title: 14089817 - cpb20-1 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / cpb20-1 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: cpb20-1 Repet 1

extract_protocol: cpb20-1 Repet 1:10ug. (Qiagen_RNeasy.pdf)

value: mutant (cpb20-1)


title: 14054609 - cpb80 Repet 2 vs Col-0 Repet 2

status: Public on Jun 26 2013

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the endogenous RNA substrates co-regulated by RQC and PTGS pathways?

hyb_protocol: Col-0 Repet 2 Cy5 / cpb80 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Col-0 Repet 2

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

growth_protocol: aerial - Media=S-Medium Bouturage (Douchefa Biochemie) hygrometry=60%  Temperature=18C  Light=16 hours

extract_protocol: Col-0 Repet 2:20ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype/variation

value: wild type (control)

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

source_name: cpb80 Repet 2

extract_protocol: cpb80 Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (cbp80 sail_1227_e07)


title: 14054611 - dcl-4-1 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / dcl-4-1 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: dcl-4-1 Repet 2

extract_protocol: dcl-4-1 Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14089818 - Col-0 Repet 1 vs cpb20-1 Repet 1

hyb_protocol: cpb20-1 Repet 1 Cy5 / Col-0 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col-0 Repet 1

extract_protocol: Col-0 Repet 1:20ug. (Qiagen_RNeasy.pdf)


title: 14089819 - cpb80 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / cpb80 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: cpb80 Repet 1

extract_protocol: cpb80 Repet 1:10ug. (Qiagen_RNeasy.pdf)


title: 14054604 - Col-0 Repet 2 vs cpb20-1 Repet 2

hyb_protocol: cpb20-1 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: cpb20-1 Repet 2

extract_protocol: cpb20-1 Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14054610 - Col-0 Repet 2 vs dcl-4-1 Repet 2

hyb_protocol: dcl-4-1 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054608 - Col-0 Repet 2 vs cpb80 Repet 2

hyb_protocol: cpb80 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054613 - 35S:RTL2.11.1.18 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / 35S:RTL2.11.1.18 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 35S:RTL2.11.1.18 Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14054614 - Col-0 Repet 2 vs 35S:RTL2.30.1.41 Repet 2

hyb_protocol: 35S:RTL2.30.1.41 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 35S:RTL2.30.1.41 Repet 2:10ug. (Qiagen_RNeasy.pdf)


title: 14054601 - Col-0 Repet 2 vs xrn3-3 Repet 2

hyb_protocol: xrn3-3 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: xrn3-3 Repet 2

extract_protocol: xrn3-3 Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn3-3 sail1172c07)


title: 14054616 - 35S:RTL2.30.1.41 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / 35S:RTL2.30.1.41 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054605 - cpb20-1 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / cpb20-1 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054603 - vcs Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / vcs Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: vcs Repet 2

extract_protocol: vcs Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (vcs sail_1257h12)


title: 14054612 - Col-0 Repet 2 vs 35S:RTL2.11.1.18 Repet 2

hyb_protocol: 35S:RTL2.11.1.18 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054598 - xrn2-2 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / xrn2-2 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: xrn2-2 Repet 2

extract_protocol: xrn2-2 Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn2-2 sail_781e02)


title: 14092646 - xrn2-2 Repet 1 vs Col-0 Repet 1

hyb_protocol: Col-0 Repet 1 Cy5 / xrn2-2 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: xrn2-2 Repet 1

extract_protocol: xrn2-2 Repet 1:10ug. (Qiagen_RNeasy.pdf)


title: 14054600 - xrn3-3 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / xrn3-3 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054602 - Col-0 Repet 2 vs vcs Repet 2

hyb_protocol: vcs Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054599 - Col-0 Repet 2 vs xrn2-2 Repet 2

hyb_protocol: xrn2-2 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14054596 - xrn2-1 Repet 2 vs Col-0 Repet 2

hyb_protocol: Col-0 Repet 2 Cy5 / xrn2-1 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: xrn2-1 Repet 2

extract_protocol: xrn2-1 Repet 2:10ug. (Qiagen_RNeasy.pdf)

value: mutant (xrn2-1 salk_041148)


title: 14054597 - Col-0 Repet 2 vs xrn2-1 Repet 2

hyb_protocol: xrn2-1 Repet 2 Cy5 / Col-0 Repet 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: BC07_19, NonPABC, ER neg, Stroma, Stroma

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

country: USA

institute: Cleveland Clinic

description:
Gene expression data of  breast normal stroma cells a from a Non-PABC patient
Raw data file: harvell_19_BC07_19_LightStroma_HG-U133_Plus_2.CEL

hyb_protocol: Fragmented and biotin-labeled targets were hybridized to HG-U133 Plus 2.0 (Affymetrix) gene chips for analysis of over 54,000 probe sets.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 - 7G.

data_processing: The data were analyzed with R-Bioconductor (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Homo sapiens

source_name: Normal

label_protocol: RNA was amplified with the WT-Ovation FFPE System based on Ribo-SPIA technology (Nugen Technologies, Inc.). Target preparation for microarray analysis used 5ug of amplified cDNA, which was then fragmented and labeled using FL-Ovation cDNA Biotin Module V2 (Nugen)

extract_protocol: RNA was isolated using the PicoPure RNA isolation Kit (Arcturus) according to the manufacturers instructions.

