTR#3670, CGH#364


title: NSCB_CGH_12x135K_357_HDFa

source_name: HDFa-TK5 p45 DNA563

value: HDFa-TK5 p45 DNA563

value: human induced pluripotent stem (hiPSC) cell line CTR#3491, CGH#357


title: Strawberry #2 42 day

description: no additional information

source_name: Honey bee samples at 42 days after the installation of the hive #2 into strawberry greenhouse

value: whole body

value: hive #2

value: strawberry greenhouse

value: 42 days


title: Strawberry #2 14 day

description: no additional information

source_name: Honey bee samples at 14 days after the installation of the hive #2 into strawberry greenhouse

value: 14 days


title: Strawberry #1 70day

description: no additional information

source_name: Honey bee samples at 70 days after the installation of the hive #1 into strawberry greenhouse

value: hive #1

value: 70 days


title: Strawberry #2 0 day

description: no additional information

source_name: Honey bee samples prior to the installation of the hive #2 into strawberry greenhouse

value: prior to installation


title: Strawberry #1 42 day

description: no additional information

source_name: Honey bee samples at 42 days after the installation of the hive #1 into strawberry greenhouse


title: NSCB_CGH_12x135K_362_HDFa

source_name: HDFa-TK5 p17 DNA572

value: HDFa-TK5 p17 DNA572

value: human induced pluripotent stem (hiPSC) cell line CTR#3667, CGH#362


title: NSCB_CGH_12x135K_356_HDFa

source_name: HDFa-YK16 p29 DNA560

value: HDFa-YK16 p29 DNA560

value: human induced pluripotent stem (hiPSC) cell line CTR#3485, CGH#356

value: human embryonic stem (hES) cell line WA01 [reference]


title: Control RWPE-1-AR cells at 3h, biological rep3

description: Gene expression data from RWPE-1-AR cell line treated wih vehicle for 3h (control).

source_name: Control RWPE-1-AR cells at 3h

value: RWPE-1-AR prostatic cell line was steroid-depleted for 48h and treated with vehicle (ethanol) for 3h


title: NSCB_CGH_12x135K_355_HDFa

source_name: HDFa-TK6 p29 DNA559

value: HDFa-TK6 p29 DNA559

value: human induced pluripotent stem (hiPSC) cell line CTR#3483, CGH#355


title: NSCB_CGH_12x135K_354_HDFa

source_name: HDFa-TK3 p31 DNA558

value: HDFa-TK3 p31 DNA558

value: human induced pluripotent stem (hiPSC) cell line CTR#3482, CGH#354


title: NSCB_CGH_12x135K_353_iPS

source_name: iPS-IMR90-1 p52 DNA557

value: iPS-IMR90-1 p52 DNA557

value: human induced pluripotent stem (hiPSC) cell line CTR#3481, CGH#353


title: Control RWPE-1-AR cells at 3h, biological rep1


title: Strawberry #1 14 day

description: no additional information

source_name: Honey bee samples at 14 days after the installation of the hive #1 into strawberry greenhouse

value: whole body

value: strawberry greenhouse


title: NSCB_CGH_12x135K_352_ICF

source_name: ICF-TK7 p33 DNA556

value: ICF-TK7 p33 DNA556

value: human induced pluripotent stem (hiPSC) cell line CTR#3480, CGH#352


title: NSCB_CGH_12x135K_347_ICF

source_name: ICF p13 DNA547

value: ICF p13 DNA547

value: human induced pluripotent stem (hiPSC) cell line CTR#3402, CGH#347


title: Control RWPE-1-AR cells at 3h, biological rep2


title: Strawberry #1 0 day

description: no additional information

source_name: Honey bee samples prior to the installation of the hive #1 into strawberry greenhouse

value: hive #1

value: prior to installation


title: NSCB_CGH_12x135K_349_iPS

source_name: iPS-foreskin-2 p17 DNA553

value: iPS-foreskin-2 p17 DNA553

value: human induced pluripotent stem (hiPSC) cell line CTR#3477, CGH#349

value: human embryonic stem (hES) cell line WA09 [reference]


title: NSCB_CGH_12x135K_350_iPS

source_name: iPS-foreskin-4 p21 DNA554

value: iPS-foreskin-4 p21 DNA554

value: human induced pluripotent stem (hiPSC) cell line CTR#3478, CGH#350


title: NSCB_CGH_12x135K_351_ICF

source_name: ICF-TK1 p34 DNA555

value: ICF-TK1 p34 DNA555

value: human induced pluripotent stem (hiPSC) cell line CTR#3479, CGH#351

value: human embryonic stem (hES) cell line WA01 [reference]


