title: 534330A03 - 10_TREATMENT1_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 10_TREATMENT1_48H_REP1 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.

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: caulin leaf - Growth conditions (Media/hygrometry/Temperature/Light) -peat+perlite (4:1). RH 65%. 20+/-2°C. Daylight + HQI light

treatment_protocol: Name:WATER_48H - compound based treatment - pathogen infection,water:.

treatment_protocol: Name:T1_48H - compound based treatment - pathogen infection,water inoculation:.


title: 534330A08 - 8_WATER_48H_REP1 vs 12_TREATMENT3_48H_REP1

status: Public on Apr 17 2017

type: RNA

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Biological question (15 lines max): Identification of grape genes regulated in response to resistance inducer treatments. This transcriptomic analysis should provide insight in the mode of action of the compounds under study and yield generic data relevant to grape defense reaction.

hyb_protocol: 12_TREATMENT3_48H_REP1 Cy5 / 8_WATER_48H_REP1 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: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Vitis vinifera

treatment_protocol: Name:T3_48H - compound based treatment - pathogen infection,water inoculation:.

tag: vitis vinifera  - age


title: 534330A04 - 8_WATER_48H_REP1 vs 10_TREATMENT1_48H_REP1

hyb_protocol: 10_TREATMENT1_48H_REP1 Cy5 / 8_WATER_48H_REP1 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: 561856A02 - 44_ADJ_24H_REP1 vs 43_WATER_24H_REP1

hyb_protocol: 43_WATER_24H_REP1 Cy5 / 44_ADJ_24H_REP1 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.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  . (PT-SIGMA-01_30-10-2012_T.pdf)

growth_protocol: caulin leaf - peat+perlite (4:1). RH 65%. 20+/-2°C. Daylight + HQI light

treatment_protocol: Name:WATER_24H - compound based treatment - water,water:.

treatment_protocol: Name:ADJUVANT_24H - compound based treatment - control,adjuvant:.


title: 534330A11 - 14_TREATMENT5_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 14_TREATMENT5_48H_REP1 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.

treatment_protocol: Name:T5_48H - compound based treatment - pathogen infection,water inoculation:.


title: 534108A09 - 22_WATER_48H_REP2 vs 27_TREATMENT4_48H_REP2

hyb_protocol: 27_TREATMENT4_48H_REP2 Cy5 / 22_WATER_48H_REP2 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.

treatment_protocol: Name:T4_48H - compound based treatment - pathogen infection,water inoculation:.


title: 534330A12 - 8_WATER_48H_REP1 vs 14_TREATMENT5_48H_REP1

hyb_protocol: 14_TREATMENT5_48H_REP1 Cy5 / 8_WATER_48H_REP1 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: 534108A08 - 26_TREATMENT3_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 26_TREATMENT3_48H_REP2 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: 534330A09 - 13_TREATMENT4_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 13_TREATMENT4_48H_REP1 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: 534330A05 - 11_TREATMENT2_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 11_TREATMENT2_48H_REP1 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.

treatment_protocol: Name:T2_48H - compound based treatment - pathogen infection,water inoculation:.


title: 534330A07 - 12_TREATMENT3_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 12_TREATMENT3_48H_REP1 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: 534330A06 - 8_WATER_48H_REP1 vs 11_TREATMENT2_48H_REP1

hyb_protocol: 11_TREATMENT2_48H_REP1 Cy5 / 8_WATER_48H_REP1 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: 534108A03 - 22_WATER_48H_REP2 vs 24_TREATMENT1_48H_REP2

hyb_protocol: 24_TREATMENT1_48H_REP2 Cy5 / 22_WATER_48H_REP2 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.

treatment_protocol: Name:ADJUVANT_48H - compound based treatment - pathogen infection,adjuvant:.


title: 534108A10 - 27_TREATMENT4_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 27_TREATMENT4_48H_REP2 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: 561856A01 - 43_WATER_24H_REP1 vs 44_ADJ_24H_REP1

hyb_protocol: 44_ADJ_24H_REP1 Cy5 / 43_WATER_24H_REP1 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: 534108A11 - 22_WATER_48H_REP2 vs 28_TREATMENT5_48H_REP2

hyb_protocol: 28_TREATMENT5_48H_REP2 Cy5 / 22_WATER_48H_REP2 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: 534330A10 - 8_WATER_48H_REP1 vs 13_TREATMENT4_48H_REP1

hyb_protocol: 13_TREATMENT4_48H_REP1 Cy5 / 8_WATER_48H_REP1 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: 534108A07 - 22_WATER_48H_REP2 vs 26_TREATMENT3_48H_REP2

hyb_protocol: 26_TREATMENT3_48H_REP2 Cy5 / 22_WATER_48H_REP2 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: 534108A12 - 28_TREATMENT5_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 28_TREATMENT5_48H_REP2 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: 534108A04 - 24_TREATMENT1_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 24_TREATMENT1_48H_REP2 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: 534108A05 - 22_WATER_48H_REP2 vs 25_TREATMENT2_48H_REP2

hyb_protocol: 25_TREATMENT2_48H_REP2 Cy5 / 22_WATER_48H_REP2 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: 534108A06 - 25_TREATMENT2_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 25_TREATMENT2_48H_REP2 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: 534105A12 - 42_TREATMENT5_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 42_TREATMENT5_48H_REP3 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: 534105A10 - 41_TREATMENT4_48H_REP3 vs 36_WATER_48H_REP3

type: mixed

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 41_TREATMENT4_48H_REP3 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.