treatment_protocol: Not treated

tag: tissue

value: breast

tag: cell type

value: normal stroma cells

tag: patient

value: Non-PABC patient


title: BC08-103, PABC, ER neg, Stroma, Normal Stroma (19)

description:
Gene expression data of  breast normal stroma cells a from a PABC patient
Raw data file: harvell_19_HG-U133_Plus_2.CEL

value: PABC patient


title: BC07_19, NonPABC, ER neg, Epithelial, Normal Epithelial

description:
Gene expression data of  breast normal epithelial cells a from a Non-PABC patient
Raw data file: harvell_17_BC07_19_Normal_HG-U133_Plus_2.CEL

value: normal epithelial cells


title: BC08-103, PABC, ER neg, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a patient with PABC
Raw data file: harvell_18_HG-U133_Plus_2.CEL

source_name: Tumor

value: tumor epithelial cells


title: BC07_47, PABC, ER pos, Epithelial, Normal Epithelial

description:
Gene expression data of breast normal epithelial cells from a PABC patient
Raw data file: harvell_14_BC07_43_Normal_HG-U133_Plus_2.CEL


title: BC07_29, PABC, ER neg, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a patient with PABC
Raw data file: harvell_12_BC07_29_Stroma_HG-U133_Plus_2.CEL

value: tumor associated stroma cells


title: BC08-49, NonPABC, ER pos, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a Non-PABC patient
Raw data file: harvell_15_HG-U133_Plus_2.CEL


title: BC08-103, PABC, ER neg, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a patient with PABC
Raw data file: harvell_22_HG-U133_Plus_2.CEL


title: BC08-24, NonPABC, ER neg, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a Non-PABC patient
Raw data file: harvell_16_HG-U133_Plus_2.CEL


title: BC06-21, NonPABC, ER pos, Epithelial, Normal Epithelial

description:
Gene expression data of  breast normal epithelial cells a from a Non-PABC patient
Raw data file: harvell_10_HG-U133_Plus_2.CEL


title: BC08-55, PABC, ER pos, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a patient with PABC
Raw data file: harvell_13_HG-U133_Plus_2.CEL


title: BC07_47, PABC, ER pos, Stroma, Stroma

description:
Gene expression data of breast normal stroma cells from a PABC patient
Raw data file: harvell_16_BC07_47_DarkStroma_HG-U133_Plus_2.CEL


title: BC08-103, PABC, ER neg, Epithelial, Normal Epithelial

description:
Gene expression data of breast normal epithelial cells from a PABC patient
Raw data file: harvell_20_HG-U133_Plus_2.CEL


title: BC08-72, PABC, ER pos, Stroma, Normal Stroma (08)

description:
Gene expression data of  breast normal stroma cells a from a PABC patient
Raw data file: harvell_08_HG-U133_Plus_2.CEL


title: BC08-49, NonPABC, ER pos, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a Non-PABC patient
Raw data file: harvell_14_HG-U133_Plus_2.CEL


title: BC08-103, PABC, ER neg, Stroma, Normal Stroma (21)

description:
Gene expression data of  breast normal stroma cells a from a PABC patient
Raw data file: harvell_21_HG-U133_Plus_2.CEL


title: BC08-55, PABC, ER pos, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a patient with PABC
Raw data file: harvell_12_HG-U133_Plus_2.CEL


title: BC07_29, PABC, ER neg, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a patient with PABC
Raw data file: harvell_11_BC07_29_Epi_HG-U133_Plus_2.CEL


title: BC06_52, PABC, ER pos, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a patient with PABC
Raw data file: harvell_8_BC06_52_Epi_HG-U133_Plus_2.CEL


title: BC08-24, NonPABC, ER neg, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells a from a Non-PABC patient
Raw data file: harvell_17_HG-U133_Plus_2.CEL


title: BC08-72, PABC, ER pos, Epithelial, Normal Epithelial

description:
Gene expression data of breast normal epithelial cells from a PABC patient
Raw data file: harvell_09_HG-U133_Plus_2.CEL


title: BC08-72, PABC, ER pos, Stroma, Normal Stroma (07)

description:
Gene expression data of  breast normal stroma cells a from a PABC patient
Raw data file: harvell_07_HG-U133_Plus_2.CEL


title: BC07_37, NonPABC, ER neg, Stroma, Stroma

description:
Gene expression data of  breast normal stroma cells a from a Non-PABC patient
Raw data file: harvell_5_BC07_37_LightStroma_HG-U133_Plus_2.CEL


title: BC07_37, NonPABC, ER neg, Epithelial, Normal Epithelial

description:
Gene expression data of breast normal epithelial cells from a Non-PABC patient
Raw data file: harvell_3_BC07_37_Epi_HG-U133_Plus_2.CEL


title: BC07_20, PABC, ER neg, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a patient with PABC
Raw data file: harvell_1_BC07_20_Epi_HG-U133_Plus_2.CEL


title: BC06_57, NonPABC, ER pos, Epithelial, Epithelial

description:
Gene expression data of  breast tumor epithelial cells a from a Non-PABC patient
Raw data file: harvell_6_BC06_57_Epi_HG-U133_Plus_2.CEL


title: BC06_57, NonPABC, ER pos, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a Non-PABC patient
Raw data file: harvell_7_BC06_57_Stroma_HG-U133_Plus_2.CEL


title: BC06-25, NonPABC, ER pos, Stroma, DCIS Stroma

description:
Gene expression data of  breast tumor associated stroma cells a from a Non-PABC patient
Raw data file: harvell_04_HG-U133_Plus_2.CEL


title: BC08-72, PABC, ER pos, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a patient with PABC
Raw data file: harvell_06_HG-U133_Plus_2.CEL


title: BC06_52, PABC, ER pos, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a patient with PABC
Raw data file: harvell_9_BC06_52_Stroma_HG-U133_Plus_2.CEL


title: BC06-25, NonPABC, ER pos, Epithelial, DCIS Epithelial

description:
Gene expression data of breast tumor epithelial cells from a Non-PABC patient
Raw data file: harvell_03_HG-U133_Plus_2.CEL


title: BC08-72, PABC, ER pos, Epithelial, Epithelial

description:
Gene expression data of breast tumor epithelial cells from a patient with PABC
Raw data file: harvell_05_HG-U133_Plus_2.CEL


title: Drosophila Imagoes at LDC 20d rotational control (1g-rot) females, biological rep2

city: Madrid

first: Raúl

last: Herranz

state: Madrid

address: Ramiro de Maeztu 9

department: Plant Cell Nucleolus, proliferation and microgravity

country: Spain

institute: Centro Investigaciones Biológicas

description:
DmImagoe_L0R.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations

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

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G System

data_processing: Analysis was performed using FIESTA viewer (bioinfogp.cnb.csic.es/tools/FIESTA). Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma). P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini and Hochberg, 1995; Reiner et al., 2003).

organism: Drosophila melanogaster

source_name: Drosophila imagoes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: OreR young (2 days-old)/mature (2 week-old) male/females were exposed to different gravitational facilities at 14C or 24C during 3-5 days.