title: Healthy control, Subject 10

city: Los Angeles

first: Yu-Hsiang

last: Lee

address: 10833 Le Conte Avenue

department: Dental Research Institute

institute: UCLA

description: Gene expression data of human salivary transcriptomes

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized at 45oC for 16 h on GeneChip Human Genome U133 plus 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed by GeneChip Robust Multiarray Averaging (GCRMA) using bioconductor gcrma package default settings and quantile as normalization method.

molecule: polyA RNA

source_name: Biofluid from healthy control subject # 10

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix; GeneChip IVT Labeling Kit).

growth_protocol: Unstimulated whole saliva were collected between 9 AM and 10 AM. All subjects were asked to refrain from eating, drinking, smoking, and oral hygiene activities for at least 1 h before collection.

extract_protocol: Extraction of saliva transcriptoms was performed using MagMAX Viral RNA Isolation Kit® according to the manufacturer's instructions.

treatment_protocol: Cell-free saliva supernatants were collected by centrifugating the whole saliva at 2,600 × g and 4°C for 15 min. The supernatants were aspirated from the pellets and then stored at -80oC in the presence of RNase inhibitor until use.

tag: tumor stage

tag: biofluid

value: Cell-free saliva

tag: gender

value: Female

tag: ethnicity

value: Korean


title: Healthy control, Subject 8

source_name: Biofluid from healthy control subject # 8


title: NSCB_CGH_12x135K_348_iPS

source_name: iPS-foreskin-1 p25 DNA552

value: iPS-foreskin-1 p25 DNA552

value: human induced pluripotent stem (hiPSC) cell line CTR#3476, CGH#348


title: NSCB_CGH_12x135K_345_iPS

source_name: iPS-foreskin-3 p20 DNA525

value: iPS-foreskin-3 p20 DNA525

value: human induced pluripotent stem (hiPSC) cell line CTR#3386, CGH#345


title: Healthy control, Subject 9

source_name: Biofluid from healthy control subject # 9


title: Healthy control, Subject 11

source_name: Biofluid from healthy control subject # 11


title: NSCB_CGH_12x135K_344_IMR90

source_name: IMR90-YZ1 p38 DNA542

value: IMR90-YZ1 p38 DNA542

value: human induced pluripotent stem (hiPSC) cell line CTR#3421, CGH#344


title: NSCB_CGH_12x135K_342_iPS_IMR90_3

source_name: iPS-IMR90-3 p31 DNA540

value: iPS-IMR90-3 p31 DNA540

value: human induced pluripotent stem (hiPSC) cell line CTR#3419, CGH#342


title: NSCB_CGH_12x135K_343_iPS_IMR90_4

source_name: iPS-IMR90-4 p31 DNA541

value: iPS-IMR90-4 p31 DNA541

value: human induced pluripotent stem (hiPSC) cell line CTR#3420, CGH#343


title: Healthy control, Subject 7

source_name: Biofluid from healthy control subject # 7


title: NSCB_CGH_12x135K_340_IMR90

source_name: IMR90-TZ1 p23 DNA 530

value: IMR90-TZ1 p23 DNA 530

value: human induced pluripotent stem (hiPSC) cell line CTR#3394, CGH#340


title: NSCB_CGH_12x135K_338_HDFa

source_name: HDFa-TK2 p54 DNA528

value: HDFa-TK2 p54 DNA528

value: human induced pluripotent stem (hiPSC) cell line CTR#3389, CGH#338


title: NSCB_CGH_12x135K_346_foreskin

source_name: foreskin p5 DNA546

value: foreskin p5 DNA546

value: human induced pluripotent stem (hiPSC) cell line CTR#3433, CGH#346

value: human embryonic stem (hES) cell line WA09 [reference]


title: Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18) Replicate 4

city: Fayetteville

first: Byung-whi

last: Kong

state: AR

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

description:
CEF_P4_P18_Rep4
Biological replicate 4 of 4. Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18)

hyb_protocol: An equal amount (825 ng) of Cy3 and Cy5 labeled cRNA probes were mixed with gene expression hybridization kit (Agilent, part No. 5188-5242) and hybridized on a 4X44K Agilent custom chicken oligo microarray (array ID: 015068). The hybridized slides were washed using a commercial kit package (Agilent).

