title: 14286604 - C58tral_2days_BR1 vs C58WT_2days_BR1

hyb_protocol: C58WT_2days_BR1 Cy5 / C58tral_2days_BR1 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: 14286435 - C58tral_18days_BR3 vs C58accR_18days_BR3

status: Public on Sep 01 2013

type: RNA

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: What are the functions and the regulatory pathways of the bacterial quorum-sensing system in the context of Agrobacterium/Arabidopsis interactions?

hyb_protocol: C58accR_18days_BR3 Cy5 / C58tral_18days_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

molecule: total RNA

organism: Arabidopsis thaliana

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: stem - Media=soil hygrometry=greenhouse Temperature Light=greenhouse

treatment_protocol: Name:wounding+C58 accR infection 18days - wounding - infection,c58 accr:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).

tag: ecotype

value: columbia (Col0)

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

treatment_protocol: Name:wounding+C58 tral infection 18days - wounding - infection,c58 tral:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286599 - C58WT_2days_BR3 vs C58accR_2days_BR3

hyb_protocol: C58accR_2days_BR3 Cy5 / C58WT_2days_BR3 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:wounding + C58 accR infection 2days - wounding - infection,c58 accr:time 2day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).

treatment_protocol: Name:wounding + C58 WT infection 2days - wounding - infection,c58 wt:time 2day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286432 - C58accR_18days_BR1 vs C58tral_18days_BR1

hyb_protocol: C58tral_18days_BR1 Cy5 / C58accR_18days_BR1 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: 14286416 - C58accR_2days_BR3 vs C58tral_2days_BR3

hyb_protocol: C58tral_2days_BR3 Cy5 / C58accR_2days_BR3 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:wounding + C58 tral infection 2days - wounding - infection,c58 tral:time 2day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: 14286420 - C58WT_18days_BR2 vs Control_18days_BR2

hyb_protocol: Control_18days_BR2 Cy5 / C58WT_18days_BR2 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:wounding 18days - wounding - wounding,wounding:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle.

treatment_protocol: Name:wounding+C58 WT infection 18days - wounding - infection,c58 wt:time 18day . Base of plant stems (about stage 5.10) were poked five times with a needle. Wounds were inoculated with fresh Agrobacterium culture (grown 48h on LBm medium (Bactotryptone 1%, Yeast Extracts 0,5%, NaCl 0,5%, agar 1,5%).


title: Line C24, replicate 2

city: Nouzilly

first: Julie

last: Collet

address: Centre INRAE

institute: INRAE

hyb_protocol: Hybridization was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was normalised via a log (base 10) transformation. Prior to data analysis, we determined the mean of the two replicates per probe.

organism: Drosophila serrata

source_name: Line C24, replicate 2

label_protocol: Labeling was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

growth_protocol: Samples were collected from a panel of 41 inbred lines of D. serrata, where whole-body samples of adult males were used. All flies were reared in 10ml vials of a standard yeast medium and maintained at 25°C with a 12 hour day/night cycle. Each line was propagated by single pair matings (1 virgin male with 1 virgin female) in each of 4 replicate vials; pairs were left to mate and lay eggs for 96 hours. Male offspring were collected as virgins from each replicate vial per line, and held in groups of 5 flies until 4 days post ecolsion. Two replicate pools of 20 flies per line were collected without the use of CO2 anaesthesia and snap frozen in liquid nitrogen.

extract_protocol: Each whole-body pool was homogenised in Trizol® and immediately stored at -80 degrees Celsius. Total RNA extraction was performed using Trizol® as per the manufacturer's (Invitrogen) protocol. RNA was then purified using RNeasy kits® according to manufacturer's (Qiagen) instructions.

tag: line

value: Line C24

tag: tissue

value: whole body

tag: gender

value: male

tag: developmental stage

value: adult


title: 14286601 - C58tral_2days_BR1 vs C58accR_2days_BR1

hyb_protocol: C58accR_2days_BR1 Cy5 / C58tral_2days_BR1 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: 14286417 - C58tral_2days_BR3 vs C58accR_2days_BR3

hyb_protocol: C58accR_2days_BR3 Cy5 / C58tral_2days_BR3 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: 14286434 - C58accR_18days_BR2 vs C58tral_18days_BR2

hyb_protocol: C58tral_18days_BR2 Cy5 / C58accR_18days_BR2 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: 14286414 - C58tral_2days_BR2 vs C58accR_2days_BR2

hyb_protocol: C58accR_2days_BR2 Cy5 / C58tral_2days_BR2 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: 14286418 - C58WT_18days_BR1 vs Control_18days_BR1

hyb_protocol: Control_18days_BR1 Cy5 / C58WT_18days_BR1 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: 14286415 - C58accR_2days_BR2 vs C58tral_2days_BR2

hyb_protocol: C58tral_2days_BR2 Cy5 / C58accR_2days_BR2 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: Line C63, replicate 2

source_name: Line C63, replicate 2

value: Line C63


title: 14248881 - C58WT_18days_BR2 vs C58accR_18days_BR2

hyb_protocol: C58accR_18days_BR2 Cy5 / C58WT_18days_BR2 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: Line C95, replicate 2

source_name: Line C95, replicate 2

value: Line C95


title: Line C53, replicate 2

source_name: Line C53, replicate 2

value: Line C53


title: Line C39, replicate 2

source_name: Line C39, replicate 2

value: Line C39


title: Line C4, replicate 2

source_name: Line C4, replicate 2

value: Line C4


title: Line C10, replicate 2

source_name: Line C10, replicate 2

value: Line C10


title: Line C56, replicate 2

source_name: Line C56, replicate 2

value: Line C56


title: 14248879 - C58WT_18days_BR1 vs C58accR_18days_BR1

hyb_protocol: C58accR_18days_BR1 Cy5 / C58WT_18days_BR1 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: Line C37, replicate 2

source_name: Line C37, replicate 2

value: Line C37


title: 14248880 - C58accR_18days_BR1 vs C58WT_18days_BR1

hyb_protocol: C58WT_18days_BR1 Cy5 / C58accR_18days_BR1 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: 14286426 - C58tral_18days_BR1 vs C58WT_18days_BR1

hyb_protocol: C58WT_18days_BR1 Cy5 / C58tral_18days_BR1 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: 14248882 - C58accR_18days_BR2 vs C58WT_18days_BR2

hyb_protocol: C58WT_18days_BR2 Cy5 / C58accR_18days_BR2 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: Line C48, replicate 2

source_name: Line C48, replicate 2

value: Line C48


title: Line C82, replicate 2

source_name: Line C82, replicate 2

value: Line C82


title: Line C33, replicate 2

source_name: Line C33, replicate 2

value: Line C33


title: Line C99, replicate 2

source_name: Line C99, replicate 2

value: Line C99


title: 14248888 - C58accR_18days_BR3 vs C58WT_18days_BR3

hyb_protocol: C58WT_18days_BR3 Cy5 / C58accR_18days_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia (Col0)


title: Line C17, replicate 2

source_name: Line C17, replicate 2

value: Line C17


title: 14286429 - C58WT_18days_BR3 vs C58tral_18days_BR3

hyb_protocol: C58tral_18days_BR3 Cy5 / C58WT_18days_BR3 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: Line C12, replicate 2

source_name: Line C12, replicate 2

value: Line C12

value: whole body


title: Line C7, replicate 2

source_name: Line C7, replicate 2

value: Line C7

value: male

value: adult


title: 14248887 - C58WT_18days_BR3 vs C58accR_18days_BR3

hyb_protocol: C58accR_18days_BR3 Cy5 / C58WT_18days_BR3 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: Line C18, replicate 2

source_name: Line C18, replicate 2

value: Line C18


title: Line C69, replicate 2

source_name: Line C69, replicate 2

value: Line C69


title: Line C68, replicate 2

source_name: Line C68, replicate 2

value: Line C68


title: Line C3, replicate 2

source_name: Line C3, replicate 2

value: Line C3


title: Line C93, replicate 2

source_name: Line C93, replicate 2

value: Line C93


title: Line C2, replicate 2

source_name: Line C2, replicate 2

value: Line C2


title: Line C20, replicate 2

source_name: Line C20, replicate 2

value: Line C20


title: Line C32, replicate 2

source_name: Line C32, replicate 2

value: Line C32


title: Line C85, replicate 2

source_name: Line C85, replicate 2

value: Line C85


title: Line C44, replicate 2

source_name: Line C44, replicate 2

value: Line C44


title: Line C87, replicate 2

source_name: Line C87, replicate 2

value: Line C87


title: Line C35, replicate 2

source_name: Line C35, replicate 2

value: Line C35


title: Line C84, replicate 2

source_name: Line C84, replicate 2

value: Line C84


title: Line C57, replicate 2

source_name: Line C57, replicate 2

value: Line C57

value: whole body


title: Line C79, replicate 2

source_name: Line C79, replicate 2

value: Line C79

value: male


title: Ets3_1

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

description: Biological replicate 1 of 2. Control L3262, untreated, harvested in early-log phase.