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

treatment_protocol: Flies were exposed to different altered gravity simulators (RPM, Magnetic levitator, centrifgue) and inmediately after the treatment were placed on ice in the Trizol solution (GibcoBRL).

tag: developmental stage

value: imago

tag: gender

value: females

tag: strain

value: Oregon R

tag: age

value: 20 days-old

tag: g level

tag: temperature


title: Drosophila Imagoes outside LDC 20d (1g) females, biological rep2

description:
DmImagoe_L1R.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: BC07_20, PABC, ER neg, Stroma, Stroma

description:
Gene expression data of  breast tumor associated stroma cells from a patient with PABC
Raw data file: harvell_2_BC07_20_Stroma_HG-U133_Plus_2.CEL


title: Drosophila Imagoes outside LDC 20d (1g) females, biological rep1

description:
DmImagoe_L1Q.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC 20d rotational control (1g-rot) females, biological rep1

description:
DmImagoe_L0Q.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: MPH2 P4

city: Shanghai

first: Linyu

last: Shi

address: 320 Yueyang Road

country: China

institute: Institute of Biochemistry and Cell Biology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences

description:
M12-P4
Gene expression data from  PG-haESCs

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079,Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Macaca fascicularis

source_name: haploid embryonic stem cells derived from parthenogenic blastocysts

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Monkey parthenogenic haploid embryonic stem cells (PG-haESCs) were cultured on feeder in ES medium supplemented with Y27635 and Thiazovivin.

extract_protocol: Total RNA was extracted and purified using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA,US) according to the manufacturer's instructions.

treatment_protocol: ES cells were washed by DPBS (GIBCO), trypsinized, and collected by centrifugation.

tag: karotype

value: haploid

value: embryonic stem cells

tag: passage


title: MPH1 P9

description:
M2-P9
Gene expression data from  PG-haESCs


title: MES1 P12

description:
M5-P12
Gene expression data from ICSI-derived ESCs

source_name: embryonic stem cells derived from ICSI blastocysts

value: diploid


title: MES2 P4

description:
M22-P4
Gene expression data from ICSI-derived ESCs


title: Drosophila Imagoes at LDC 20d (2g) females, biological rep4

description:
DmImagoe_L2Z.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC 20d (2g) females, biological rep2

description:
DmImagoe_L2X.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside LDC (1g) females, biological rep2

description:
DmImagoe_H1R.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations

value: 5 days-old


title: MES3 P4

description:
M24-P4
Gene expression data from ICSI-derived ESCs


title: MPH1 P11

description:
M1-P11
Gene expression data from  PG-haESCs


title: MPH1 P7

description:
M2-P7
Gene expression data from  PG-haESCs


title: Drosophila Imagoes at LDC rotational control (1g-rot) females, biological rep2

description:
DmImagoe_H0R.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: MPH1 P8

description:
M1-P8
Gene expression data from  PG-haESCs


title: MF rep2

description:
118-2
Gene expression data from female somatic fibroblasts

source_name: female somatic fibroblasts

value: somatic cells


title: 14092647 - Col-0 Repet 1 vs xrn2-2 Repet 1

description: What are the endogenous RNA substrates co-regulated by RQC and PTGS pathways?

hyb_protocol: xrn2-2 Repet 1 Cy5 / Col-0 Repet 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia

value: mutant (xrn2-2 sail_781e02)

value: wild type (control)


title: Drosophila Imagoes outside LDC (1g) females, biological rep1

description:
DmImagoe_H1Q.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC rotational control (1g-rot) females, biological rep1

description:
DmImagoe_H0Q.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC 20d (2g) females, biological rep3

description:
DmImagoe_L2Y.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: MF rep1

description:
118-1
Gene expression data from female somatic fibroblasts


title: Drosophila Imagoes at LDC (2g) females, biological rep3

description:
DmImagoe_H2Y.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC (2g) females, biological rep4

description:
DmImagoe_H2Z.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC 20d (2g) females, biological rep1

description:
DmImagoe_L2V.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet 80h (1g 24ºC) females, biological rep3

description:
DmImagoe_3oI.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC (2g) females, biological rep1

description:
DmImagoe_H2V.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at LDC (2g) females, biological rep2

description:
DmImagoe_H2X.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet 80h (1g 24ºC) females, biological rep1

description:
DmImagoe_3oG.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet 80h (1g 24ºC) females, biological rep2

description:
DmImagoe_3oH.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet (1g 24ºC) females, biological rep2

description:
DmImagoe_3oE.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet 80h (0g*) females, biological rep1

description:
DmImagoe_30G.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet (1g) females, biological rep2

description:
DmImagoe_3cF.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet (1g) females, biological rep1

description:
DmImagoe_3cD.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (2g*) females, biological rep1

description:
DmImagoe_32D.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet (1g 24ºC) females, biological rep1

description:
DmImagoe_3oD.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (2g*) females, biological rep3

description:
DmImagoe_32F.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet 80h (1g*) females, biological rep1

description:
DmImagoe_31G.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet 80h (1g*) females, biological rep2

description:
DmImagoe_31H.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (1g*) females, biological rep2

description:
DmImagoe_31E.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside the magnet (1g 24ºC) females, biological rep3

description:
DmImagoe_3oF.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet 80h (0g*) females, biological rep2

description:
DmImagoe_30H.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at RPM (0g) males, biological rep3

description:
DmImagoe_90G.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations

value: males


title: Drosophila Imagoes at the magnet (2g*) females, biological rep2

description:
DmImagoe_32E.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (1g*) females, biological rep3

description:
DmImagoe_31F.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (1g*) females, biological rep1

description:
DmImagoe_31D.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at RPM (0g) males, biological rep1

description:
DmImagoe_90E.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at RPM (0g) males, biological rep4

description:
DmImagoe_90H.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside RPM (1g) males, biological rep2