scan_protocol: Scanned on an Genepix 4000B scanner (Molecular Devices Corporation)

data_processing:
Gene Pix Pro (v 6.1) with Acuity software (v 4.0)
There are 320 control spots on the 44K whole genes. The expression values of the 320 control genes were collected in 10 groups, and the average values of each group were calculated. The mean values were compared to the reference values published by Zahurak et al in 2007. From the 10 compared mean values, one constant were deducted for a normalization, and same precesses were performed for each replicate. Finally all spots were normalized with those constants.

organism: Gallus gallus

source_name: CEF (P4)

label_protocol: 2 µg of total RNA were used for this experiment, and all procedures were followed to manufacturer's instructions.

growth_protocol: Cells were grown in a Dulbecco’s Modified Eagle’s Medium (DMEM, 0.45% glucose) plus 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine in 10 cm tissue culture plates (Sarstedt Inc., Newton, NC, USA).

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

treatment_protocol: Cells were passaged every 3-4 days when it was fully confluent until passage 18.

tag: developmental stage

value: embryo

value: chicken embryo fibroblast cells (CEF)

tag: cell passage

source_name: CEF (P18)


title: Healthy control, Subject 5

source_name: Biofluid from healthy control subject # 5

value: Cell-free saliva

value: Female

value: Korean


title: Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18) Replicate 2

description:
CEF_P4_P18_Rep2
Biological replicate 2 of 4. Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18)


title: NSCB_CGH_12x135K_341_iPS_IMR90

source_name: iPS-IMR90-2 p30 DNA531

value: iPS-IMR90-2 p30 DNA531

value: human induced pluripotent stem (hiPSC) cell line CTR#3395, CGH#341

value: human embryonic stem (hES) cell line WA01 [reference]


title: NSCB_CGH_12x135K_339_HDFa

source_name: HDFa-TK8 p63 DNA529

value: HDFa-TK8 p63 DNA529

value: human induced pluripotent stem (hiPSC) cell line CTR#3393, CGH#339


title: Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18) Replicate 3

description:
CEF_P4_P18_Rep3
Biological replicate 3 of 4. Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18)


title: NSCB_CGH_12x135K_337_HDFa

source_name: HDFa-YK26 p90 DNA527

value: HDFa-YK26 p90 DNA527

value: human induced pluripotent stem (hiPSC) cell line CTR#3388, CGH#337


title: Healthy control, Subject 4

source_name: Biofluid from healthy control subject # 4


title: Healthy control, Subject 6

source_name: Biofluid from healthy control subject # 6


title: Healthy control, Subject 3

source_name: Biofluid from healthy control subject # 3


title: NSCB_CGH_12x135K_334_ICF

source_name: ICF-TK4 p32 DNA523

value: ICF-TK4 p32 DNA523

value: human induced pluripotent stem (hiPSC) cell line CTR#3384, CGH#334


title: NSCB_CGH_12x135K_335_ICF

source_name: ICF-TK4 p34 DNA524

value: ICF-TK4 p34 DNA524

value: human induced pluripotent stem (hiPSC) cell line CTR#3385, CGH#335


title: Healthy control, Subject 2

source_name: Biofluid from healthy control subject # 2


title: NSCB_CGH_12x135K_336_HDFa

source_name: HDFa-YK22 p34 DNA526

value: HDFa-YK22 p34 DNA526

value: human induced pluripotent stem (hiPSC) cell line CTR#3387, CGH#336


title: Chicken embryo fibroblast cells vs. Immortal chicken embryo fibroblast cells (DF-1) Replicate 2

description:
CEF_DF-1_Rep2
Biological replicate 2 of 4. chicken embryo fibroblast cells vs. immortal chicken embryo fibroblast cells (DF-1).

source_name: CEF

treatment_protocol: The CEF cells were splitted every 3-4 days when they were fully confluent.

value: embryo

value: chicken embryo fibroblast cells (CEF)


title: Chicken embryo fibroblast cells vs. Immortal chicken embryo fibroblast cells (DF-1) Replicate 1

description:
CEF_DF-1_Rep1
Biological replicate 1 of 4. chicken embryo fibroblast cells vs. immortal chicken embryo fibroblast cells (DF-1).