hyb_protocol: Oligoarray control targets and hybridization buffer (Aminoallyl post DNA Labeling kit ,GeneChem, Daejeon, Korea) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: ScanArray 5000 scanner (Packard, Billerica, CA, USA)

data_processing: Raw microarray data were lowess normalized and analyzed by using ArrayNorm (http://genome.tugraz.at/), a platform-independent Java tool for normalization and statistical analysis

organism: Saccharomyces cerevisiae

source_name: Ets2 and Ets3 is obtained ethanol tolerant strains through screening a mutant library of SPT15 of Saccharomyces cerevisiae L3262

label_protocol: 40-50 µg of total RNA were primed with 2 µl of 100 µM oligo-dT primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h using Aminoallyl post DNA Labeling kit (GeneChem, Daejeon, Korea) and a superscript reverse transcriptase (Invitrogen, Carlsbad, CA, USA).

growth_protocol: Yeast cells (S. cerevisiae L3262, Ets2, and Ets3) were initially inoculated at 0.1 OD600, and incubated to 0.3 OD600 for 3 hours in YSCD-Ura.

extract_protocol: Total RNA extraction and RNA quality control for microarray analysis were performed as Ho-phenol method (reference : Appl Environ Microbiol, 2007).

tag: strain

tag: substrain

source_name: Total RNA from S. cerevisiae L3262 in early-log phase

tag: growth phase

value: early-log phase (OD600=0.3)


title: Infected_Boechera stricta_forming_pseudoflowers_replicate_3_of_3

city: Norwich

first: Liliana

middle: Maria

last: Cano

state: Norfolk

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

description: This sample is of infected leaves of Boechera stricta with Puccinia monoica

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

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

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

organism: Boechera stricta

source_name: Infected  Boechera stricta with Puccinia monoica forming pseudoflowers

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

growth_protocol: Samples of uninfected and infected material was grinded in liquid nitrogen and frozen prior RNA extraction.

extract_protocol: Total RNA was extracted using the RNAesy Plant Mini Kit (Qiagen, Cat No. 74904) and DNA was removed by DNase digestion with the RNase-Free DNase set (Qiagen, Cat No. 79254). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at NimbleGen.

treatment_protocol: All samples were collected from the field (Gothic,Colorado, USA) in 5ml bottles of RNAlater stabilization solution (Invitrogen, Cat No. AM7023) and stored at -4C prior RNA extraction.

value: Infected leaves


title: Ets3_2

description: Biological replicate 2 of 2. Control L3262, untreated, harvested in early-log phase.


title: Uninfected_flowers_of_Bochera_stricta_replicate_1_of_2

description: This sample is of uninfected flowers of Boechera stricta

source_name: Flowers of uninfected Boechera stricta

value: Uninfected flowers


title: Line C28, replicate 2

hyb_protocol: Hybridization was performed by The Centre for Genomics and Bioinformatics, Bloomington, IN USA, following standard NimbleGen operating protocol. See www.nimblegen.com.

source_name: Line C28, replicate 2

value: Line C28

value: adult


title: Line C23, replicate 2

source_name: Line C23, replicate 2

value: Line C23


title: Ets2_1


title: Infected_Boechera stricta_forming_pseudoflowers_replicate_1_of_3


title: Ets2_2


title: Line C58, replicate 2

source_name: Line C58, replicate 2

value: Line C58


title: Uninfected_stem_and_leaves_of_Bochera_stricta_replicate_3_of_3

description: This sample is of uninfected stem and leaves of Boechera stricta

source_name: Stem and leaves of uninfected Boechera stricta

value: Uninfected stem and leaves


title: Line C50, replicate 2

source_name: Line C50, replicate 2

value: Line C50


title: Uninfected_flowers_of_Bochera_stricta_replicate_2_of_2


title: PC-3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Subconfluent prostate cells were used in this study.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with the mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

organism: Homo sapiens

source_name: Prostate cancer cell line, PC3

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark).

growth_protocol: Normal human prostate cell lines (epithelial cells, RWPE-1; stromal cells, PrSc) and prostate cancer cell lines (LNCaP, PC3, and DU145) were obtained from the American Type Culture Collection (ATCC, Manassas, VA USA). All of the cell lines were cultured under an atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA from the cell lines were extracted using ISOGEN (NipponGene, Tokyo, Japan) according to the manufacturer's instructions.

tag: cell line

tag: cell type

value: prostate cancer cells


title: LNCap

source_name: Prostate cancer cell line, LNCap

value: LNCap


title: RW PE-1

source_name: Prostate cell line, RWPE-1

value: normal prostate epithelial cells


title: DU145

source_name: Prostate cancer cell line, DU145


title: PrSC

source_name: Prostate cell line, PrSC

value: PrSC

value: normal prostate stromal cells


title: Line C22, replicate 2

source_name: Line C22, replicate 2

value: Line C22

value: whole body


title: Line C15, replicate 2

source_name: Line C15, replicate 2

value: Line C15

value: male


title: Line C34, replicate 2

source_name: Line C34, replicate 2

value: Line C34


title: Line C84, replicate 1

source_name: Line C84, replicate 1

value: Line C84


title: Line C3, replicate 1

source_name: Line C3, replicate 1

value: Line C3


title: Line C100, replicate 1

source_name: Line C100, replicate 1

value: Line C100

value: adult


title: Infected_Boechera stricta_forming_pseudoflowers_replicate_2_of_3

source_name: Infected  Boechera stricta with Puccinia monoica forming pseudoflowers

value: Infected leaves


title: Uninfected_stem_and_leaves_of_Bochera_stricta_replicate_2_of_3

value: Uninfected stem and leaves


title: Uninfected_stem_and_leaves_of_Bochera_stricta_replicate_1_of_3


title: Line C77, replicate 1

source_name: Line C77, replicate 1

value: Line C77


title: Line C77, replicate 2

source_name: Line C77, replicate 2


title: start_cont_48_r1

city: Leuven

first: Mieke

last: Jansen

address: Ch. Deberiotstraat 32

department: Biology

country: Belgium

institute: KULeuven

description:
64_61009
This Sample uses the array with Stratagene controls.

hyb_protocol: Arrays were hybridized overnight at 42°C. See Vandenbrouck et al. 2009 (PMID 19187980) for more details.

scan_protocol: Genepix personal 4100 Scanner and Genepix pro 4.1 software (Axon Instruments).

data_processing: Statistical analysis was performed using the R package limma (Smyth, 2004). Spots for which red or green FG < BG + 2SD (Sclep et al., 2007) on all arrays were deleted before analysis (FG: median foreground intensity, BG: average local background intensity calculated over the full microarray, SD: standard deviation of local background intensities). Median intensity data were background corrected using a normal-exponential convolution model using the function backgroundCorrect with method 'normexp', offset = 50 (Ritchie et al., 2007). Data were loess-normalized using the function normalizeWithinArrays, method = 'loess' (Smyth & Speed, 2003). Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method (Smyth, 2004). Each stressor was contrasted against the controls. These contrasts were fitted to the linear models and cut off at p < 0.05 and log2FC > 0.75 or log2FC < -0.75 (log2 fold change).

organism: Daphnia magna

source_name: start, r1

label_protocol: cDNA collection and sample labelling were done according to Soetaert et al. (2007) and Vandenbrouck et al. (2009). Briefly, total RNA (5µg) together with 2µl mRNA spike from the Lucidea Universal Scorecard (Amersham Biosciences) or from the Spotreport Alien cDNA Array Validation System (Agilent Technologies' Stratagene products) was converted into cDNA using random primers (Invitrogen), a dNTP labelling mix containing aminoallyl-dUTPs and 400U Superscript II reverse transcriptase (Invitrogen). Cy5 and Cy3 (Amersham Biosciences) were covalently coupled to the aminoallyl cDNA samples. After a cleanup reaction (QIAquick PCR purification kit, Qiagen, USA) removing all non-incorporated dyes, the quality of the labelled cDNA was checked spectrophotometrically using the Nanodrop. A total amount of 50 pmol labelled cDNA with a frequency of incorporation between 20 and 50 was vacuum dried to use as probe.

growth_protocol: P 32,85 clone cultured in standard conditions to avoid maternal effects (see Jansen et al.).