description:
DmImagoe_91G.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside RPM (1g) males, biological rep1

description:
DmImagoe_91E.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside RPM (1g) males, biological rep3

description:
DmImagoe_91H.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (0g*) females, biological rep3

description:
DmImagoe_30F.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (0g*) females, biological rep1

description:
DmImagoe_30D.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at RPM (0g) males, biological rep2

description:
DmImagoe_90F.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside RPM (1g) females, biological rep3

description:
DmImagoe_91C.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at the magnet (0g*) females, biological rep2

description:
DmImagoe_30E.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside RPM (1g) females, biological rep1

description:
DmImagoe_91A.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes outside RPM (1g) females, biological rep2

description:
DmImagoe_91B.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Drosophila Imagoes at RPM (0g) females, biological rep3

description:
DmImagoe_90C.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations


title: Pupae outside LDC (1g) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_R6B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

source_name: Drosophila pupae before imagoes hatch

growth_protocol: OreR late larvae were developed at 24C during 3.5 days into different gravitational and environmental conditions

treatment_protocol: Early pupae were exposed to a cold step (ΔT) previous to the gravitational treatment or not. During the gravitational treatment pupae have a limite amount of oxigen (↓O2) in a closed container or not. Flies were exposed to different altered gravity simulators (RPM, Magnetic levitator, centrifgue) and inmediately after the treatment were placed on ice in the Trizol solution (GibcoBRL).

value: late pupae

value: late pupae just before eclosion

tag: environment (Δt)

value: suboptimal

tag: environment (↓o2)

tag: magnetic field (*)

value: No


title: Drosophila Imagoes at RPM (0g) females, biological rep1

description:
DmImagoe_90A.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations

value: imago


title: Pupae at LDC rotational control (1g-rot) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_RCA.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_RCB.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) constrained (↓O2), biological rep2

description:
DmPupae_Q6B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: normal


title: Pupae outside LDC (1g) constrained (↓O2), biological rep1

description:
DmPupae_Q6A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: Oregon R


title: Pupae at LDC rotational control (1g-rot) constrained (↓O2), biological rep3

description:
DmPupae_QCC.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Drosophila Imagoes at RPM (0g) females, biological rep2

description:
DmImagoe_90B.CEL
Gene expression data under altered gravity in different Drosophila imagoes populations

value: females


title: Pupae at LDC (12g) constrained biological rep1

description:
DmPupae_R9E.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (↓O2), biological rep1

description:
DmPupae_Q9A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (6g) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_R8H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_R9F.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (↓O2), biological rep3

description:
DmPupae_Q9C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (↓O2), biological rep2

description:
DmPupae_Q9B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (6g) constrained (↓O2), biological rep1

description:
DmPupae_Q8H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_R6A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (6g) constrained (↓O2), biological rep2

description:
DmPupae_Q8I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) constrained (ΔT), biological rep2

description:
DmPupae_R1H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) constrained (ΔT), biological rep3

description:
DmPupae_R1I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) constrained (↓O2), biological rep3

description:
DmPupae_Q6C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) constrained (ΔT), biological rep1

description:
DmPupae_R0A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) constrained (↓O2), biological rep2

description:
DmPupae_QCB.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) constrained (ΔT), biological rep1

description:
DmPupae_R1A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (6g) constrained (ΔT), biological rep2

description:
DmPupae_R3I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) constrained (ΔT), biological rep3

description:
DmPupae_R0I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) constrained (↓O2), biological rep1

description:
DmPupae_QCA.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (6g) constrained (ΔT), biological rep1

description:
DmPupae_R3H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) constrained (ΔT), biological rep2

description:
DmPupae_R0H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside LDC (1g) without constrains, biological rep1

description:
DmPupae_Q1A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (ΔT), biological rep3

description:
DmPupae_R4C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) without constrains, biological rep3

description:
DmPupae_Q0I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC rotational control (1g-rot) without constrains, biological rep2

description:
DmPupae_Q0H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (ΔT), biological rep1

description:
DmPupae_R4A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) constrained (ΔT), biological rep2

description:
DmPupae_R4B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (6g) without constrains, biological rep1

description:
DmPupae_Q3H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T6, biological rep1

city: Taiyuan City

first: Xiao Chun

last: Wei

state: Shanxi Shanxi

address: No.382, Wuyi Road,Taiyuan City.

department: Department of Orthopaedics

institute: the Second Hospital of Shanxi Medical University

description: Rattus norvegicus_T6-1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100 (Affymetrix Expression Expression Console v.1.1).

label: Biotin

organism: Rattus norvegicus

source_name: knee articular cartilage in latter-stage elderly

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

growth_protocol: The cartilage that was harvested individually from the right knee joint were stored at liquid nitrogen temperatures at once with protected by Rnasin inhibitor.

treatment_protocol: After grinded under the ice, cartilage tissue were collected for further total RNA extraction.

value: Sprague-Dawley

value: latter-stage elderly

tag: time point

value: T6 (18-month)

value: knee articular cartilage


title: knee articular cartilage at T6, biological rep2

description: Rattus norvegicus_T6-2


title: knee articular cartilage at T6, biological rep3

description: Rattus norvegicus_T6-3


title: knee articular cartilage at T5, biological rep2

description: Rattus norvegicus_T5-2

source_name: knee articular cartilage in early-stage elderly

value: early-stage elderly

value: T5 (12-month)


title: knee articular cartilage at T5, biological rep3

description: Rattus norvegicus_T5-3


title: Pupae at LDC (6g) without constrains, biological rep2

description:
DmPupae_Q3I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T5, biological rep1

description: Rattus norvegicus_T5-1


title: knee articular cartilage at T4, biological rep1

description: Rattus norvegicus_T4-1

source_name: knee articular cartilage in middle-aged

value: middle-aged

value: T4 (6-month)


title: Pupae outside LDC (1g) without constrains, biological rep2

description:
DmPupae_Q1H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T4, biological rep3