molecule: other


title: 534105A09 - 36_WATER_48H_REP3 vs 41_TREATMENT4_48H_REP3

hyb_protocol: 41_TREATMENT4_48H_REP3 Cy5 / 36_WATER_48H_REP3 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: 534105A08 - 40_TREATMENT3_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 40_TREATMENT3_48H_REP3 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: 534105A11 - 36_WATER_48H_REP3 vs 42_TREATMENT5_48H_REP3

hyb_protocol: 42_TREATMENT5_48H_REP3 Cy5 / 36_WATER_48H_REP3 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: 534105A06 - 39_TREATMENT2_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 39_TREATMENT2_48H_REP3 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: 534105A07 - 36_WATER_48H_REP3 vs 40_TREATMENT3_48H_REP3

hyb_protocol: 40_TREATMENT3_48H_REP3 Cy5 / 36_WATER_48H_REP3 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: 534105A05 - 36_WATER_48H_REP3 vs 39_TREATMENT2_48H_REP3

hyb_protocol: 39_TREATMENT2_48H_REP3 Cy5 / 36_WATER_48H_REP3 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: 534330A02 - 8_WATER_48H_REP1 vs 9_ADJ_48H_REP1

hyb_protocol: 9_ADJ_48H_REP1 Cy5 / 8_WATER_48H_REP1 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: 534105A04 - 38_TREATMENT1_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 38_TREATMENT1_48H_REP3 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: 534105A03 - 36_WATER_48H_REP3 vs 38_TREATMENT1_48H_REP3

hyb_protocol: 38_TREATMENT1_48H_REP3 Cy5 / 36_WATER_48H_REP3 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: 534108A01 - 22_WATER_48H_REP2 vs 23_ADJ_48H_REP2

hyb_protocol: 23_ADJ_48H_REP2 Cy5 / 22_WATER_48H_REP2 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: SK-LMS-1 MEF2A shRNA#4 biological rep1

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

description: SK-LMS-1 sh MEF2A #4 repA

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with the Lumi package in R.

label: biotin

organism: Homo sapiens

source_name: SK-LMS-1 MEF2A shRNA#4

label_protocol: Aliquots of RNAs were amplified and labelled according to the specifications of the Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: SK-LMS-1 and SK-UT-1 cells were grown in DMEM (Euroclone) supplemented with 10%FBS, L-glutamine (2mM), penicillin (100U/ml) and streptomycin (100μg/ml) (Lonza) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy columns (QIAGEN, Hilden, Germany)

treatment_protocol: SK-LMS-1 and SK-UT-1 cells stably KD for MEF2D and MEF2A or expressing a shRNA control were generated through lentiviral infection. The resulting polyclonal populations were grown for 48h in adhesion.

tag: cell line

tag: cell type

value: Human leiomyosarcoma cell line

tag: infected with

value: shRNA against MEF2A


title: 534108A02 - 23_ADJ_48H_REP2 vs 22_WATER_48H_REP2

hyb_protocol: 22_WATER_48H_REP2 Cy5 / 23_ADJ_48H_REP2 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: SK-UT-1 control shRNA biological rep2

description: SK-UT-1 sh CT repB

source_name: SK-UT-1 control shRNA

value: a control shRNA


title: SK-UT-1 MEF2D shRNA#1 biological rep1

description: SK-UT-1 sh MEF2D #1 repA

source_name: SK-UT-1 MEF2D shRNA#1

value: shRNA against MEF2D


title: SK-UT-1 MEF2D shRNA#2 biological rep2

description: SK-UT-1 sh MEF2D #2 repB

source_name: SK-UT-1 MEF2D shRNA#2


title: 534330A01 - 9_ADJ_48H_REP1 vs 8_WATER_48H_REP1

hyb_protocol: 8_WATER_48H_REP1 Cy5 / 9_ADJ_48H_REP1 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: SK-UT-1 MEF2A shRNA#4 biological rep1

description: SK-UT-1 sh MEF2A #4 repA

source_name: SK-UT-1 MEF2A shRNA#4


title: SK-LMS-1 MEF2A shRNA#4 biological rep2

description: SK-LMS-1 sh MEF2A #4 repB


title: 534105A01 - 36_WATER_48H_REP3 vs 37_ADJ_48H_REP3

hyb_protocol: 37_ADJ_48H_REP3 Cy5 / 36_WATER_48H_REP3 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: 534105A02 - 37_ADJ_48H_REP3 vs 36_WATER_48H_REP3

hyb_protocol: 36_WATER_48H_REP3 Cy5 / 37_ADJ_48H_REP3 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: Untreated Control [miRNA]

city: Beijing

first: SHUAI

last: HUANG

address: Nanwei Road NO2

country: China

institute: Institute of Materia Medica,Chinese Academy of Medical Sciences/Peking Union Medical College

description:
C1
Expression data from Huh7 cells not treated with CA.

hyb_protocol: The Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that had intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: Huh7 cells without CA treatment

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline.

growth_protocol: The human hepato cancer cell line Huh7 was cultured in the DMEM medium supplemented with 10% fetal calf serum (FBS), penicillin (100 U/mL), and streptomycin (100 μg/mL).

extract_protocol: Trizol extraction of total RNA and purified with RNeasy mini kit (QIAGEN) was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with CA (25 μΜ or 50 μΜ) for 24 hrs, trypsinized and re-suspended in serum-free medium.