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's protocol.

treatment_protocol:
Eighty juveniles per treatment were kept together in 500ml jars at a density of 1 animal/2.5ml medium and exposed to four conditions (two biological replicates per treatment): a control treatment without stress, fish kairomones (Leuciscus idus), carbaryl (5.6µg/l; measured concentration 5.74µg/l) or spores of the parasite Pasteuria ramosa (5x10^6 spores/ml).
Exposures were done every second day starting at day 0. Medium was completely renewed at the moment of a new stress pulse. The two biological samples were collected after 48h, 96h and 144h of exposure. The last pulse was given three hours before freezing the animals for gene expression analysis, respectively, on 45h-, 93h- and 141h-old Daphnia.

tag: clone

value: female

tag: treatment

value: non-exposure

tag: replicate

source_name: control, 48h, r1

value: control

tag: time point


title: Line C87, replicate 1

source_name: Line C87, replicate 1

value: Line C87


title: fish_par_144_r2

description:
61_61009
This Sample uses the array with Stratagene controls.

source_name: fish exposed, 144h, r2

value: fish exposure

source_name: parasite exposed, 144h, r2

value: parasite exposure


title: par_cont_144_r2

description:
63_61009
This Sample uses the array with Stratagene controls.

source_name: control, 144h, r2


title: par_ref_96_r1

description:
62_61009
This Sample uses the array with Stratagene controls.

source_name: parasite exposed, 96h, r1

source_name: reference sample

value: reference


title: Line C10, replicate 1

source_name: Line C10, replicate 1

value: Line C10

value: whole body


title: Line C32, replicate 1

source_name: Line C32, replicate 1

value: Line C32

value: male


title: Line C22, replicate 1

source_name: Line C22, replicate 1

value: Line C22


title: Line C23, replicate 1

source_name: Line C23, replicate 1

value: Line C23


title: Line C85, replicate 1

source_name: Line C85, replicate 1

value: Line C85

value: adult


title: cont_ref_48_r1

description:
69_61009
This Sample uses the array with Stratagene controls.


title: Line C93, replicate 1

source_name: Line C93, replicate 1

value: Line C93


title: carb_ref_48_r2

description:
66_61009
This Sample uses the array with Stratagene controls.

source_name: carbaryl exposed, 48h, r2

value: carbaryl exposure


title: Line C79, replicate 1

source_name: Line C79, replicate 1

value: Line C79


title: ref_fish_96_r1

description:
67_61009
This Sample uses the array with Stratagene controls.

value: female

source_name: fish exposed, 96h, r1


title: Line C82, replicate 1

source_name: Line C82, replicate 1

value: Line C82


title: carb_par_96_1

description:
50_20409(2)
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 96h, r1

source_name: parasite exposed, 96h, r2


title: par_ref_144_1

description:
7_250309(2)
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 144h, r1


title: Line C88, replicate 2

source_name: Line C88, replicate 2

value: Line C88


title: cont_carb_96_1

description:
52_020409(2)
This Sample uses the array with Lucidea controls.

source_name: control, 96h, r1

value: control


title: carb_fish_144_2

description:
53_030409
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 144h, r2

source_name: fish exposed, 144h, r2

value: fish exposure


title: Line C44, replicate 1

source_name: Line C44, replicate 1

value: Line C44


title: fish_ref_48_r2

description:
68_61009
This Sample uses the array with Stratagene controls.

source_name: fish exposed, 48h, r2

source_name: reference sample

value: reference


title: 14248878 - C58tral_18days_BR3 vs C58WT_18days_BR3

description: What are the functions and the regulatory pathways of the bacterial quorum-sensing system in the context of Agrobacterium/Arabidopsis interactions?

hyb_protocol: C58WT_18days_BR3 Cy5 / C58tral_18days_BR3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: columbia (Col0)


title: par_fish_48_1

description:
51_010409
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 48h, r1

value: parasite exposure

source_name: fish exposed, 48h, r1


title: Line C50, replicate 1

source_name: Line C50, replicate 1

value: Line C50

value: whole body

value: male


title: carb_cont_48_2

description:
55_030409
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 48h, r2


title: Line C88, replicate 1

source_name: Line C88, replicate 1


title: Line C68, replicate 1

source_name: Line C68, replicate 1

value: Line C68


title: Line C24, replicate 1

source_name: Line C24, replicate 1

value: Line C24

value: adult


title: Line C53, replicate 1

source_name: Line C53, replicate 1

value: Line C53


title: Line C2, replicate 1

source_name: Line C2, replicate 1

value: Line C2


title: Line C58, replicate 1

source_name: Line C58, replicate 1

value: Line C58


title: Line C34, replicate 1

source_name: Line C34, replicate 1

value: Line C34


title: Line C4, replicate 1

source_name: Line C4, replicate 1

value: Line C4


title: Line C15, replicate 1

source_name: Line C15, replicate 1

value: Line C15


title: ref_carb_48_1

description:
33_300309
This Sample uses the array with Lucidea controls.

value: female

source_name: carbaryl exposed, 48h, r1

value: carbaryl exposure


title: Line C48, replicate 1

source_name: Line C48, replicate 1

value: Line C48


title: Line C100, replicate 2

source_name: Line C100, replicate 2

value: Line C100


title: Line C20, replicate 1

source_name: Line C20, replicate 1

value: Line C20


title: Line C33, replicate 1

source_name: Line C33, replicate 1

value: Line C33


title: Line C35, replicate 1

source_name: Line C35, replicate 1

value: Line C35

value: whole body


title: Line C7, replicate 1

source_name: Line C7, replicate 1

value: Line C7

value: male


title: Line C69, replicate 1

source_name: Line C69, replicate 1

value: Line C69

value: adult


title: Line C39, replicate 1

source_name: Line C39, replicate 1

value: Line C39


title: Line C95, replicate 1

source_name: Line C95, replicate 1

value: Line C95


title: Line C18, replicate 1

source_name: Line C18, replicate 1

value: Line C18


title: Line C63, replicate 1

source_name: Line C63, replicate 1

value: Line C63


title: Line C17, replicate 1

source_name: Line C17, replicate 1

value: Line C17


title: Line C99, replicate 1

source_name: Line C99, replicate 1

value: Line C99


title: Line C12, replicate 1

source_name: Line C12, replicate 1

value: Line C12


title: Line C28, replicate 1

source_name: Line C28, replicate 1

value: Line C28


title: Line C37, replicate 1

source_name: Line C37, replicate 1

value: Line C37


title: ref_cont_48_2

description:
31_010409
This Sample uses the array with Lucidea controls.

source_name: reference sample

value: female

value: reference

source_name: control, 48h, r2

value: control


title: Line C56, replicate 1

source_name: Line C56, replicate 1

value: Line C56

value: whole body


title: Line C57, replicate 1

source_name: Line C57, replicate 1

value: Line C57

value: male


title: carb_ref_144_2

description:
2_270309(2)
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 144h, r2

value: carbaryl exposure


title: ref_start_1

description:
23_300309
This Sample uses the array with Lucidea controls.

source_name: start, r1

value: non-exposure


title: cont_fish_48_2

description:
54_030409
This Sample uses the array with Lucidea controls.

source_name: fish exposed, 48h, r2

value: fish exposure


title: ref_carb_144_1

description:
5_270309(2)
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 144h, r1


title: cont_ref_96_1

description:
20_300309
This Sample uses the array with Lucidea controls.

source_name: control, 96h, r1


title: carb_par_144_1

description:
39_020409(2)
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 144h, r1

value: parasite exposure


title: ref_par_144_2

description:
34_070409
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 144h, r2


title: start_ref_2

description:
1_240309
This Sample uses the array with Lucidea controls.

source_name: start, r2


title: carb_par_48_1

description:
27_010409
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 48h, r1

source_name: parasite exposed, 48h, r1


title: cont_carb_144_1

description:
38_030409(2)
This Sample uses the array with Lucidea controls.

source_name: control, 144h, r1


title: ref_carb_96_1

description:
8_270309(2)
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 96h, r1


title: fish_ref_144_2

description:
29_010409
This Sample uses the array with Lucidea controls.

source_name: fish exposed, 144h, r2


title: cont_start_144_2_1

description:
58_030409
This Sample uses the array with Lucidea controls.

source_name: control, 144h, r2


title: par_carb_96_2

description:
49_020409
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 96h, r2

source_name: carbaryl exposed, 96h, r2


title: ref_fish_144_1

description:
17_300309
This Sample uses the array with Lucidea controls.