description: Rattus norvegicus_T4-3


title: knee articular cartilage at T4, biological rep2

description: Rattus norvegicus_T4-2


title: Pupae outside LDC (1g) without constrains, biological rep3

description:
DmPupae_Q1I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T3, biological rep2

description: Rattus norvegicus_T3-2

source_name: knee articular cartilage in adult

value: adult

value: T3 (3-month)


title: Pupae at LDC (6g) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_R8I.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: late pupae just before eclosion


title: Pupae outside the magnet (1g) constrained (ΔT), biological rep3

description:
DmPupae_5oC.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: suboptimal

value: No


title: Pupae at LDC (12g) without constrains, biological rep1

description:
DmPupae_Q4A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: normal


title: Pupae outside the magnet (1g) constrained (ΔT), biological rep2

description:
DmPupae_5oB.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: Oregon R


title: knee articular cartilage at T3, biological rep3

description: Rattus norvegicus_T3-3


title: Pupae at LDC rotational control (1g-rot) without constrains, biological rep1

description:
DmPupae_Q0A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at LDC (12g) without constrains, biological rep2

description:
DmPupae_Q4B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside the magnet (1g) constrained (ΔT), biological rep1

description:
DmPupae_5oA.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside the magnet (1g) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_5cB.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T3, biological rep1

description: Rattus norvegicus_T3-1


title: knee articular cartilage at T2, biological rep3

description: Rattus norvegicus_T2-3

source_name: knee articular cartilage in youth

value: youth

value: T2 (week 4)


title: Pupae at the magnet (2g*) constrained (ΔT & ↓O2), biological rep3

description:
DmPupae_52C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: Yes


title: Pupae outside the magnet (1g) constrained (ΔT & ↓O2), biological rep3

description:
DmPupae_5cC.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside the magnet (1g) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_5cA.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at the magnet (2g*) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_52B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T2, biological rep1

description: Rattus norvegicus_T2-1

value: Sprague-Dawley


title: knee articular cartilage at T0, biological rep3

description: Rattus norvegicus_T0-3

source_name: knee articular cartilage in newborn

value: newborn

value: T0 (day 0)

value: knee articular cartilage


title: knee articular cartilage at T1, biological rep2

description: Rattus norvegicus_T1-2

source_name: knee articular cartilage in childhood

value: childhood

value: T1 (week 1)


title: knee articular cartilage at T1, biological rep1

description: Rattus norvegicus_T1-1


title: knee articular cartilage at T1, biological rep3

description: Rattus norvegicus_T1-3


title: knee articular cartilage at T0, biological rep2

description: Rattus norvegicus_T0-2


title: Pupae at the magnet (1g*) constrained (ΔT & ↓O2), biological rep3

description:
DmPupae_51C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at the magnet (1g*) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_51B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at the magnet (1g*) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_51A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T0, biological rep1

description: Rattus norvegicus_T0-1


title: Pupae at the magnet (2g*) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_52A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: knee articular cartilage at T2, biological rep2

description: Rattus norvegicus_T2-2


title: Pupae at the magnet (0g*) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_50B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at the magnet (0g*) constrained (ΔT & ↓O2), biological rep3

description:
DmPupae_50C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae outside the magnet (1g) without constrains, biological rep3

description:
DmPupae_6oC.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: MPH2-P5 vs adipose

type: genomic

description: CNV analysis of MPH2-P5 vs adipose

hyb_protocol: Array  hybridization  was  performed  using  Agilent  Oligo  aCGH  Hybridization  Kit (Cat#5188-5380,  Agilent  technologies,  Santa  Clara,  CA,  US)in  Hybridization  Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 65℃, 20rpm for 24 hours. Array  wash  was  performed  using  Agilent  Oligo  aCGH  Wash  Buffer  1  and  2  set (Cat#5188-5226,  Agilent  technologies,  Santa  Clara,  CA,  US)  in  staining  dishes (Cat#121,  Thermo  Shandon,  Waltham,  MA,  US)  follow  the  manufacturer’s instructions.

scan_protocol: Slides  were  scanned  by  Agilent  Microarray  Scanner  (Cat#G2565BA,  Agilent technologies, Santa Clara, CA, US),scan  resolution= 3μm, PMT 100% to generate tiff image.

data_processing: Raw data was acquired  and  normalized (algorithm:  LOWESS) using  Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Calculate Z-score for each CNV region using DNA Analytics 4.0.81 software (Agilent technologies, Santa Clara, CA, US), window size is set to 1M and Z-score threshold is set to 4.0.

molecule: genomic DNA

source_name: female adipose cells

label_protocol: Experimental  sample  and  control  sample  were  labeled  with  Cy5  NHS  ester(Cat#PA15100,  GE  healthcare  Biosciences,  Pittsburgh,  PA,  US)  and  Cy3  NHS  ester(Cat#PA13105,  GE  healthcare  Biosciences,  Pittsburgh,  PA,  US)  respectively,  using Agilent Genomic DNA Labeling Kit PLUS (Cat#5188-5309, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions. Labeled DNA fragments were purified  using  Amicon  Ultra-0.5,  Ultracel-30  Membrane,30  kDa(Cat#UFC5030BK, Millipore,  Billerica,  MA,  US).  Measured  the  absorbance  at A260nm  (DNA),A550nm (Cyanine 3),and A650nm(Cyanine 5)of purified DNA fragments to calculate the Specific Activity.

extract_protocol: The genomic DNA was extracted using Promega Genomic DNA Purification Kit (A1620).