title: Chicken embryo fibroblast cells vs. Immortal chicken embryo fibroblast cells (DF-1) Replicate 3

description:
CEF_DF-1_Rep3
Biological replicate 3 of 4. chicken embryo fibroblast cells vs. immortal chicken embryo fibroblast cells (DF-1).


title: Chicken embryo fibroblast cells vs. Immortal chicken embryo fibroblast cells (DF-1) Replicate 4

description:
CEF_DF-1_Rep4
Biological replicate 4 of 4. chicken embryo fibroblast cells vs. immortal chicken embryo fibroblast cells (DF-1).


title: Healthy control, Subject 1

source_name: Biofluid from healthy control subject # 1

value: Cell-free saliva

value: Female


title: Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18) Replicate 1

description:
CEF_P4_P18_Rep1
Biological replicate 1 of 4. Healthy chicken embryo fibroblast cells (P4) vs. Senescent chicken embryo fibroblast cells (P18)


title: NSCB_CGH_12x135K_333_HDFa

source_name: HDFa p5 DNA533

value: HDFa p5 DNA533

value: human induced pluripotent stem (hiPSC) cell line CTR#3401, CGH#333


title: NSCB_CGH_12x135K_331_IMR

description: This CGH experiment is designed to detect deletion, insertation, amplication, etc. in the sample relative to the reference.

source_name: IMR90 p5 DNA532

value: IMR90 p5 DNA532

value: human induced pluripotent stem (hiPSC) cell line CTR#3400, CGH#331

value: human embryonic stem (hES) cell line WA01 [reference]


title: Ovarian cancer at 3C, Patient 10

source_name: Biofluid from ovarian cancer patient # 10

value: IIIC

value: Korean


title: TET-tapetum-rep3

first: Koichiro

last: Aya

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and Biotechnology Center

description: Gene expression in the rice tapetum at tetrad stage, collected by lasar microdissection

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 277 - 1500ng of labeled and fragmented cRNA was hybridized to Agilent Rice 44K custom array (G2519F) using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2565BA according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). Obtained background subtracted Signal intensities (gBGSubSignal) were normalized by variance stabilization (VSN) using R software (http://www.r-project.org/).

organism: Oryza sativa

source_name: Tapetum at tetrad stage, replicate 3

label_protocol: Cy3-labeled cRNA were prepared from total RNA using Low RNA Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification. The cDNA synthesis reaction time was extended to 6 hrs.

growth_protocol: Rice (O. sativa L. ssp. japonica cv. Nipponbare) plants were grown in a greenhouse under normal conditions.

extract_protocol: Total RNA was extracted from each cell type and tissue with a PicoPure™ RNA isolation kit (Molecular Devices, Ontario, Canada) following the manufacturer's recommendations. Total RNA was quantified with a Quant-iT™ RiboGreen RNA reagent and kit (Invitrogen, San Diego, CA, USA).

treatment_protocol: The anthers were fixed in Farmer's fixative (ethanol : acetate = 3 : 1) overnight at 4°C. Dehydration and paraffin embedding were performed by using a microwave processor. Paraffin-embedded sections were cut to a thickness of 16 μm and mounted on PEN membrane glass slides (Molecular Devices, Ontario, Canada) for LM. To remove the paraffin, slides were immersed in 100% xylene (twice), 50% xylene/50% ethanol and 100% ethanol (v/v) for 5 min each, and then air-dried completely at room temperature. Three or four individual flowers were used for each LM experiment. LM was performed using the Veritas Laser Microdissection System LCC1704 (Molecular Devices). Selected areas were captured by an infrared laser (IR laser) onto CapSure Macro LCM Caps (Molecular Devices), and were subsequently cut by a UV laser. The target cells that fused to the LCM cap were collected by removing the cap from the tissue section.