source_name: reference sample

source_name: fish exposed, 144h, r1


title: fish_ref_96_2

description:
19_240309
This Sample uses the array with Lucidea controls.

source_name: fish exposed, 96h, r2


title: ref_cont_96_2

description:
10_270309(2)
This Sample uses the array with Lucidea controls.

source_name: control, 96h, r2


title: ref_par_48_2

description:
14_010409
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 48h, r2


title: par_ref_48_1

description:
26_300309
This Sample uses the array with Lucidea controls.


title: fish_carb_48_144_2

description:
57_030409
This Sample uses the array with Lucidea controls.

source_name: fish exposed, 48h, r2

source_name: carbaryl exposed, 144h, r2


title: ref_fish_48_1

description:
21_300309
This Sample uses the array with Lucidea controls.

source_name: fish exposed, 48h, r1


title: start_cont_96_2

description:
3_270309(2)
This Sample uses the array with Lucidea controls.

source_name: start, r2


title: ref_par_96_2

description:
18_300309(2)
This Sample uses the array with Lucidea controls.


title: fish_cont_48_96_1

description:
28_010409
This Sample uses the array with Lucidea controls.

source_name: control, 96h, r1


title: ref_cont_144_2

description:
4_250309(2)
This Sample uses the array with Lucidea controls.


title: cont_ref_144_1

description:
9_270309(2)
This Sample uses the array with Lucidea controls.


title: par_fish_144_1

description:
40_020409(2)
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 144h, r1


title: carb_ref_96_2

description:
6_250309(2)
This Sample uses the array with Lucidea controls.


title: carb_par_96_48_2

description:
47_020409(2)
This Sample uses the array with Lucidea controls.


title: par_fish_96_1

description:
48_020409
This Sample uses the array with Lucidea controls.

source_name: parasite exposed, 96h, r1

source_name: fish exposed, 96h, r1


title: cont_fish_96_2

description:
46_020409
This Sample uses the array with Lucidea controls.


title: fish_cont_96_144_1

description:
41_20409(2)
This Sample uses the array with Lucidea controls.

source_name: control, 144h, r1


title: fish_par_96_2

description:
42_030409(2)
This Sample uses the array with Lucidea controls.


title: cont_carb_48_1

description:
44_020409(2)
This Sample uses the array with Lucidea controls.

source_name: control, 48h, r1

source_name: carbaryl exposed, 48h, r1


title: par_carb_48_2

description:
45_020409
This Sample uses the array with Lucidea controls.

source_name: carbaryl exposed, 48h, r2


title: MycRas_1

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

country: USA

institute: UCSF

description: A0007691: MYC-RAS over-expressor

hyb_protocol: Hybridization, washing, staining, imaging, and signal extraction were performed according to Affymetrix-recommended procedures, except that the 20X GeneChip Eukaryotic Hybridization Control cocktail was omitted from the hybridization.

scan_protocol: The fluorecence data is extracted at 1.4 micron pixel resolution using the Affymetrix 3000 7G scanner.

data_processing:
The signal processing implemented is a multi-step process involving probe specific signal detection calls, background estimate and correction, constant variance stabilization and either array scaling or global normalization. For each probe, an estimated background value is subtracted that is derived from the median signal of a set of G-C-matched anti-genomic controls. Arrays within a specific analysis experiment were normalized together according to the variance stabilization method described by Huber et al. (Huber et al., 2002). Detection calls were based on a Wilcoxon rank-sum test of the miRNA probe signal compared to the distribution of signals from GC-content matched anti-genomic probes.
For statistical hypothesis testing, a two-sample t-Test, with assumption of equal variance, was applied. One-way ANOVA was used. These tests define which probes are considered to be significantly differentially expressed, or significant, based on a default p-value of 0.05 and log2 difference > 1. The post-normalized data scale is reported as generalized log2 data.

label: biotin

organism: Mus musculus

source_name: tumor tissue from LT2/MYC/RAS mouse

label_protocol: The 3’ ends of the RNA molecules were tailed and biotin-labeled using the mirVana™ miRNA Labeling Kit (Ambion Inc., Austin, TX). The kit’s dNTP mixture in the tailing reaction was replaced with a proprietary nucleotide mixture containing biotin-modified nucleotides (PerkinElmer, Waltham, MA).

growth_protocol: Mice were kept on doxy diet to keep oncogenes switched off

extract_protocol: Total RNA extracted using mirVANA kit from Ambion. The miRNA-enriched fraction of small RNAs was purified from total RNA by polyacrylamide gel electrophoresis using Ambion’s flashPAGE™ kits, Ambion Inc., Austin, TX.

treatment_protocol: Doxycycline chow was replaced with regular chow to switch on oncogene expression

tag: strain background

value: FVB

tag: genotype/variation

value: MYC-RAS over-expressor

value: liver tumor


title: MycRas_2

description: A0007692: MYC-RAS over-expressor


title: MycRas_3

description: A0007693: MYC-RAS over-expressor


title: RAS_2

description: A0007688: RAS over-expressor

source_name: tumor tissue from LT2/RAS mouse

value: RAS over-expressor


title: LT2_5

description: A0009920: Normal

source_name: tumor tissue from LT2 mouse

value: Normal

value: normal liver


title: LT2_3

description: A0007697: Normal


title: MycRas_5

description: A0009919: MYC-RAS over-expressor


title: RAS_3

description: A0007689: RAS over-expressor


title: LT2_1

description: A0007695: Normal


title: WT-Leaf_4week_AmbientNO_rep2

city: Nueherberg

first: Gitto

middle: Thomas

last: Kuruthukulangarakoola

address: Ingolsteadter Landstrasse 1

department: Biochemical Plant Pathology

country: Germany

institute: Helmholtz Zentrum München

description: Gene expression after 4 weeks of exposure to ambient NO_Rosette leaves

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis thaliana Oligonucleotide Microarrays (G4102A) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37 °C GE Wash buffer 2 (Agilent), 10 seconds in Acetonitrile (Sigma-Aldrich) and then for 30 seconds in Stabililazation and Drying Solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k microarrays (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 029132_D_F_20110524) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Leaf_4 Week after germination_Ambient NO_Replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 10 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The wild type Arabidopsis thaliana seeds were sowed on soil mixed with sand (5:1 proportion) in 5.5 cm x 6 cm x 5.5 cm (length x breadth x height) plastic pots. Five seeds per pot were sowed and the pots were arranged in rectangular trays. The trays were covered with thin plastic foils and were subjected to seed stratification (incubation at 4°C for at least 72 hours in the dark) before moving them to the growth chambers.

extract_protocol: Total RNA was isolated using Qiagen Plant RNeasy Mini Kit following the manufacturer's recommendation.  The protocol includes an on-column DNase digestion. Isolated Total RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: After stratification sowed seeds containing trays were transferred into NO fumigation chamber (Day - Temp: 20 °C, rHumidity: 80%, Light: 300 µmol/m2/s in PAR, UV: 17 mWm-2; Night - Temp: 16 °C, rHumidity: 80%). On the 5th day the thin plastic foils were removed. The group named Ambient NO were fumigated with Ambient air and the other group named 3ppmNO was fumigated with ambient air mixed with 3 ppm NO gas. The treatment was for 24 hours daily till samples were harvested.

value: Whole Rosette Leaves


title: RAS_4

description: A0007690: RAS over-expressor


title: WT-Leaf_4week_3ppmNO_rep3

description: Gene expression after 4 weeks of exposure to 3 ppm NO_Rosette leaves

source_name: Leaf_4 Week after germination_3 ppm NO_Replicate 4


title: WT-Leaf_4week_AmbientNO_rep1

source_name: Leaf_4 Week after germination_Ambient NO_Replicate 1


title: WT-Leaf_4week_AmbientNO_rep3

source_name: Leaf_4 Week after germination_Ambient NO_Replicate 3


title: LT2_2

description: A0007696: Normal


title: WT-Leaf_4week_3ppmNO_rep1

source_name: Leaf_4 Week after germination_3 ppm NO_Replicate 2


title: WT-Leaf_4week_3ppmNO_rep2

source_name: Leaf_4 Week after germination_3 ppm NO_Replicate 3


title: Reference 05 Ref05_01

type: mixed

city: Chicago

first: Nathan

last: Schoettler

state: IL

address: 924 E 57th Street, R402

institute: University of Chicago

hyb_protocol: Prior to hybridization, microarrays were re-hydrated, washed (Wash Buffers A, B and C, ArrayIt), prehybridized for two hours (BlockIt Blocking Buffer, ArrayIt) and washed again. Hybridizations were performed with 10 ng of the labeled reference sample added to 1.5 μg labeled cDNA and 2 μg human Cot-1 DNA (Invitrogen). DNA was mixed with HybIt 2 hybridization buffer (ArrayIt) at 1x concentration to a final volume of 20 μL, denatured at 80°C for 3 minutes and hybridized overnight at 37.0°C for 14-16 hours.