value: hepato cancer cell line

tag: treatment


title: CA 25uM [miRNA]

description:
C2
Expression data from Huh7 cells treated with CA 25uM.

source_name: Huh7 cells with CA 25uM treatment

value: CA 25uM


title: SK-UT-1 MEF2A shRNA#4 biological rep2

description: SK-UT-1 sh MEF2A #4 repB


title: SK-UT-1 control shRNA biological rep1

description: SK-UT-1 sh CT repA


title: SK-LMS-1 MEF2D shRNA#2 biological rep2

description: SK-LMS-1 sh MEF2D #2 repB

source_name: SK-LMS-1 MEF2D shRNA#2


title: SK-LMS-1 control shRNA biological rep2

description: SK-LMS-1 sh CT repB

source_name: SK-LMS-1 control shRNA


title: SK-LMS-1 MEF2D shRNA#1 biological rep1

description: SK-LMS-1 sh MEF2D #1 repA

source_name: SK-LMS-1 MEF2D shRNA#1


title: SK-LMS-1 MEF2A shRNA#3 biological rep2

description: SK-LMS-1 sh MEF2A #3 repB

source_name: SK-LMS-1 MEF2A shRNA#3


title: SK-UT-1 MEF2A shRNA#3 biological rep1

description: SK-UT-1 sh MEF2A #3 repA

source_name: SK-UT-1 MEF2A shRNA#3


title: CA 50uM [miRNA]

description:
C3
Expression data from Huh7 cells treated with CA 50uM.

source_name: Huh7 cells with CA 50uM treatment

value: CA 50uM


title: SK-UT-1 MEF2A shRNA#3 biological rep2

description: SK-UT-1 sh MEF2A #3 repB


title: SK-LMS-1 MEF2A shRNA#3 biological rep1

description: SK-LMS-1 sh MEF2A #3 repA


title: SK-UT-1 MEF2D shRNA#1 biological rep2

description: SK-UT-1 sh MEF2D #1 repB


title: SK-LMS-1 MEF2D shRNA#1 biological rep2

description: SK-LMS-1 sh MEF2D #1 repB


title: SK-LMS-1 MEF2D shRNA#2 biological rep1

description: SK-LMS-1 sh MEF2D #2 repA


title: SK-LMS-1 control shRNA biological rep1

description: SK-LMS-1 sh CT repA


title: CA 100uM [mRNA]

description:
C3
Expression data from Huh7 cells treated with CA 100uM.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 x Blocking Agent and 2.2 μl of 25xFragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. The hybridized arrays were washed, fixed.

scan_protocol: The chips were scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Huh7 cells with CA 100uM treatment

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

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

treatment_protocol: Cells were treated with CA (50 μΜ or 100 μΜ) for 24 hrs, trypsinized and re-suspended in serum-free medium.

value: CA 100uM


title: CA 50uM [mRNA]

description:
C2
Expression data from Huh7 cells treated with CA 50uM.


title: SK-UT-1 MEF2D shRNA#2 biological rep1

description: SK-UT-1 sh MEF2D #2 repA


title: mock-infected2-2

status: Public on Apr 16 2017

city: Hong Kong

first: Philip

last: Yeung

address: Pokfulam road

country: Hong Kong

institute: The University of Hong Kong

description: small RNA

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GCOS

data_processing:
We did a shRNA library screening to screen out shRNAs that are essential for a virus replication. The shRNA targeting sequence, which is complemented with the host mRNA, were amplified and were detected in the Affymetrix platform. The amplified fragment is less than 30 base pair, which could not be processed the same way as that of the conventional affymetrix matrix.
Therefore, instead of the normalization of the data which is required for the conventional microarray experiments, we looked for absolute values of the signals.

source_name: cell line

label_protocol: biotin-labeled protocol from GeneNet (SBI)

extract_protocol: mirVanaTM small RNA isolation kit from Ambion

treatment_protocol: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% (v/v) heat-inactivated fetal calf serum (FCS), 100 units/ml of penicillin, and 100 μg/ml of streptomycin with the addition of 1 μg/ml of puromycin

tag: infection

value: uninfected


title: Untreated Control [mRNA]


title: mock-infected2-1

description: small RNA

growth_protocol: Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% (v/v) heat-inactivated fetal calf serum (FCS), 100 units/ml of penicillin, and 100 μg/ml of streptomycin


title: hSRY-OFF mouse liver rep1

city: San Francisco

first: Yun-Fai

middle: Chris

last: Lau

state: CA

address: 4150 Clement Street

department: Department of Medicine, VA Medical Center

country: USA

institute: University of California, San Francisco

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with lumi of the limma::neqc function in R.

organism: Mus musculus

source_name: hSRY-OFF mouse

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

extract_protocol: RNA was extracted with Trizol Plus RNA Purification kit. Quality control was performed with Agilent Bioanalyzer.