tag: subspecies

value: japonica

tag: cultivar

value: Nipponbare

value: tapetum


title: TET-tapetum-rep2

source_name: Tapetum at tetrad stage, replicate 2


title: Ovarian cancer at 3C, Patient 11

source_name: Biofluid from ovarian cancer patient # 11


title: Ovarian cancer at 3B, Patient 9

source_name: Biofluid from ovarian cancer patient # 9

value: IIIB


title: UN-tapetum-rep2

description: Gene expression in the rice tapetum at uninuclear stage, collected by lasar microdissection

source_name: Tapetum at uninuclear stage, replicate 2


title: UN-tapetum-rep3

source_name: Tapetum at uninuclear stage, replicate 3


title: MEI-tapetum-rep3

description: Gene expression in the rice tapetum at meiosis stage, collected by lasar microdissection

source_name: Tapetum at meiosis stage, replicate 3


title: UN-tapetum-rep1

source_name: Tapetum at uninuclear stage, replicate 1


title: Ovarian cancer at 3C, Patient 8

source_name: Biofluid from ovarian cancer patient # 8


title: Ovarian cancer at 3C, Patient 7

source_name: Biofluid from ovarian cancer patient # 7


title: TET-tapetum-rep1

source_name: Tapetum at tetrad stage, replicate 1


title: MEI-tapetum-rep2

source_name: Tapetum at meiosis stage, replicate 2


title: GMP NcstnKO replicate2

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

institute: Inserm

description: 4 weeks after polyIC injection

hyb_protocol: 3.75 mcg of biotin-labeled cDNA were hybridized for 16 hrs onto the GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix)

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using dChip program. No further adjustments were made to the data in the table.

organism: Mus musculus

source_name: Lineage negative, cKit+, Sca1- CD34+ FcgammaRII/III+ bone marrow cells from 6 weeks old NcstnKO mouse

label_protocol: 5 ng total RNA was amplified by Nugen Ovation RNA amplification system V2 and the resulting cDNA biotin-labeled using the FL-Ovation™ cDNA Biotin Module V2

extract_protocol: Qiagen RNEasy Plus mini Kit  was used to extract total cellular RNA according to the manufacturer's protocol, and the RNA was amplified and converted into cDNA using the Ovation Amplification v2 and Biotin cDNA Biotin systems

treatment_protocol: 14 days old Ncstn flox/flox and Ncstn flox/flox Mx1-cre+ littermate were injected 3 times with polyIC (20mcg/g of body weight) every other day. Mice were sacrificed and analyzed 4 weeks after injection

value: male

tag: age

value: 6 weeks

tag: genotype

value: Ncstn flox/flox Mx1-cre+


title: Ovarian cancer at 3C, Patient 6

source_name: Biofluid from ovarian cancer patient # 6


title: GMP NcstnKO replicate1

description: 4 weeks after polyIC injection

value: female


title: Ovarian cancer at 3C, Patient 1

source_name: Biofluid from ovarian cancer patient # 1

value: Cell-free saliva


title: Ovarian cancer at 3C, Patient 5

source_name: Biofluid from ovarian cancer patient # 5

value: Female


title: GMP NcstnKO replicate3

description: 4 weeks after polyIC injection


title: GMP WT replicate1

description: 4 weeks after polyIC injection

source_name: Lineage negative, cKit+, Sca1- CD34+ FcgammaRII/III+ bone marrow cells from 6 weeks old WT mouse

value: Ncstn flox/flox


title: MEI-tapetum-rep1

source_name: Tapetum at meiosis stage, replicate 1

tag: tissue


title: GMP WT replicate3

description: 4 weeks after polyIC injection


title: BC-pollen-rep5

description: Gene expression in the rice pollen at bicelluar stage, collected by lasar microdissection

source_name: Pollen at bicelluar stage, replicate 5

value: pollen


title: GMP WT replicate2

description: 4 weeks after polyIC injection


title: TC-pollen-rep2

description: Gene expression in the rice pollen at tricelluar stage, collected by lasar microdissection

source_name: Pollen at tricelluar stage, replicate 2


title: Ovarian cancer at 3C, Patient 4

source_name: Biofluid from ovarian cancer patient # 4


title: BC-pollen-rep6

source_name: Pollen at bicelluar stage, replicate 6


title: TC-pollen-rep3

source_name: Pollen at tricelluar stage, replicate 3


title: TC-pollen-rep1

source_name: Pollen at tricelluar stage, replicate 1


title: BC-pollen-rep4

source_name: Pollen at bicelluar stage, replicate 4


title: Ovarian cancer at 3C, Patient 3

source_name: Biofluid from ovarian cancer patient # 3


title: BC-pollen-rep7

source_name: Pollen at bicelluar stage, replicate 7


title: BC-pollen-rep3

source_name: Pollen at bicelluar stage, replicate 3


title: BC-pollen-rep8

source_name: Pollen at bicelluar stage, replicate 8


title: UN-microspore-rep3

description: Gene expression in the rice microspore at uninuclear stage, collected by lasar microdissection