scan_protocol: Following hybridization, microarrays were washed with Wash Buffers A, B and C for 2 minutes each, dried and scanned using an Axon GenePix 4000B scanner (Molecular Devices). All amplified and labeled cDNA samples were hybridized two times as technical replicates. cDNA labeling, prehybridization, hybridization, washing and scanning were all performed by the same individual at approximately the same time of the day.

data_processing:
Image analysis was performed using GenePix Pro 6.0 (Molecular Devices). Spot recognition and flags were checked for each spot and manually adjusted when appropriate. Because the reference sample was co-hybridized with all samples, hybridization quality could be readily observed and missing spots could be easily detected. Missing spots were consistent between arrays, and no more than 3 of 12 replicate spots per gene were missing. Therefore, only 9 replicate spots were used for analysis even though the majority of probes were spotted 12 times per array. Log2 background subtracted values (for both red and green channels) for the human light chain V genes were normalized using the LOWESS function of the MAANOVA 2.0 software (Xiangqin Cui, Hao Wu, Gary A. Churchill, The Jackson Lab) in Matlab (Mathworks).
Normalized log2 for the red channel and green channel are reported on two separate sheets.

label: Alexa 647

source_name: Standard 5: Reference sample with reverse complement of O2/O12 spiked in at 4.7% and 1-19 at 4.7%

label_protocol: Ulysis Alexa-Fluor 647 (Ch1) and Ulysis Alexa-Fluor 555 (Ch2)

extract_protocol: Total RNA was extracted using TRIZOL according to the recommended protocol

tag: disease state

tag: sample type

value: Standard 5, Reference sample with reverse complement of O2/O12 spiked in at 4.7% and 1-19 at 4.7%

label: Alexa 555

molecule: other

source_name: Reference (equal molar concentrations of the reverse complement of all human light chain probes)

tag: components

value: Synthesized DNA (oligonucleotides)


title: Reference 05 Ref05_02

value: Reference (equal molar concentrations of the reverse complement of all human light chain probes)


title: Reference 04 Ref04_01

source_name: Standard 4: Reference sample with reverse complement of O2/O12 spiked in at 2.2% and 1-19 spiked in at 11.1%

value: Standard 4, Reference sample with reverse complement of O2/O12 spiked in at 2.2% and 1-19 spiked in at 11.1%


title: RAS_1

description: A0007687: RAS over-expressor

tag: tissue


title: MYC_4

description: A0007686: MYC over-expressor

source_name: tumor tissue from LT2/MYC mouse

value: MYC over-expressor


title: Reference 01 Ref01_02

source_name: Standard 1: Reference sample with reverse complement of B3 spiked in a 5.3% and 2-13 spiked in at 26%

value: Standard 1, Reference sample with reverse complement of B3 spiked in a 5.3% and 2-13 spiked in at 26%


title: MYC_3

description: A0007685: MYC over-expressor


title: Reference 04 Ref04_02


title: Reference 01 Ref01_01


title: SLE 09 LSLE09_02

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype

value: SLE

tag: individual


title: SLE 10 LSLE10_02

value: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype


title: Reference 03 Ref03_01

source_name: Standard 3: Reference sample with reverse complement of B3 spiked in at 26.0% and 2-13 spiked in at 5.2%

value: Standard 3, Reference sample with reverse complement of B3 spiked in at 26.0% and 2-13 spiked in at 5.2%


title: PANC-1 - MeDIP

type: genomic

city: Nanjing

first: wentao

last: gao

address: 300 Guangzhou Road

department: Department of General Surgery

country: China

institute: the first affiliated hospital with nanjing medical university

description: MeDIP-chip PANC-1 cells

hyb_protocol: detailed information for MeDIP-chip protocol.doc. Briefly for hyb, 1. Set the Hybridization System to 42°C. With the cover closed, allow at least 3 hours for the temperature to stabilize.  2. Resuspend 6ug dried sample pellet in 5ul water.  3. Vortex well and spin to collect contents in bottom of the tube.  4. Using components from a NimbleGen Hybridization Kit, prepare the hybridization solution master mix according to the following table. The amounts listed in the table provide a sufficient volume to hybridize a single slide.  Hybridization Solution Master Mix Volume per Slide  2×Hybridization Buffer 29.5ul  Alignment Oligo 1.2ul  Hybridization Component A 11.8ul  Total 42.5ul  5. Add the appropriate amount of hybridization solution to each sample according to the following table:  Hybridization Solution (from step 4) 13ul  Resuspended sample (from step 2) 5ul  Total 18ul  6. Vortex well (~15 seconds) and spin to collect contents in bottom of the tube. Incubate at 95°C for 5 minutes, protected from light.  7. Vortex, spin, and place the tube in the Hybridization System sample block (pre-heated to 42°C) until ready for sample loading.

scan_protocol: Arrays were scanned on an GenePix 4000B scanner per manufacturer's protocol, briefly: 1. Turn on the scanner using the power switch on the back right side.  2. Launch the GenePix software 10 minutes before scanning to allow lasers to warm.  3. Open the scanner door and the slide carriage.  4. Place the slide in the slide carriage so that the array is face down.  5. Close the carriage and slide the scanner door shut.  6. Open the Hardware Settings dialog box. Select the following settings for scanning:  • Wavelength (532 = Cy3, 635 = Cy5)  • 532 PMT Gain = 650(Default, adjusted depending on the situation)  • 635 PMT Gain = 750(Default, adjusted depending on the situation)  • Power (%) = 33%  • Pixel size (μm) = 5  • Lines to average = 1  • Focus position (μm) = 0  7. Click Data Scan to scan the microarray. When the scan is complete, save the image for the 532nm and 635nm wavelengths.  8. Perform data extraction using GenePix Pro6.0 and export data to excel.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 MeDIP-chip data extraction.

molecule: genomic DNA

source_name: MeDIP DNA from PANC-1 cells

label_protocol: detailed information for MeDIP-chip protocol.pdf. Briefly for label, 1. Prepare the following three solutions:  10× TE (10mM Tris HCI, 1mM EDTA):  1M Tris HCl, pH 7.4 1.5ml  0.5M EDTA 0.3ml  Water  13.2ml  Total 15ml  50×dNTP Mix:  Water  250ul  10×TE 50ul  100mM dATP 50ul  100mM dGTP 50ul  100mM dTTP 50ul  100mM dCTP 50ul  Total 500ul  Random 9mer Buffer(Prepare fresh each time):  Water  8.6ml  1M Tris HCl, pH 7.4 1.25ml  1M MgCI2 125ul  β-Mercaptoethanol 17.5ul  Total ~10ml  2. Dilute Cy3 and Cy5 dye-labeled 9mers to 1 O.D./42μl Random 9mer Buffer. Aliquot to 40μl individual reaction volumes in 0.2ml thin-walled PCR tubes and store at -20°C, protected from light.  3. Assemble “MeDIP” and “Input” samples in separate 0.2ml thin-walled PCR tubes:   MeDIP Input  Sample 1ug 1ug  Cy3-9mer Primers  40ul  Cy5-9mer Primers 40ul   Water X ul X ul  Total 80ul 80ul  4. Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quick-chill in an ice-water bath for 10 minutes.  5. Prepare 20μl of the following dNTP/Klenow master mix for each sample prepared in step 4:  50×dNTP mix 10ul  Water 8ul  Klenow(50U/ul) 2ul  Total 20ul  6. Add 20μl of the dNTP/Klenow master mix to each of the denatured samples prepared in step 4. Keep on ice.   MeDIP Input  Reaction volumn from step 4 80ul 80ul  dNTP/klenow Master Mix 20 ul 20 ul  Total 100ul 100ul  7. Mix well by pipetting up and down 10 times.  8. Quick-spin to force contents to bottom of the tube.  9. Incubate for 2 hours at 37°C in a thermocycler protected from light.  10. Stop the reaction by addition of 0.5M EDTA.   MeDIP Input  Reaction volumn from step 6 100ul 100ul  Stop Solution( 0.5M EDTA) 10ul 10ul  Total 110ul 110ul  11. Add 5M NaCl to each tube.   MeDIP Input  Reaction volumn from step 10 110ul 110ul  5M NaCI 11.5ul 11.5ul  Total 121.5ul 121.5ul  12. Vortex briefly, spin, and transfer the entire contents to a 1.5ml tube containing isopropanol.   MeDIP Input  Reaction volumn from step 11 121.5ul 121.5ul  Isopropanol 110ul 110ul  Total 231.5ul 231.5ul  13. Vortex well. Incubate for 10 minutes at room temperature, protected from light.  14. Centrifuge at 12,000 x g for 10 minutes. Remove supernatant with a pipette.  15. Rinse pellet with 500μl 80% ice-cold ethanol. Dislodge pellet from tube wall.  16. Centrifuge at 12,000 x g for 2 minutes. Remove supernatant with a pipette.  17. Dry contents in a SpeedVac on low heat until dry for 5 minutes, protected from light.  18. Spin tubes briefly prior to opening. Rehydrate pellets in 25μl water.  19. Vortex for 30 seconds and quick-spin to collect contents in bottom of the tube. Continue to vortex or let sit at room temperature, protected from light, until the pellet is completely rehydrated, then vortex again and quick-spin.  20. Measure the labeled DNA using Nanodrop ND1000. Use 6ug labeled MeDIP/Input DNA per hybridization reaction.  21. Dry 6ug labeled DNA in a SpeedVac on low heat until dry for 5 minutes, protected from light.  *For spectrophotometer, the O.D. A260 /A280 ratio should be close to 1.9 for pure DNA (ratios between 1.7 and 2.0 are acceptable). The O.D. A260/A230 ratio should be more than 1.8.