tag: strain

value: FVB

tag: age

tag: Sex

value: male

tag: tissue

value: liver


title: mock-infected1-2

description: small RNA


title: EV-infected2-2

description: small RNA

value: Infected


title: EV-infected1-2

description: small RNA


title: mock-infected1-1

description: small RNA


title: EV-infected1-1

description: small RNA


title: hSRY-ON mouse liver rep1

source_name: hSRY-ON mouse


title: hSRY-OFF mouse liver rep3


title: hSRY-ON mouse liver rep3


title: hSRY-ON mouse liver rep2


title: hSRY-ON mouse lung rep2

value: lung


title: hSRY-OFF mouse lung rep3


title: hSRY-ON mouse lung rep1


title: hSRY-OFF mouse lung rep2


title: hSRY-ON mouse lung rep3


title: EV-infected2-1

description: small RNA


title: hSRY-OFF mouse lung rep1


title: hSRY-OFF mouse brain rep3

value: whole brain


title: hSRY-ON mouse heart rep3

value: heart


title: hSRY-OFF mouse heart rep3


title: hSRY-ON mouse heart rep2


title: hSRY-OFF mouse liver rep2


title: hSRY-ON mouse brain rep1


title: hSRY-ON mouse heart rep1


title: hSRY-OFF mouse heart rep1


title: hSRY-ON mouse brain rep3


title: hSRY-OFF mouse brain rep1


title: hSRY-ON mouse brain rep2


title: MCT treated lungs

status: Public on Apr 15 2017

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

institute: LC Sciences

description: wt-mct-lung

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C. After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining. Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: lung tissue, MCT treated

label_protocol: Microarray assay was performed using a service provider (LC Sciences). Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: miRNeasy Mini Kit was used for total RNA extraction following manufacturer's protocol for using the kit.

treatment_protocol: WT mice of 14-weeks old were treated with monocrotaline for a period of 30 days. The untreated mice were used as comparative control. The lungs were isolated and miRNAs were made for array analysis.

tag: genotype/variation

value: WT

value: monocrotaline (MCT)


title: Untreated WT-lungs

description: wt-lung

source_name: lung tissue, untreated


title: hSRY-OFF mouse brain rep2


title: hSRY-OFF mouse heart rep2


title: Cancerous tissue_L084

type: genomic

city: Shinjyuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35, Shinano-machi

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina iScan Protocol

data_processing: GenomeStudio software (version 1.9.0, Illumina)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Genomic DNA from liver tissue_L084

label_protocol: Standard Illumina Protocol

extract_protocol: Phenol-chloroform extraction followed by dialysis

value: Hepatocellular carcinoma

tag: gender

value: Male

tag: age by decade

tag: hepatitis virus

value: Positive


title: Cancerous tissue_L044

source_name: Genomic DNA from liver tissue_L044


title: Cancerous tissue_L062

source_name: Genomic DNA from liver tissue_L062


title: Cancerous tissue_L077

source_name: Genomic DNA from liver tissue_L077


title: Cancerous tissue_L081

source_name: Genomic DNA from liver tissue_L081


title: Cancerous tissue_L046

source_name: Genomic DNA from liver tissue_L046

value: Female


title: Cancerous tissue_L059

source_name: Genomic DNA from liver tissue_L059


title: Cancerous tissue_L058

source_name: Genomic DNA from liver tissue_L058


title: Cancerous tissue_L079

source_name: Genomic DNA from liver tissue_L079


title: Cancerous tissue_L042

source_name: Genomic DNA from liver tissue_L042


title: Cancerous tissue_L070

source_name: Genomic DNA from liver tissue_L070


title: Cancerous tissue_L080

source_name: Genomic DNA from liver tissue_L080


title: Cancerous tissue_L078

source_name: Genomic DNA from liver tissue_L078


title: Cancerous tissue_L048

source_name: Genomic DNA from liver tissue_L048


title: Cancerous tissue_L041

source_name: Genomic DNA from liver tissue_L041


title: Cancerous tissue_L056

source_name: Genomic DNA from liver tissue_L056


title: Cancerous tissue_L071

source_name: Genomic DNA from liver tissue_L071


title: Cancerous tissue_L067

source_name: Genomic DNA from liver tissue_L067


title: Cancerous tissue_L073

source_name: Genomic DNA from liver tissue_L073


title: Cancerous tissue_L057

source_name: Genomic DNA from liver tissue_L057


title: Cancerous tissue_L064

source_name: Genomic DNA from liver tissue_L064


title: Cancerous tissue_L055

source_name: Genomic DNA from liver tissue_L055


title: Cancerous tissue_L074

source_name: Genomic DNA from liver tissue_L074


title: Cancerous tissue_L075

source_name: Genomic DNA from liver tissue_L075


title: Cancerous tissue_L040

source_name: Genomic DNA from liver tissue_L040


title: Cancerous tissue_L051

source_name: Genomic DNA from liver tissue_L051


title: Cancerous tissue_L061

source_name: Genomic DNA from liver tissue_L061


title: Cancerous tissue_L072

source_name: Genomic DNA from liver tissue_L072


title: Cancerous tissue_L053

source_name: Genomic DNA from liver tissue_L053


title: Cancerous tissue_L043

source_name: Genomic DNA from liver tissue_L043


title: Cancerous tissue_L037

source_name: Genomic DNA from liver tissue_L037


title: Cancerous tissue_L034

source_name: Genomic DNA from liver tissue_L034


title: Cancerous tissue_L039

source_name: Genomic DNA from liver tissue_L039


title: Cancerous tissue_L035

source_name: Genomic DNA from liver tissue_L035


title: 169-Hy-Wk10-LG

city: Toronto

first: Nicholas

middle: J

last: Harding

state: ON

address: 101 College St

department: Informatics and Biocomputing Platform

country: Canada

institute: OICR

hyb_protocol: Hybridization was performed by Affymetrix according to the platform protocol

scan_protocol: Scanning was performed by Affymetrix

data_processing:
Quantitated intensity files (CEL files) for each array were loaded into the R statistical environment (v3.0.2).
Files generated for batch 2 (Human Transcriptome arrays) were loaded and RMA-normalized using the affy package (v1.40.0) using a custom cdf (hta20hsentrezgcdf v18.0.0)
Each batch was examined for spatial and distributional homogeneity; no outliers were identified

source_name: Fresh Frozen primary prostate tumour extraction

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tissue was digested and total RNA was extracted using the mirVana miRNA Isolation Kit (Life Technologies).