value: somatic cells

value: haploid embryonic stem cells


title: Pupae at the magnet (0g*) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_50A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae


title: MPH1-P20 vs adipose

description: CNV analysis of MPH1-P20 vs adipose


title: MPH1-P11 vs adipose

description: CNV analysis of MPH1-P11 vs adipose


title: adipose vs adipose

description: CNV analysis of adipose vs adipose


title: Pupae outside the magnet (1g) without constrains, biological rep2

description:
DmPupae_6oB.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae just before eclosion


title: Pupae outside the magnet (1g) constrained (↓O2), biological rep3

description:
DmPupae_6cC.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: suboptimal


title: Pupae outside the magnet (1g) without constrains, biological rep1

description:
DmPupae_6oA.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: No


title: Pupae outside the magnet (1g) constrained (↓O2), biological rep2

description:
DmPupae_6cB.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: normal


title: SD_HippocampalSliceCulture_BDV_23 days_rep1

city: Freiburg

first: Martin

last: Schwemmle

address: Hermann-Herder-Str. 11

country: Germany

institute: University Freiburg

description: Gene expression in BDV infected after 23 days

hyb_protocol: Hybridization was performed with 0.6 mg of labeled cDNA per array at a temperature of 65°C overnight

scan_protocol: The hybridized microarrays are scanned with a laser scanner (Axon 4000A) using one color scan setting for 4x44k array slides

data_processing: The Feature Extraction Software 9.5.3.1 was then used to process and analyze array images. The software returns a series of spot quality measures to evaluate the quality and reliability of spot intensity estimates. The raw data were analyzed using GeneSpring GX 10.0

source_name: Hippocampal slice culture, 23 days, BDV infected

label_protocol: 0.5 µg of total RNA was reverse transcribed into cDNA and labeled with Cy3 using the one-color Quick Amp Labeling Kit (Agilent).

growth_protocol: Hippocampal slice cultures were prepared from newborn Lewis and SD rats (P0-P2). Intact slices were placed on humidified porous membranes (CM50; Millipore) in 6-well plates containing 1.2 ml of serum-based nutrient medium (25% heat-inactivated horse serum, 50% MEM and 25% Hanks’ balanced salt solution supplemented with GlutamaxTM at 2 mM final concentration). The medium was changed 3 times per week for various periods (1, 2, 3 or 4 weeks).

extract_protocol: RNA from 4 Hippocampal slice cultures was extracted with 1 ml TriFast (peqGOLD) for 10 min at room temperature and then mixed with 200 µl Chloroform with vortexting for 15 sec. The mixture was incubated at room temperature for 10 min followed by 10-min centrifugation at >10000g. The upper transparent phase was collected, mixed with 500 µl isopropanol containing glycogen and incubated on ice for 30 min. RNA was then pelleted with 10000g of centrifugation for 30mins, washed with 80% ethanol. Finally, RNA was air-dry and dissolved in diethylpyrocarbonate-treated water. The RNA amount was determined by NanoDrop (NanoDrop Technologies).

treatment_protocol: Slices were infected immediately after preparation with 1 µl of BDV virus stock, corresponding to ca. 1000 focus forming units (FFU). Control cultures received normal medium but without BDV infection.

value: Sprague Dawley

value: Hippocampus slice culture

tag: infection

value: BDV


title: SD_HippocampalSliceCulture_BDV_23 days_rep2


title: SD_HippocampalSliceCulture_BDV_23 days_rep3


title: Pupae outside the magnet (1g) constrained (↓O2), biological rep1

description:
DmPupae_6cA.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: Oregon R


title: LEW_HippocampalSliceCulture_BDV_23 days_rep2

value: Lewis


title: LEW_HippocampalSliceCulture_BDV_23 days_rep3


title: Wnt5a 2

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

hyb_protocol: The arrays were hybridized overnight at 45oC, and then washed, stained, and scanned the next day. Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

scan_protocol: Gene expression levels were extracted using AGCC (Affymetrix GeneChip Command Console). Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).

data_processing: The data was analyzed with Genesprings using the default settings. The summarized probeset was generated using RMA summarization algorithm. Quantile normalization was used.

organism: Mus musculus

source_name: 4T1 Wnt5a transduced

label_protocol: Detailed genechip analysis procedures are presented in the Manufacturer’s GeneChip Expression Technical Manual (Affymetrix).  Briefly, 50ng of total RNA from each sample was used in a two cycle cDNA amplification protocol using T7-linked oligo dT primers as per the manufacturer’s instructions.  After the first round of cDNA synthesis an in vitro transcription step was utilized to amplify the RNA following which a second round of cDNA synthesis was performed.  Subsequently, cRNA was generated and biotin was incorporated into the cRNA strand by standard methods (Affymetrix) followed by cRNA fragmentation, and preparation of hybridization cocktail.

growth_protocol: Vector and Wnt5a expressing 4T1 cells were passaged and grown according to ATCC standard instructions for 4T1 cells. When cells were 70% confluent RNA was extracted.

extract_protocol: RNA was extracted from the cells in culture using the standard Trizol method.  RNA was Dnase treated and then tested using RT-PCR to assure there was no DNA contamination in the samples.

tag: cell line

tag: genotype/variation


title: SD_HippocampalSliceCulture_uninf_23 days_rep2

description: Gene expression in uninfected after 23 days

source_name: Hippocampal slice culture, 23 days, uninfected

tag: tissue

value: uninfected


title: Pupae at the magnet (2g*) constrained (↓O2), biological rep2

description:
DmPupae_62B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: Yes


title: LEW_HippocampalSliceCulture_BDV_23 days_rep1


title: Pupae at the magnet (1g*) constrained (↓O2), biological rep3

description:
DmPupae_61C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at the magnet (2g*) constrained (↓O2), biological rep3

description:
DmPupae_62C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Pupae at the magnet (2g*) constrained (↓O2), biological rep1

description:
DmPupae_62A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Wnt5a 1


title: vector 1

source_name: 4T1 vector transduced

value: Control


title: LEW_HippocampalSliceCulture_uninf_23 days_rep3


title: SD_HippocampalSliceCulture_uninf_23 days_rep1


title: vector 2


title: SD_HippocampalSliceCulture_uninf_23 days_rep3


title: LEW_HippocampalSliceCulture_uninf_23 days_rep2


title: LEW_HippocampalSliceCulture_uninf_23 days_rep1


title: Pupae at the magnet (1g*) constrained (↓O2), biological rep1

description:
DmPupae_61A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Glutamine synthetase subcompartment of hepatic acinus 2PV

city: St. John's

first: John

middle: Thomas

last: Brosnan

state: NL

address: 232 Elizabeth Avenue

department: Biochemistry

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: A total of 1.5 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with strepavidini-Cy3 prior to visualization.