growth_protocol: cultured in DMEM medium

extract_protocol: detailed information for MeDIP protocol.pdf. Briefly for extraction, 1. Add 500ul of phenol/chloroform/isoamylalcohol (25:24:1) to each “MeDIP”,  “negative control” and “input” sample and shake tubes vigorously by hand.  2. Centrifuge for 5 minutes 13000Xg at RT. Transfer the aqueous phase into a new 1.5ml tube.  3. Add 500ul of chloroform/isoamylalcohol (24:1), shake tubes vigorously by hand.  4. Centrifuge for 5 minutes 13000Xg at RT. Transfer the aqueous phase into a new 1.5ml tube.  5. Add 5M NaCl to a final concentration of 200mM, 30ug Glycogen and 1000ul EtOH.  6. Precipitate at -80°C for 30 minutes.   7. Centrifuge at 13000Xg for 20 minutes at 4°C to pellet DNA samples.  8. Wash the samples with 500ul of 70%EtOH.  9. Dry the samples for 10min at RT. Re-suspend each sample in 20ul of 10mM Tris-HCl pH 8.0.  10. Use Nanodrop to measure concentration.

value: pancreas/duct

tag: age

tag: gender

value: male

tag: pancreas pathology

value: pancreatic adenocarcinoma

tag: primary disease

tag: chip antibody

value: Anti-5-methyl cytidine(Mouse)

source_name: input DNA from PANC-1

value: none, input DNA


title: SLE 09 LSLE09_01

tag: cell type


title: Reference 02 Ref02_02

source_name: Standard 2: Reference sample withreverse complement of B3 spiked in at 10.8% and 2-13 spiked in at 10.8%

value: Standard 2, Reference sample withreverse complement of B3 spiked in at 10.8% and 2-13 spiked in at 10.8%


title: SLE 08 LSLE08_02


title: MYC_1

description: A0007683: MYC over-expressor

value: FVB

value: liver tumor


title: Reference 02 Ref02_01


title: SLE 08 LSLE08_01


title: Colorectal Tumor Tissue-010912-01TB-CytoScanHD

city: Riyadh

first: Sathish

last: Periyasamy

state: Select a State or Province

department: Bioinformatics

country: Saudi Arabia

institute: NGHA

description:
010912-01TB
Hybridized to CytoScanHD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Nexus Copy Number 6.0 (Biodiscovery, Inc., CA, USA) was used to assess genome wide copy number frequencies for the 15 patients. Aroma.affymetrix - another CBS implemented as part of BioConductor’s DNACopy library- and the underlying TumorBoost algorithm were also used to identify genomic events and normalize allele specific copy number with paired normals
Primary data description: CNV calls, LOH (see supplementary file linked on Series record)

label: Biotin

source_name: Colorectal Tumor Tissue-121011-01TB

label_protocol: CytoScanHD kit and Reagent kit bundle from Affymetrix

growth_protocol: NONE (Tissue samples were used)

extract_protocol: DNA and RNA were extracted from the same tissue using Macherey Nagel trio kit (Germany).10-30mg of tissue sample was homogenized using Qiagen Tissue lyzer. The lysate was loaded on centrifuge columns. After washing nucleic acids were eluted as per the manufacturers protocol.

value: Tumor

value: Male

value: Colon

tag: tnm

tag: Stage

value: II


title: Reference 03 Ref03_02

value: Reference (equal molar concentrations of the reverse complement of all human light chain probes)

value: Synthesized DNA (oligonucleotides)


title: SLE 07 LSLE07_02

value: SLE


title: SLE 07 LSLE07_01

value: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype


title: Normal pancreas tissue - MeDIP

description: MeDIP-chip Normal pancreas tissue

source_name: MeDIP DNA from normal pancreas tissue

value: female

value: normal pancreas

value: adenoma of duodenal papilla

source_name: input DNA from normal pancreas


title: col-2

city: Ikoma

first: Diana

middle: Mihaela

last: Buzas

state: Nara

address: 8916-5 Takayama

department: Biological Sciences

institute: NAIST

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

growth_protocol: All plants were grown on MS agar plates in a 16h light: 8h dark photoperiod under fluorescent lights at 22°C for 12 days.T1 siFIE plants (in C24 ecotype) were selected on plates supplemented with kanamycin (50 mgL-1). The swn-7 clf-28 mutant is sterile and was selected from the progeny of swn-7 clf-28/+ plants.

extract_protocol: RNA was extracted from intermediate phenotype siFIE plants (Additional file Figure S1), C24, clf-7 swn-28 and Col using Qiagen Plant RNeasy mini kit. For each sample, three pools of 10-12 plants were used. The siFIE plants were analysed for FIE mRNA by RT-qPCR; the maximum level of FIE mRNA was found to be 10% of wildtype C24.

tag: genotype

value: Wild-type

tag: phenotype

value: normal

tag: accession


title: siFIE-2

value: T1 siFIE knock-down (about 10% of wt mRNA level )

value: pleiotropic


title: Colorectal Tumor Tissue-112611-02TB-CytoScanHD

description:
112611-02TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-112611-02TB


title: siFIE-3


title: Colorectal Tumor Tissue-100811-01TB-CytoScanHD

description:
100811-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-100811-01TB

value: Female

value: Recto-sigmoid

value: IV


title: Colorectal Tumor Tissue-112611-01TB-CytoScanHD

description:
112611-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-112611-01TB

value: Tumor

value: Sigmoid


title: clf-7swn-28-1


title: SLE 06 LSLE06_02


title: clf-7swn-28-2


title: Colorectal Tumor Tissue-092811-01TB-CytoScanHD

description:
092811-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-092811-01TB

value: Rectal

value: I


title: SLE 05 LSLE05_01

value: Reference (equal molar concentrations of the reverse complement of all human light chain probes)

value: Synthesized DNA (oligonucleotides)


title: Colorectal Tumor Tissue-101011-01TB-CytoScanHD

description:
101011-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-101011-01TB


title: siFIE-1


title: SLE 04 LSLE04_02

value: SLE

value: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype

source_name: Reference (equal molar concentrations of the reverse complement of all human light chain probes)


title: col-1


title: Colorectal Tumor Tissue-100311-03TB-CytoScanHD

description:
100311-03TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-100300-03TB

value: Colon


title: col-3


title: Colorectal Tumor Tissue-062011-01TB-CytoScanHD

description:
062011-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-062011-01TB


title: SLE 03 LSLE03_02


title: SLE 03 LSLE03_01


title: Colorectal Tumor Tissue-051611-01TB-CytoScanHD

description:
051611-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-051611-01TB

value: Male


title: Colorectal Tumor Tissue-092611-01TB-CytoScanHD

description:
092611-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-092611-01TB


title: Colorectal Tumor Tissue-121011-01TB-CytoScanHD

description:
121011-01TB
Hybridized to CytoScanHD


title: Colorectal Tumor Tissue-042412-01TB-CytoScanHD

description:
042412-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-042412-01TB