treatment_protocol: For RNA extractions, ice cold tumour tissue maintained on RNAase-free microscope slides was macro-dissected from 10 µm sections and transferred to an Eppendorf tube on ice.

value: prostrate


title: Non-cancerous tissue_L075

value: Non-cancerous liver  tissue


title: 58-Ox-Wk0-LG


title: Cancerous tissue_L036

source_name: Genomic DNA from liver tissue_L036


title: Non-cancerous tissue_L084

source_name: Genomic DNA from liver tissue_L084


title: Non-cancerous tissue_L081

source_name: Genomic DNA from liver tissue_L081


title: Non-cancerous tissue_L077

source_name: Genomic DNA from liver tissue_L077


title: Cancerous tissue_L033

source_name: Genomic DNA from liver tissue_L033


title: 169-Ox-Wk10-LG


title: Non-cancerous tissue_L072


title: 169-Ox-Wk0-LG


title: Non-cancerous tissue_L078

source_name: Genomic DNA from liver tissue_L078


title: Non-cancerous tissue_L064

source_name: Genomic DNA from liver tissue_L064


title: Non-cancerous tissue_L074

source_name: Genomic DNA from liver tissue_L074


title: Non-cancerous tissue_L080

source_name: Genomic DNA from liver tissue_L080


title: Non-cancerous tissue_L073

source_name: Genomic DNA from liver tissue_L073


title: Non-cancerous tissue_L079

source_name: Genomic DNA from liver tissue_L079


title: Non-cancerous tissue_L071

source_name: Genomic DNA from liver tissue_L071


title: Vec-Ox-Wk10-LG


title: Non-cancerous tissue_L070

source_name: Genomic DNA from liver tissue_L070


title: Non-cancerous tissue_L061

source_name: Genomic DNA from liver tissue_L061


title: Non-cancerous tissue_L067

source_name: Genomic DNA from liver tissue_L067


title: Vec-Hy-Wk10-LG


title: Non-cancerous tissue_L055

source_name: Genomic DNA from liver tissue_L055


title: Non-cancerous tissue_L059

source_name: Genomic DNA from liver tissue_L059


title: Non-cancerous tissue_L058

source_name: Genomic DNA from liver tissue_L058


title: Non-cancerous tissue_L056

source_name: Genomic DNA from liver tissue_L056


title: Vec-Ox-Wk0-LG

source_name: Fresh Frozen primary prostate tumour extraction


title: Non-cancerous tissue_L062

source_name: Genomic DNA from liver tissue_L062


title: Gastric-Tumor-BYS-24-SNP_6.0

city: Boston

first: Steven

middle: E

last: Schumacher

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Hybridized to SNP 6.0 array

hyb_protocol: Each sample was genotyped using the Sty I chip of the 500K Human Mapping Array wet (Affymetrix), containing probes to 238,270 SNP loci, according to manufacturer’s instructions. In brief, 250 ng of genomic DNA was digested with the StyI restriction enzyme (New England Biolabs), ligated to an adaptor with T4 ligase (New England Biolabs), and PCR-amplified using a 9700 Thermal Cycler I (Applied Biosystems) and Titanium Taq (Clontech) to achieve fragments ranging from 200-1100 bp. These fragments were pooled, concentrated, processed through a clean-up step, and further fragmented with DNaseI (Affymetrix) before being labeled, denatured, and hybridized to arrays

scan_protocol: Arrays were washed and scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using five closest normal method, in which tumor signal intensities are divided by the geometric mean of the five normal samples closest to the tumor in Euclidean log2 ratio space (as described in Weir et al, Nature 2007).  Cancer samples were normalized against the plate normals included in this submission and also normals used in the TCGA ovarian cancer study (TCGA network, Nature, 2011). The attached data matrix files contains the resulting normalized copy-number values.
Normalized copy number data for samples can be found in tumor-type matrix files. Genotype Call (SNP call) data are not provided and are not used in this study.

label: Biotin

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: DNA was obtained from cell line pellets or tumors frozen at the time of surgical dissection and maintained at -80C until use.

tag: cancer type

value: gastric adenocarcinoma

tag: batch

value: DAVIT


title: Normal-Tissue-BYS-N24-SNP_6.0

description: Hybridized to SNP 6.0 array

value: non-malignant cells


title: Cancerous tissue_L038

source_name: Genomic DNA from liver tissue_L038


title: CPCG0361-F2


title: Non-cancerous tissue_L057

source_name: Genomic DNA from liver tissue_L057


title: CPCG0346-F2


title: Normal-Tissue-BYS-N42-SNP_6.0

description: Hybridized to SNP 6.0 array

data_processing:
Probe-level signal intensities were normalized to a common reference array using quantile normalization and combined to form SNP-level signal intensities using the dChip model-based expression (PM/MM) method . Genome-wide copy number estimates were obtained using five closest normal method, in which tumor signal intensities are divided by the geometric mean of the five normal samples closest to the tumor in Euclidean log2 ratio space (as described in Weir et al, Nature 2007).  Cancer samples were normalized against the plate normals included in this submission and also normals used in the TCGA ovarian cancer study (TCGA network, Nature, 2011). The attached data matrix files contains the resulting normalized copy-number values.
Normalized copy number data for samples can be found in GEW_SNP6_normalized_data_matrix.txt file. Genotype Call (SNP call) data are not provided and are not used in this study.