scan_protocol: BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.

data_processing: After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value).  Both non-normalized and normalized (qspline) data were generated for each tissue type.

source_name: Liver

label_protocol: Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.

extract_protocol: RNA was extracted from all tissues using a standard protocol and Tri-reagent.

treatment_protocol: Liver tissue was prepared and fixed on a glass slide, and laser capture microdissection was used to collect specific cell types.  Three types of samples were analyzed:peri-venous, non-peri-venous, and an entire scrape of tissue from the slide.


title: Pupae at the magnet (0g*) constrained (↓O2), biological rep3

description:
DmPupae_60C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Glutamine synthetase subcompartment of hepatic acinus 1PV


title: nivh70

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

value: Male

tag: population

value: Nivkhs

tag: region

value: Sakhalin Island


title: Glutamine synthetase subcompartment of hepatic acinus PV3


title: 032652

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
Amela-429 vs. Amela cell line 429
Date:2007/04/04

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

scan_protocol: Scanned on a GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide normalization: quantile, Intraslide normalization: printtiploess, Background normalization: Kooperberg, Software used: rscript. VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion

extract_protocol: Other

value: TiRP Ink4a/ArfF/F B10.D2

tag: sample

value: nonpigmented amelanotic melanoma

source_name: Amela cell line 429

value: Amela cell line 429

value: Amela 429

tag: cell type

value: nonpigmented amelanotic melanoma cells


title: chukchi113 v2

tag: gender

value: Female

value: Chukchis

value: Northeast Siberia


title: 032653

description:
Amela-288 vs. Amela cell line 288
Date:2007/04/04

tag: strain

source_name: Amela cell line 288

value: Amela cell line 288

value: Amela 288


title: koryakE84 v2

value: Koryaks


title: Pupae at the magnet (1g*) constrained (↓O2), biological rep2

description:
DmPupae_61B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

source_name: Drosophila pupae before imagoes hatch

tag: developmental stage

value: late pupae

value: Oregon R

tag: age

value: late pupae just before eclosion

tag: g level

value: normal

value: suboptimal

value: Yes


title: Pupae at the magnet (0g*) constrained (↓O2), biological rep2

description:
DmPupae_60B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

tag: environment (Δt)


title: Zones 1+2 of hepatic acinus 1NPV

value: Zones 1+2 of hepatic acinus


title: Pupae at the magnet (0g*) constrained (↓O2), biological rep1

description:
DmPupae_60A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

tag: environment (↓o2)


title: even838

value: blood

value: Male

value: Evens

value: Sakha


title: Zones 1+2 of hepatic acinus 2NPV


title: even2694

value: Female


title: 016674

description:
CTRL vs. Amela-396
Date:2006/09/05

hyb_protocol: CGH-Agilent-4rpm : 750.0 ng at 62 degree_C during 17 hours

data_processing: Interslide normalization: scale, Intraslide normalization: printtiploess, Background normalization: Kooperberg, Software used: rscript. VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: CTRL

extract_protocol: Roche

value: TiRP Ink4a/ArfF/F B10.D2

value: CTRL

value: healthy tail skin

value: nonpigmented amelanotic melanoma


title: even2754


title: Pupae outside RPM (1g) constrained (ΔT & ↓O2), biological rep4

description:
DmPupae_71H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

tag: magnetic field (*)

value: No


title: nivh120

value: Nivkhs

value: Sakhalin Island


title: Pupae outside RPM (1g) constrained (ΔT & ↓O2), biological rep3

description:
DmPupae_71G.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R

value: late pupae just before eclosion


title: 016675

description:
Amela-491 vs. CTRL
Date:2006/09/05


title: even2763


title: Slide scrape of liver 1SC

value: Slide scrape of liver


title: 016481

description:
Mela-281 vs. Amela-353
Date:2006/09/01

value: pigmented melanotic melanoma


title: Pupae outside RPM (1g) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_71F.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: suboptimal


title: nihv69

value: blood

value: Male


title: 016671

description:
Amela-353 vs. CTRL
Date:2006/09/05


title: Slide scrape of liver 2SC


title: Pupae outside RPM (1g) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_71E.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: Dolgan1708

value: Dolgans

value: Sakha


title: 016520

description:
Amela-491 vs. Mela-493
Date:2006/09/08

value: TiRP Ink4a/ArfF/F B10.D2


title: Slide scrape of liver SC3


title: Zones 1+2 of hepatic acinus NPV3

value: Zones 1+2 of hepatic acinus


title: U2-OS cells with OGE

city: Taichung

first: Jer-Yuh

last: Liu

address: Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

description: Gene expression data from Osteosarcoma U2-OS cells exposure to 600 μg/mL OGE for 24 hours

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were hybridized to 11 mg of labeled, amplified cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007)

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

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

label_protocol: 100ng of total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

growth_protocol: The human osteosarcoma HOS and U2-OS cells and the human osteoblast hFOS cells were maintained in DMEM supplemented with 10% FBS and 100 μg/ml penicillin/streptomycin at 37oC (the human osteoblast hFOS cells at 34 oC) in a humidified atmosphere containing 5% CO2. Cells were seeded in culture plates at an initial density of 1x105 cells/ml and grown to approximately 80% confluence.

treatment_protocol: The culture was treated with OGE at indicated concentrations for 24, 48 or 72 h and subsequently washed with phosphate-buffered saline (PBS; 25 mM sodium phosphate, 150 mM NaCl, pH 7.2). The resulting cells were collected for following analyses.