value: III


title: SLE 02 LSLE02_01

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype


title: SLE 05 LSLE05_02


title: SLE 02 LSLE02_02


title: SLE 01 LSLE01_02


title: Colorectal Tumor Tissue-031912-01TB-CytoScanHD

description:
031912-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-031912-01TB

value: II


title: SLE 04 LSLE04_01


title: Colorectal Tumor Tissue-011112-01TB-CytoScanHD

description:
011112-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-011112-01TB


title: Colorectal Tumor Tissue-033112-01TB-CytoScanHD

description:
033112-01TB
Hybridized to CytoScanHD

source_name: Colorectal Tumor Tissue-033112-01TB


title: SLE 01 LSLE01_01


title: Colorectal Normal Tissue-121011-01NB-CytoScanHD

description:
121011-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-121011-01NB

value: Adjacent Normal


title: Colorectal Normal Tissue-112611-01NB-CytoScanHD

description:
112611-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-112611-01NB


title: Colorectal Normal Tissue-010912-01NB-CytoScanHD

description:
010912-01NB
Hybridized to CytoScanHD


title: Colorectal Normal Tissue-112611-02NB-CytoScanHD

description:
112611-02NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-112611-02NB


title: Healthy 10 LH10_02

value: Healthy


title: Colorectal Normal Tissue-100811-01NB-CytoScanHD

description:
100811-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-100811-01NB

value: Female


title: Colorectal Normal Tissue-100311-03NB-CytoScanHD

description:
100311-03NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-100300-03NB


title: clf-7swn-28-3

value: pleiotropic


title: Colorectal Normal Tissue-101011-01NB-CytoScanHD

description:
101011-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-101011-01NB

value: IV


title: Healthy 09 LH09_02


title: Healthy 10 LH10_01


title: Healthy 09 LH09_01


title: Healthy 08 LH08_02


title: Healthy 08 LH08_01


title: Healthy 07 LH07_02


title: Healthy 07 LH07_01


title: Healthy 06 LH06_02


title: Colorectal Normal Tissue-051611-01NB-CytoScanHD

description:
051611-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-051611-01NB


title: Colorectal Normal Tissue-062011-01NB-CytoScanHD

description:
062011-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-062011-01NB


title: Healthy 05 LH05_02

source_name: Reference (equal molar concentrations of the reverse complement of all human light chain probes)


title: Healthy 06 LH06_01


title: Colorectal Normal Tissue-042412-01NB-CytoScanHD

description:
042412-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-042412-01NB

value: Recto-sigmoid


title: Colorectal Normal Tissue-033112-01NB-CytoScanHD

description:
033112-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-033112-01NB

value: Sigmoid


title: Colorectal Normal Tissue-031912-01NB-CytoScanHD

description:
031912-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-031912-01NB


title: Healthy 05 LH05_01


title: Colorectal Normal Tissue-092811-01NB-CytoScanHD

description:
092811-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-092811-01NB

value: Rectal


title: Healthy 04 LH04_01

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype


title: Colorectal Normal Tissue-092611-01NB-CytoScanHD

description:
092611-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-092611-01NB


title: Healthy 04 LH04_02


title: Healthy 03 LH03_02


title: Colorectal Normal Tissue-011112-01NB-CytoScanHD

description:
011112-01NB
Hybridized to CytoScanHD

source_name: Colorectal Normal Tissue-011112-01NB


title: Healthy 03 LH03_01


title: Healthy 01 LH01_01


title: Healthy 01 LH01_02


title: SLE 10 KSLE10_02

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa+IgLambda- phenotype


title: expA-DM stat rep3

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

country: Finland

institute: University of Helsinki

description:
Ch1: 140911-array7-1.gpr
Ch2: 140911-array8-1.gpr

hyb_protocol: 200 ng of each labelled aRNA samples (one sample per dye and biological triplicate) were hybridized to the array according to the manufacturer's (Agilent Technologies) instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5, page 31 onwards).

scan_protocol: The microarray slide was washed after hybridization according to the manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v6.5). The microarray slide was scanned using a Genepix 4110AL scanner (Axon Instruments). Using green dye channel for Cy5 labelled samples, red dye channel for Cy3 labelled samples and blue dye channel for Alexa488 labelled samples, using 100% PMT and a resolution of 5 um.

data_processing:
The resulting images were analyzed with Agilent Genepix pro 6.1. Data generated from the scanning was then analyzed using Bioconductor with the limma software package for the R programming language. Normalization was achieved using a combination of print-tip loess normalization within the arrays and quantile normalization between the arrays, and empirical Bayesian variance shrinkage for statistical analysis, combining data from all probes for each gene. A false discovery rate (fdr) value of 0.05 was used as cut-off for significance in statistical analysis.

The data matrix ('normalized_avrg_data.txt' available on Series records) contains normalized log2-ratio of Ch1/Ch2 (average of 3 replicates).

organism: Pectobacterium wasabiae

source_name: expA knock out replicate 3 stat

label_protocol: Aminoallyl-UTP containing aRNA was then hybridized to HyPer-5 (Cy5, Amersham), Cy3 (Amersham) or Alexa488 (Invitrogen) one dye per biological replicate. 5 µg of aRNA of each biological replicate of a sample was dried in a vacuum centrifuge, then resuspended in 7 µl sterile MQ water and 9 µl Na2CO3 buffer at pH 9.3, then 4 µl of dye was added. The samples were subsequently incubated at RT in darkness for 1 hour, then 4.5 µl 4M hydroxylamine was added and the samples were left to incubate at RT in darkness for an additional 15 minutes. Finally the samples were purified using the PureLink PCR purification kit (Invitrogen).

growth_protocol: Bacteria colonies of SCC3193 wild type, expA mutant, rsmA mutant and expA rsmA double mutant were grown in liquid hrp inducing minimal medium (supplemented with 0.4% polygalacturonic acid) cultures with 200 rpm shaking at 28 degrees celsius. Cells from all strains were grown to stationary phase.

extract_protocol: Total RNA from SCC3193 strains were isolated using the RNA extraction protocol by Summers et al (1970). The RNA was further treated with Superase I (supplier: Ambion) to remove genomic DNA traces according to the suppliers instructions. The RNA was further treated using the MinElute cleanup kit (Qiagen) for enzyme removal and RNA purification. The RNA quality and quantity was checked using a NanoDrop and a Agilent BioAnalyzer (RNA Nano 6000 chip). Subsequently, 16S and 23S rRNA were removed from the samples, leaving mainly bacterial mRNA, using the Ambion MICROBExpress kit according to the manufacturer's protocol. Quality and quantity were checked after this step using Agilent BioAnalyzer and NonDrop. After this, the sampels were treated with the Ambion MessageAmp(TM) II Bacteria RNA Amplification kit, supplemented with 5-(3-aminoallyl)-UTP, according to the manufacturer's instructions to synthesize antisense RNA (aRNA) from the original RNA samples.

tag: strain background

tag: genotype/variation

value: expA inactivation mutant

tag: growth stage

value: early stationary growth phase

source_name: rsmA expA double knock-out replicate 3 stat

value: rsmA expA double mutant


title: expA-rsmA stat rep3

source_name: rsmA KO replicate 3 stat

value: rsmA inactivation mutant


title: DM-rsmA stat rep2

description:
Ch1: 140911-array7-1.gpr
Ch2: 140911-array7-1.gpr

source_name: rsmA expA double knock-out replicate 2 stat

source_name: rsmA KO replicate 2 stat


title: expA-DM stat rep1

description:
Ch1: 140911-array5-2.gpr
Ch2: 140911-array5-2.gpr

source_name: expA knock out replicate 1 stat

source_name: rsmA expA double knock-out replicate 1 stat


title: DM-rsmA stat rep1

description:
Ch1: 140911-array5-2.gpr
Ch2: 140911-array6-1.gpr

source_name: rsmA KO replicate 1 stat


title: SLE 09 KSLE09_02

tag: disease state

value: SLE

value: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa+IgLambda- phenotype

source_name: Reference (equal molar concentrations of the reverse complement of all human light chain probes)

tag: components

tag: sample type

value: Synthesized DNA (oligonucleotides)


title: Healthy 02 LH02_01

tag: individual

value: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype

value: Reference (equal molar concentrations of the reverse complement of all human light chain probes)