title: Normal-Tissue-BYS-N43-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0334-F2


title: Non-cancerous tissue_L044

source_name: Genomic DNA from liver tissue_L044


title: CPCG0398-F2


title: Non-cancerous tissue_L043

source_name: Genomic DNA from liver tissue_L043


title: Non-cancerous tissue_L046

source_name: Genomic DNA from liver tissue_L046


title: Non-cancerous tissue_L051

source_name: Genomic DNA from liver tissue_L051


title: CPCG0266-F2


title: Non-cancerous tissue_L048

source_name: Genomic DNA from liver tissue_L048


title: Non-cancerous tissue_L042

source_name: Genomic DNA from liver tissue_L042


title: Normal-Tissue-BYS-N40-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0241-F2


title: Normal-Tissue-BYS-N39-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N38-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N37-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N41-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N35-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N34-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N36-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Non-cancerous tissue_L053

source_name: Genomic DNA from liver tissue_L053


title: Normal-Tissue-BYS-N32-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0416-F2


title: CPCG0395-F2


title: Normal-Tissue-BYS-N31-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0415-F2


title: CPCG0396-F2


title: Normal-Tissue-BYS-N29-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Non-cancerous tissue_L040

source_name: Genomic DNA from liver tissue_L040


title: Normal-Tissue-BYS-N23-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N21-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Tgfbr2 KO biological rep3

city: Tianjin

first: Yuechen

last: Luo

address: 288 Nanjing Road, Tianjin, 300020, P.R. China

institute: Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Gene expression data of Treg cells from Foxp3CreTgfbr2 f/f  mice
Tgfbr2 KO 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MoGene-2_0-st Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 30007G

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software

source_name: CD4+YFP+ Treg cells

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

treatment_protocol: CD4+YFP+ Treg cells were sorted from spleen and lymph nodes for RNA extraction with Trizol reagent

value: spleen and lymph nodes

value: CD4+YFP+ Treg cells

value: male

tag: genotype

value: Foxp3CreTgfbr2 f/f


title: CPCG0414-F2


title: Normal-Tissue-BYS-N22-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Non-cancerous tissue_L037

source_name: Genomic DNA from liver tissue_L037


title: Non-cancerous tissue_L041

source_name: Genomic DNA from liver tissue_L041


title: Normal-Tissue-BYS-N20-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N27-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Tgfbr2 KO biological rep1

description:
Gene expression data of Treg cells from Foxp3CreTgfbr2 f/f  mice
Tgfbr2 KO 1

growth_protocol: CD4+YFP+ Treg cells were sorted from spleen and lymph nodes


title: Non-cancerous tissue_L039

source_name: Genomic DNA from liver tissue_L039


title: Non-cancerous tissue_L035

source_name: Genomic DNA from liver tissue_L035


title: Non-cancerous tissue_L036

source_name: Genomic DNA from liver tissue_L036


title: Normal-Tissue-BYS-N19-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Tgfbr2 KO biological rep2

description:
Gene expression data of Treg cells from Foxp3CreTgfbr2 f/f  mice
Tgfbr2 KO 2


title: CPCG0413-F2

source_name: Fresh Frozen primary prostate tumour extraction


title: Tgfbr2 WT biological rep2

description:
Gene expression data of Treg cells from Foxp3Cre mice
Tgfbr2 WT 2


title: CPCG0412-F2


title: Normal-Tissue-BYS-N17-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Non-cancerous tissue_L038

source_name: Genomic DNA from liver tissue_L038


title: Normal-Tissue-BYS-N18-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Non-cancerous tissue_L034

source_name: Genomic DNA from liver tissue_L034


title: CPCG0411-F2


title: Normal-Tissue-BYS-N15-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N16-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N13-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N14-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N12-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Tgfbr2 WT biological rep3

description:
Gene expression data of Treg cells from Foxp3Cre mice
Tgfbr2 WT 3


title: CPCG0410-F2


title: Normal-Tissue-BYS-N10-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N09-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N08-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Tgfbr2 WT biological rep1

description:
Gene expression data of Treg cells from Foxp3Cre mice
Tgfbr2 WT 1


title: Normal-Tissue-BYS-N06-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N07-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0409-F2


title: LKB1 KO biological rep3

description:
Gene expression data of Treg cells from Foxp3Cre/+Lkb1f/f  mice
LKB1 KO 3

value: female


title: Normal-Tissue-BYS-N01-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Normal-Tissue-BYS-N04-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0408-F2


title: Gastric-Tumor-BYS-78-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-77-SNP_6.0

description: Hybridized to SNP 6.0 array


title: LKB1 KO biological rep1

description:
Gene expression data of Treg cells from Foxp3Cre/+Lkb1f/f  mice
LKB1 KO 1


title: CPCG0407-F2


title: LKB1 KO biological rep2

description:
Gene expression data of Treg cells from Foxp3Cre/+Lkb1f/f  mice
LKB1 KO 2


title: CPCG0401-F2


title: LKB1 WT  biological rep3

description:
Gene expression data of Treg cells from Foxp3Cre/+ mice
LKB1 WT 3


title: Gastric-Tumor-BYS-76-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Lung_persistent_2

city: Seoul

first: Soomin

last: Park

address: 50 Yonsei-ro, Seodaemun-gu

department: department of microbiology

country: South Korea

institute: Yonsei university college of medicine

description: Gene expression data from Mtb-infected mouse lung with drug treatment