source_name: Microspore at uninuclear stage, replicate 3

value: microspore


title: LSK WT replicate2c

description: 4 weeks after polyIC injection

source_name: Lineage negative, cKit+, Sca1+ bone marrow cells from 6 weeks old WT mouse


title: LSK WT replicate1c

description: 4 weeks after polyIC injection


title: LSK WT replicate3c

description: 4 weeks after polyIC injection


title: BC-pollen-rep2

source_name: Pollen at bicelluar stage, replicate 2


title: Ovarian cancer at 3C, Patient 2

source_name: Biofluid from ovarian cancer patient # 2


title: BC-pollen-rep1

source_name: Pollen at bicelluar stage, replicate 1


title: LSK N1IC replicate3

description: 2 weeks after polyIC injection

source_name: Lineage negative, cKit+, Sca1+ bone marrow cells from 5 weeks old N1-IC+ mouse

treatment_protocol: 21 days old Ncstn flox/flox and Ncstn flox/flox Mx1-cre+ littermate were injected 3 times with polyIC (20mcg/g of body weight) every other day. Mice were sacrificed and analyzed 2 weeks after the last injection. LSK cells were sorted.

value: 5 weeks

value: lox-stop-lox N1-IC Mx1-cre+


title: UN-microspore-rep1

source_name: Microspore at uninuclear stage, replicate 1


title: UN-microspore-rep2

source_name: Microspore at uninuclear stage, replicate 2


title: LSK N1IC replicate1

description: 2 weeks after polyIC injection


title: Co-culture 1

city: Singapore

first: Siew-Min

last: Ong

address: 8A Biomedical Grove, Immunos Level 4

country: Singapore

institute: Singapore Immunology Network (SIgN)

description: Biological replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with R/Bioconductor

source_name: cell line and blood monocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Spheroids were cultured in IMDM with 5% human serum for 8 days

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: tumor cells cultured with macrophages


title: LSK WT replicate1b

description: 2 weeks after polyIC injection

source_name: Lineage negative, cKit+, Sca1+ bone marrow cells from 5 weeks old WT mouse


title: 2-phenylethyl ITC spiked - EC10 vs. Acetone Control  EC10-2_AC4_F.candida_2-phenITC

city: Amsterdam

first: Elaine

last: van Ommen Kloeke

address: De Boelelaan 1085

department: Ecological Science

country: Netherlands

institute: VU University Amsterdam

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma package in the R (2.9.0) software environment (http://www.r-project.org/), which consisted of normexp background correction (set off = 30), loess normalization and aquantile normalization. Contrast ratios were obtained by fitting linear models using empirical Bayes methods.

organism: Folsomia candida

source_name: 2-phenylethyl ITC spiked soil - EC10 exposure

label_protocol: 500 ng input was used for amplification and labeling with the Agilent Low-Input Fluorescent Linear Amplification Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

value: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with 2-phenylethyl isothiocyanate EC10 (6.21 nmol/g (DW)).

tag: treatment

value: whole organism

tag: strain

value: Berlin

source_name: Acetone Control soil exposure

value: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with only acetone (acetone control).

value: Acetone Control soil exposure


title: Co-culture 2

description: Biological replicate 2


title: 2-phenylethyl ITC spiked - EC10 vs. 2-phenylethyl ITC spiked - EC50 EC10-3_EC50-2_F.candida_2-phenITC

value: 2-phenylethyl ITC spiked soil - EC10 exposure

source_name: 2-phenylethyl ITC spiked soil - EC50 exposure

value: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with 2-phenylethyl isothiocyanate EC50 (10.7 nmol/g (DW)).