title: SLE 08 KSLE08_02


title: expA-DM stat rep2

description:
Ch1: 140911-array6-1.gpr
Ch2: 140911-array7-1.gpr

source_name: expA knock out replicate 2 stat


title: expA-rsmA stat rep2


title: SLE 10 KSLE10_01


title: expA-wt stat rep2

description:
Ch1: 140911-array6-1.gpr
Ch2: 140911-array6-1.gpr

source_name: wildtype cells replicate 2 stat

value: wildtype


title: SLE 10 LSLE10_01


title: expA-rsmA stat rep1


title: expA-wt stat rep1

source_name: wildtype cells replicate 1 stat


title: DM-wt stat rep3

description:
Ch1: 140911-array8-1.gpr
Ch2: 140911-array8-1.gpr

source_name: wildtype cells replicate 3 stat


title: DM-rsmA stat rep3


title: Healthy 02 LH02_02

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa-IgLambda+ phenotype

value: Healthy


title: SLE 08 KSLE08_01


title: SLE 07 KSLE07_02


title: DM-wt stat rep2

description:
Ch1: 140911-array7-1.gpr
Ch2: 140911-array6-1.gpr


title: SLE 07 KSLE07_01


title: SLE 06 KSLE06_02


title: SLE 06 KSLE06_01


title: SLE 09 KSLE09_01


title: expA-wt stat rep3


title: rsmA-wt stat rep2


title: SLE 05 KSLE05_02


title: rsmA-wt stat rep1

description:
Ch1: 140911-array6-1.gpr
Ch2: 140911-array5-2.gpr


title: SLE 05 KSLE05_01


title: SLE 04 KSLE04_02


title: expA-DM LL rep3

description:
Ch1: 140911-array4-1.gpr
Ch2: 140911-array4-1.gpr

source_name: expA knock out replicate 3 Late-Log

value: late-logarithmic growth phase

source_name: rsmA expA double knock-out replicate 3 Late-Log


title: SLE 04 KSLE04_01

source_name: FACS sorted peripheral blood B cells with the CD20+CD138-IgKappa+IgLambda- phenotype


title: DM-rsmA LL rep3

source_name: rsmA KO replicate 3 Late-Log


title: SLE 03 KSLE03_02


title: DM-rsmA LL rep1

description:
Ch1: 140911-array2-1.gpr
Ch2: 140911-array1-2.gpr

source_name: rsmA expA double knock-out replicate 1 Late-Log

source_name: rsmA KO replicate 1 Late-Log


title: expA-DM LL rep2

description:
Ch1: 140911-array2-1.gpr
Ch2: 140911-array3-2.gpr

source_name: expA knock out replicate 2 Late-Log

source_name: rsmA expA double knock-out replicate 2 Late-Log


title: rsmA-wt stat rep3

source_name: rsmA KO replicate 3 stat


title: expA-DM LL rep1

description:
Ch1: 140911-array1-2.gpr
Ch2: 140911-array2-1.gpr

source_name: expA knock out replicate 1 Late-Log


title: DM-wt stat rep1

source_name: rsmA expA double knock-out replicate 1 stat


title: SLE 02 KSLE02_02

source_name: Reference (equal molar concentrations of the reverse complement of all human light chain probes)


title: SLE 03 KSLE03_01


title: SLE 02 KSLE02_01


title: expA-rsmA LL rep3


title: SLE 01 KSLE01_01


title: expA-rsmA LL rep2

source_name: rsmA KO replicate 2 Late-Log


title: Healthy 10 KH10_02


title: expA-wt LL rep3

description:
Ch1: 140911-array4-1.gpr
Ch2: 140911-array3-2.gpr

source_name: wildtype cells replicate 3 mid-log


title: expA-rsmA LL rep1

description:
Ch1: 140911-array1-2.gpr
Ch2: 140911-array1-2.gpr


title: expA-wt LL rep2

description:
Ch1: 140911-array2-1.gpr
Ch2: 140911-array2-1.gpr

source_name: wildtype cells replicate 2 late-log


title: SLE 01 KSLE01_02


title: Healthy 10 KH10_01


title: MYC_2

description: A0007684: MYC over-expressor

source_name: tumor tissue from LT2/MYC mouse

value: FVB

value: MYC over-expressor

tag: tissue

value: liver tumor


title: DM-rsmA LL rep2

description:
Ch1: 140911-array3-2.gpr
Ch2: 140911-array3-2.gpr


title: Healthy 09 KH09_02


title: DM-wt LL rep3


title: Healthy 08 KH08_02


title: Healthy 09 KH09_01


title: expA-wt LL rep1

source_name: wildtype cells replicate 1 late-log


title: Healthy 07 KH07_01


title: Healthy 07 KH07_02


title: Healthy 06 KH06_02


title: rsmA-wt LL rep1


title: rsmA-wt LL rep3


title: rsmA-wt LL rep2

description:
Ch1: 140911-array3-2.gpr
Ch2: 140911-array2-1.gpr


title: Healthy 08 KH08_01


title: DM-wt LL rep1


title: Healthy 05 KH05_02


title: Healthy 06 KH06_01


title: Healthy 05 KH05_01


title: Healthy 03 KH03_02


title: Healthy 04 KH04_02


title: Healthy 04 KH04_01


title: DM-wt LL rep2


title: Healthy 02 KH02_01


title: Healthy 03 KH03_01


title: Healthy 02 KH02_02


title: MMN+Glucose+NH4/36hrs (R1)

city: Lund

first: Tomas

last: Johansson

address: Sölvegatan 37

country: Sweden

institute: Lund University

description: Treat MMN+Glucose+NH4/36hrs; Replicate 1 (subarray A10)

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization kit (#05 583 683 001) according to their Gene Expression v5.0 protocol (www.nimblegen.com).

scan_protocol: Scanning was performed at single-label (Cy3) wavelength (532nm) on an Agilent High-Resolution Microarray Scanner set at 2 um resolution and 40% PMT.

data_processing: The bursted and gridded tif-files (.tif file) were directly subjected data extraction, background reduction and quantile normalization using the RMA (Robust Multi-Chip Average) algoritm as implemented by the NimbleScan software package, version 2.5.26 (Roche NimbleGen, Inc.)(www.nimblegen.com).

organism: Paxillus involutus

source_name: Treat MMN+Glucose+NH4/36hrs

label_protocol: Single-color labeling was performed using the Roche/NimbleGen One-Color DNA Labeling kit (# 05 223 55 001) following their Gene Expression v5.0 protocol (www.nimblegen.com).

growth_protocol: Paxillus involutus (Batsch) Fr. (ATCC 200175) was grown axenically in Petri dishes on a layer of glass beads immersed in medium. The fungus was first grown for 9 days on a Minimum Melin Norkrans (MMN)+glucose medium (in RT and in the dark). The cultures were then starved for nitrogen during 24 hrs, by replacing the medium by the same medium but excluding the nitrogen source (NH4Cl).

extract_protocol: Harvest mycelium was immediately dropped into liquid nitrogen and homogenized in a mortar on dry ice. Total RNA was extracted using the Plant RNeasy Mini kit (www.qiagen.com) and concentrated using RNA MinElute kit (www.qiagen.com). RNA quality/integrity and concentration was assessed by analysis on a RNA 6000 Nano chip using the 2100 Bioanalyzer (Agilent). From total RNA, cDNA was produced using the SuperScript double-stranded cDNA Synthesis kit (Invitrogen, #11917-0xx) according to the NimbleGen Gene Expression v5.0 protocol (www.nimblegen.com).

treatment_protocol: After starvation the medium was replaced with BSA dissolved in MMN+glucose (inorganic N source excluded) and followed by incubation for 4 days. After this period of time there was either no addition or addition of 5mg of NH4Cl and continued incubation for either 14 or 36 hrs prior harvest (3 replicates for each).

tag: strain

value: mycelium patch


title: MMN+Glucose-NH4/36hrs (R3)

description: Treat MMN+Glucose-NH4/36hrs; Replicate 3 (subarray A09)

source_name: Treat MMN+Glucose-NH4/36hrs


title: MMN+Glucose-NH4/36hrs (R2)

description: Treat MMN+Glucose-NH4/36hrs; Replicate 2 (subarray A08)


title: MMN+Glucose+NH4/36hrs (R2)

description: Treat MMN+Glucose+NH4/36hrs; Replicate 2 (subarray A11)


title: MMN+Glucose+NH4/14hrs (R3)

description: Treat MMN+Glucose+NH4/14hrs; Replicate 3 (subarray A06)

source_name: Treat MMN+Glucose+NH4/14hrs


title: MMN+Glucose-NH4/36hrs (R1)

description: Treat MMN+Glucose-NH4/36hrs; Replicate 1 (subarray A07)