tag: treatment

value: exposure to 600 ug/mL OGE

tag: tumor

value: Human osterogenic sarcoma

value: Bone; osteosarcoma


title: 032654

description:
Amela-491 vs. Amela cell line 486
Date:2007/04/04

value: nonpigmented amelanotic melanoma

source_name: Amela cell line 486

value: Amela cell line 486

value: nonpigmented amelanotic melanoma cells

tag: cell line

value: Amela 486


title: even2682

value: Female

value: Evens


title: Pupae at RPM (0g) constrained (ΔT & ↓O2), biological rep4

description:
DmPupae_70H.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R

value: late pupae just before eclosion

value: No


title: Pupae at RPM (0g) constrained (ΔT & ↓O2), biological rep2

description:
DmPupae_70F.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: suboptimal


title: even1574

value: blood

value: Sakha


title: ket14

value: Kets

value: Central Siberia


title: Pupae at RPM (0g) constrained (ΔT & ↓O2), biological rep3

description:
DmPupae_70G.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis


title: 032926

description:
Amela cell line 486 vs. Amela-491
Date:2007/04/04

value: TiRP Ink4a/ArfF/F B10.D2


title: even2759

value: Male


title: Dolgan3865

value: Dolgans


title: 016605

description:
Mela-493 vs. Amela-491
Date:2006/09/01

value: pigmented melanotic melanoma

value: nonpigmented amelanotic melanoma


title: HOS cells

description: Gene expression data from Osteosarcoma HOS cells exposure to 0 μg/mL OGE for 24 hours

value: HOS

value: exposure to 0 ug/mL OGE

value: human osteosarcoma

value: Bone; osteosarcoma


title: Pupae at RPM (0g) constrained (ΔT & ↓O2), biological rep1

description:
DmPupae_70E.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R


title: even2737

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChips (Illumina).

value: Female

value: Evens


title: 016526

description:
Amela-514 vs. Mela-TBD35
Date:2006/09/01


title: U2-OS cells

description: Gene expression data from Osteosarcoma U2-OS cells exposure to 0 μg/mL OGE for 24 hours

value: Human osterogenic sarcoma


title: Dolgan3840

value: blood

value: Sakha


title: shor123

value: Shors

value: South Siberia


title: HOS cells with OGE

description: Gene expression data from Osteosarcoma HOS cells exposure to 600 μg/mL OGE for 24 hours

value: exposure to 600 ug/mL OGE


title: ket3

value: Kets

value: Central Siberia


title: Pupae outside RPM (1g) constrained (ΔT), biological rep3

description:
DmPupae_71C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae just before eclosion

value: suboptimal

value: normal

value: No


title: shor125


title: shor122


title: 032863

description:
Amela-353 vs. Amela cell line 429
Date:2007/04/04

value: TiRP Ink4a/ArfF/F B10.D2

value: nonpigmented amelanotic melanoma

value: Amela cell line 429

value: Amela 429

value: nonpigmented amelanotic melanoma cells


title: colon_NMS_D_4

city: Perugia

first: Stefano

last: Fiorucci

address: Via E dal Pozzo

department: Dipartimento di Medicina Clinica e Sperimentale

country: Italy

institute: Universita di Perugia

hyb_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to Agilent Whole Rat Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006). Cotrol probes were not included in the processing.

label_protocol: 100 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Male, Wistar rats  (200-250 g, Charles River, Monza, Italy) were housed in plastic cages and maintained under controlled conditions. All experimental procedures were approved by our institutional animal research committees and were in accordance with nationally approved guidelines for the treatment of laboratory animals. All experiments were conducted in blind manner in that the observers  were not aware of the identity of drugs administered to each animal. Pups in the NMS group were separated from their mothers and placed into individual cages in another room for 180 min daily from postnatal day 2 to day 14, whereas normally-handled (NH) pups were maintained in their home cage with the dam. All rats were treated daily by gavage with placebo or VSL#3 at the dose of 18 billions in 100 μL saline according to the experimental design. Microarray studies were conducted on in Group 2 (healthy, CRD, Group C), Group 4 (NMS, CRD, Group M) and Group 5 (NMS, VSL#3 administered from day 3 to day 60, CRD, Group D).  At the end of the studies (postnatal day 60), animals were sacrificed and the colon collected.

extract_protocol: The RNA was isolated by using standard RNA extraction protocols (Trizol, Sigma-Aldrich) and the RNA quality checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies). Only RNAs with calculated RNA Integrity Numbers (RIN) higher than 6 were accepted.

value: Wistar rats

tag: gener

value: male

tag: weight

value: colon

tag: neonatal maternal separation (nms)

value: yes

value: daily by gavage with VSL#3 (18x10E9 VSL#3/100 ul saline)

tag: treatment period

value: day 3 to day 60


title: colon_NMS_D_3

tag: tissue


title: Pupae outside RPM (1g) constrained (ΔT), biological rep2

description:
DmPupae_71B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R


title: 032864

description:
Amela cell line 429 vs. Amela-429
Date:2007/04/04

tag: sample

tag: cell type


title: colon_NMS_D_2

tag: strain


title: Pupae outside RPM (1g) constrained (ΔT), biological rep1

description:
DmPupae_71A.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

tag: developmental stage

value: late pupae just before eclosion


title: Yakut3185

value: blood

tag: gender

value: Female

tag: population

value: Yakuts

tag: region

value: Sakha


title: 016575

description:
CTRL vs. Mela-493
Date:2006/09/08

value: TiRP Ink4a/ArfF/F B10.D2

value: CTRL

value: healthy tail skin

value: pigmented melanotic melanoma


title: 016513

description:
Mela-442 vs. Amela-396
Date:2006/09/01

value: nonpigmented amelanotic melanoma


title: Pupae at RPM (0g) constrained (ΔT), biological rep3

description:
DmPupae_70C.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

tag: age

tag: g level

tag: environment (Δt)

value: suboptimal

tag: environment (↓o2)

value: normal

value: No


title: colon_NMS_D_1

value: Wistar rats

value: male

value: colon

value: yes

tag: treatment

value: daily by gavage with VSL#3 (18x10E9 VSL#3/100 ul saline)


title: colon_NMS_M_4

tag: gener

value: daily by gavage with placebo (100 ul saline)

value: day 3 to day 60


title: Pupae at RPM (0g) constrained (ΔT), biological rep2

description:
DmPupae_70B.CEL
Gene expression data under altered gravity and altered environmental conditions during Drosophila metamorphosis

value: late pupae

value: Oregon R

value: late pupae just before eclosion

tag: magnetic field (*)


title: shor117

value: blood

value: Male

value: Shors

value: South Siberia