title: Co-culture 3

description: Biological replicate 3


title: Co-culture 4

description: Biological replicate 4


title: MEI-microspore-rep2

description: Gene expression in the rice microspore at meiosis stage, collected by lasar microdissection

source_name: Microspore at meiosis stage, replicate 2

value: japonica

value: Nipponbare


title: MEI-microspore-rep1

source_name: Microspore at meiosis stage, replicate 1


title: Tumor-sorted 4

description: Biological replicate 4

value: tumor cells  which have interacted with macrophages


title: TET-microspore-rep1

description: Gene expression in the rice microspore at tetrad stage, collected by lasar microdissection

source_name: Microspore at tetrad stage, replicate 1


title: LSK N1IC replicate2

description: 2 weeks after polyIC injection

value: female


title: MEI-microspore-rep3

source_name: Microspore at meiosis stage, replicate 3


title: MEI-microspore-rep4

source_name: Microspore at meiosis stage, replicate 4


title: 2-phenylethyl ITC spiked - EC50 vs. 2-phenylethyl ITC spiked - EC10 EC50-4_EC10-4_F.candida_2-phenITC

value: 2-phenylethyl ITC spiked soil - EC50 exposure


title: LSK WT replicate2b

description: 2 weeks after polyIC injection


title: TET-microspore-rep3

source_name: Microspore at tetrad stage, replicate 3


title: 2-phenylethyl ITC spiked - EC50 vs. Control  EC50-3_C4_F.candida_2-phenITC

source_name: Control soil exposure

value: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil non-spiked (control).

value: Control soil exposure


title: Pre_anther_rep3

description: Gene expression in the rice anther at premeiosis, collected by lasar microdissection

source_name: Anther at PreMEI stage, replicate 3

value: anther


title: TET-microspore-rep2

source_name: Microspore at tetrad stage, replicate 2

value: microspore


title: Acetone Control  vs. 2-phenylethyl ITC spiked - EC50 AC3_EC50-1_F.candida_2-phenITC


title: Tumor-sorted 2

description: Biological replicate 2


title: Tumor-sorted 3

description: Biological replicate 3


title: Tumor-sorted 1

description: Biological replicate 1


title: LSK Ncstn KO replicate2

description: 4 weeks after polyIC injection

source_name: Lineage negative, cKit+, Sca1+ bone marrow cells from 6 weeks old Ncstn KO mouse

value: male

value: 6 weeks

value: Ncstn flox/flox Mx1-cre+


title: Control  vs. 2-phenylethyl ITC spiked - EC10 C2_EC10-1_F.candida_2-phenITC

value: whole organism

value: Berlin

value: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with 2-phenylethyl isothiocyanate EC10 (6.21 nmol/g (DW)).


title: LSK WT replicate3

description: 2 weeks after polyIC injection

value: 5 weeks


title: Pre_anther_rep2

source_name: Anther at PreMEI stage, replicate 2


title: Acetone Control  vs. Control  AC2_C3_F.candida_2-phenITC

value: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with only acetone (acetone control).

value: Acetone Control soil exposure


title: LSK Ncstn KO replicate1

description: 4 weeks after polyIC injection


title: LSK WT replicate2

description: 4 weeks after polyIC injection

source_name: Lineage negative, cKit+, Sca1+ bone marrow cells from 6 weeks old WT mouse

value: Ncstn flox/flox


title: Control  vs. Acetone Control  C1_AC1_F.candida_2-phenITC


title: Pre_anther_rep1

source_name: Anther at PreMEI stage, replicate 1

value: japonica

value: Nipponbare


title: LSK WT replicate1

description: 4 weeks after polyIC injection


title: Tumor alone 1

description: Biological replicate 1

source_name: cell line

value: tumor cell


title: XSxrAY#X_1mo_control

status: Public on May 11 2011

city: Canterbury

first: Peter

middle: James

last: Ellis

state: Kent

address: Stacey Building

department: School of Biosciences

country: United Kingdom

institute: University of Kent

description:
Age-matched control for sample 4421347024_D
4421347024_E

data_processing: Quantile normalization was performed with BeadStudio (Illumina) - software package now renamed GenomeStudio

source_name: Mouse testis

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep kit for Illumina arrays

extract_protocol: RNA was extracted with TRI reagent (Sigma), followed by clean-up with QIAGEN RNeasy MinElute kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: 1 month

tag: y gene complement

value: Complete

tag: transgene

tag: number pooled


title: Wildtype_control_rep2

description:
Normal controls for shSLY, 2/3 Yqdel and XSxrAY#X genotypes
4421347011_D

value: 8 weeks


title: 2_3 Yqdel

value: 2 months

value: 2/3 Yq deleted


title: XSxrAY#X_1mo

value: Yq absent


title: shSLY3_rep3

value: shSLY RNAi construct


title: 9_10 Yqdel

description:
The 9/10 deletion arose on a Sry-negative background, necessitating a separate control
4421347024_B

value: 9/10 Yq deleted, Sry deleted

value: Sry