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Mouse Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: Lung_Mtb-infected_drug treatment

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

value: Lung


title: Gastric-Tumor-BYS-75-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0390-F2


title: CPCG0391-F2


title: Lung_persistent_3


title: LKB1 WT  biological rep2

description:
Gene expression data of Treg cells from Foxp3Cre/+ mice
LKB1 WT 2


title: Normal-Tissue-BYS-N02-SNP_6.0

description: Hybridized to SNP 6.0 array


title: LKB1 WT  biological rep1

description:
Gene expression data of Treg cells from Foxp3Cre/+ mice
LKB1 WT 1


title: Lung_persistent_1


title: CPCG0387-F2


title: Gastric-Tumor-BYS-73-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0389-F2


title: Gastric-Tumor-BYS-72-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Non-cancerous tissue_L033

source_name: Genomic DNA from liver tissue_L033


title: Gastric-Tumor-BYS-71-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-70-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Lung_chronic_3

description: Gene expression data from Mtb-infected mouse lung


title: CPCG0382-F2


title: Lung_chronic_2


title: Gastric-Tumor-BYS-69-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Lung_chronic_1


title: Gastric-Tumor-BYS-66-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-67-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-65-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0378-F2


title: Gastric-Tumor-BYS-63-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-74-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Lung_healthy_3

description: Gene expression data from non-infected mouse lung


title: Lung_healthy_2


title: Lung_healthy_1


title: Gastric-Tumor-BYS-62-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-61-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-60-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0372-F2


title: CPCG0381-F2


title: Gastric-Tumor-BYS-59-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-58-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-57-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0371-F2


title: Gastric-Tumor-BYS-68-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0375-F2


title: Gastric-Tumor-BYS-64-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-55-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0366-F2


title: Gastric-Tumor-BYS-53-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-52-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-54-SNP_6.0

description: Hybridized to SNP 6.0 array


title: KO line 2

city: Vancouver

first: Marco

middle: A

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

institute: Canada's Michael Smith Genome Sciences Centre

hyb_protocol: 5.5 ug cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada)

data_processing: RMA normalization was performed using the R/Bioconductor package oligo (version 1.34.2). Only transcript clusters that mapped to single genes were retained for further analyses.

source_name: CIC knockout monoclonal cell line derived from HEK293a

label_protocol: Biotinylated cDNA were prepared from 150 ng RNA (The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada)

growth_protocol: Cells were grown in DMEM supplemented with 10% heat-inactivated FBS

extract_protocol: RNA extraction was performed using the RNeasy Plus Mini Kit (74136, Qiagen) according to the manufacturer's instructions

treatment_protocol: Cells were washed with PBS, trypsinized, and harvested by pelleting

value: CIC knockout


title: Gastric-Tumor-BYS-51-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0365-F2


title: CPCG0373-F2


title: CPCG0364-F2


title: KO line 3


title: WT line 3

source_name: CIC wild type monoclonal cell line derived from HEK293a

value: CIC wild type


title: CPCG0362-F2


title: CPCG0363-F2


title: Gastric-Tumor-BYS-50-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-49-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-46-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0358-F2


title: WT line 2


title: Gastric-Tumor-BYS-47-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-56-SNP_6.0

description: Hybridized to SNP 6.0 array


title: KO line 1


title: CPCG0356-F2


title: Gastric-Tumor-BYS-48-SNP_6.0

description: Hybridized to SNP 6.0 array


title: WT line 1 (parental)

source_name: HEK293a cell line

value: HEK


title: CPCG0210-F2

data_processing:
Quantitated intensity files (CEL files) for each array were loaded into the R statistical environment (v3.0.2).
Files generated for batch 1 (HuGene2.0 arrays) were loaded and normalized using the RMA algorithm available in the oligo package for R (v1.26.2), using the default platform design information (pd.hugene.2.0.st v3.8.0).
Each batch was examined for spatial and distributional homogeneity; no outliers were identified
Normalized batch 1 transcript clusters were mapped to EntrezGene IDs and gene symbols using the hugene20sttranscriptcluster.db (v2.12.1) available from Bioconductor.


title: CPCG0208-F2


title: Gastric-Tumor-BYS-44-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-45-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0196-F2


title: CPCG0354-F2


title: CPCG0191-F2


title: Gastric-Tumor-BYS-41-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-42-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-40-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0355-F2


title: Gastric-Tumor-BYS-43-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-39-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-36-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-37-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-35-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0357-F2


title: CPCG0350-F2


title: CPCG0184-F2


title: Gastric-Tumor-BYS-38-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0103-F2


title: CPCG0183-F2


title: Gastric-Tumor-BYS-32-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0102-F2


title: CPCG0352-F2


title: CPCG0353-F2


title: CPCG0100-F2


title: CPCG0349-F2


title: CPCG0348-F2


title: CPCG0099-F2


title: Gastric-Tumor-BYS-30-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-29-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0344-F2


title: Gastric-Tumor-BYS-34-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-31-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-28-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0341-F2


title: CPCG0342-F2


title: CPCG0340-F2


title: Gastric-Tumor-BYS-27-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-25-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-23-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-22-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-21-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-20-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0335-F2


title: CPCG0336-F2


title: CPCG0331-F2


title: Gastric-Tumor-BYS-19-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0339-F2


title: CPCG0333-F2


title: Gastric-Tumor-BYS-15-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-18-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0267-F2


title: Gastric-Tumor-BYS-17-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0265-F2


title: CPCG0269-F2


title: Gastric-Tumor-BYS-14-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-16-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0262-F2


title: CPCG0263-F2


title: CPCG0324-F2


title: CPCG0260-F2


title: Gastric-Tumor-BYS-13-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-12-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0258-F2


title: Gastric-Tumor-BYS-11-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-10-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-05-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-08-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-07-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-06-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0248-F2


title: Gastric-Tumor-BYS-09-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-02-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-04-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-01-SNP_6.0

description: Hybridized to SNP 6.0 array


title: Gastric-Tumor-BYS-03-SNP_6.0

description: Hybridized to SNP 6.0 array


title: CPCG0249-F2


title: CPCG0236-F2


title: CPCG0246-F2


title: AP9 (Dementia 8)

status: Public on Apr 14 2017

city: Columbus

first: Haiyan

last: Fu

state: Ohio

address: 700 Children's Dive

department: Center for Gene Therapy

institute: Research Institute at Nationwide Childrens Hospital

description: gene expression in human blood

hyb_protocol: The labeled test and control RNA samples were fragmented and hybridized to the array overnight. Microarray slides were then washed and scanned with the Agilent G2505C Microarray Scanner, at 2 µM resolution.

scan_protocol: Microarray slides were washed and scanned with the Agilent G2505C Microarray Scanner, at 2 µM resolution.

data_processing: Images were analyzed with Feature Extraction 10.10 (Agilent Technologies). Median foreground intensities were then obtained for each spot and imported into the mathematical software package “R”, which was used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house for this analysis. The data was normalized by the loess method using the LIMMA (Linear models for microarray data) package in “R” as described

source_name: Peripheral blood, replica 8

label_protocol: The RNA samples were labeled with Cy3, purified using Qiagen columns and checked for labeling efficiency using the NanoDrop spectrophotometer (NanoDrop products).

extract_protocol: Paxgene Blood RNA kit (Qiagen)

treatment_protocol: peripheral blood

value: whole blood

tag: disease

value: advanced Alzheimer's disease


title: CPCG0250-F2


title: AP5 (Dementia 5)

description: gene expression in human blood

source_name: Peripheral blood, replica 5

value: Female


title: AP4 (Dementia 4)

description: gene expression in human blood

source_name: Peripheral blood, replica 4


title: AP6 (Dementia 6)

description: gene expression in human blood

source_name: Peripheral blood, replica 6


title: U251 cells transfected with Scr-shRNA, biological rep3

city: Shanghai,

first: Feng

middle: jun

last: lin

state: xvhuiqv

address: 2Institute of Health Sciences

department: Department of Pathophysiology

institute: 1Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with affmetrix expression console default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: U251 cells transfected with Scr-shRNA

growth_protocol: BRD4-shRNA-transfected and Scr-shRNA-transfected U251 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Gibco)

treatment_protocol: BRD4-shRNA-transfected and Scr-shRNA-transfected U251 cells were rinsed with PBS and placed on ice in the Trizol solution (Life Technologies).

tag: cell line


title: AP8 (Dementia 7)

description: gene expression in human blood

source_name: Peripheral blood, replica 7


title: U251 cells transfected with BRD4-shRNA, biological rep2

source_name: U251 cells transfected with BRD4-shRNA


title: CPCG0255-F2

value: prostrate


title: U251 cells transfected with BRD4-shRNA, biological rep1


title: C010 (Control 10)

description: gene expression in human blood

source_name: Peripheral blood, replica 10

value: healthy


title: AP3 (Dementia 3)

description: gene expression in human blood

source_name: Peripheral blood, replica 3


title: C05 (Control 5)

description: gene expression in human blood


title: C06 (Control 6)

description: gene expression in human blood


title: C07 (Control 7)

description: gene expression in human blood


title: C03 (Control 3)

description: gene expression in human blood


title: U251 cells transfected with BRD4-shRNA, biological rep3


title: C02 (Control 2)

description: gene expression in human blood

source_name: Peripheral blood, replica 2


title: AP10 (Dementia 9)

description: gene expression in human blood

source_name: Peripheral blood, replica 9


title: U251 cells transfected with Scr-shRNA, biological rep1


title: U251 cells transfected with Scr-shRNA, biological rep2


title: WT-adCM-rep4

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed using Bioconductor version 3.1 with oligo package version 1.32.0, pd.mogene.1.0.st.v1 package version 3.14.1 and mogene10sttranscriptcluster.db package version 8.3.1

source_name: heart

label_protocol: Affymetrix protocol

extract_protocol: Total RNAs were extracted using Trizol according to the manufacturer's instructions.

tag: cell type

value: cardiomyocytes

value: Wildtype


title: WT-adCM-rep5


title: CKO-adCM-rep3

value: cardiac conditional EED knock-out


title: AP1 (Dementia 1)

description: gene expression in human blood

source_name: Peripheral blood, replica 1


title: WT-adCM-rep2


title: AP2 (Dementia 2)

description: gene expression in human blood


title: C09 (Control 9)

description: gene expression in human blood


title: CKO-adCM-rep1


title: C08 (Control 8)

description: gene expression in human blood


title: WT-adCM-rep3