title: Schizophrenia ped125 sp385-50K Xba

description:
sp385-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped125 sp385


title: Schizophrenia ped125 sp387-50K Xba

status: Public on Jun 13 2011

type: genomic

city: Wako-city

first: Kazuo

last: Yamada

state: Saitama

address: 2-1 Hirosawa

country: Japan

institute: RIKEN Brain Science Institute

description:
sp387-50K Xba
Hybridized to 50K_Xba

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.

data_processing: CEL files were processed by manufacture's protocol. The software used to generate the SNP calls is GeneChip DNA Analysis Software (GDAS) v3.0. Matrix tables for the genetic programs were produced. Genotype data were analyzed with the GeneSpring GT (Varia) 2.0 software package developed by Agilent Technologies (Santa Clara, CA). Transmission disequilibrium test was performed using the R program (http://www.r-project.org).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Schizophrenia ped125 sp387

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood using standard phenol/chloroform extraction. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel.electrophoresis.

tag: tissue

value: peripheral blood

tag: individual

value: patient

tag: gender

value: female

tag: affection _status

value: schizophrenia


title: Schizophrenia ped123 sp381-50K Xba

description:
sp381-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped123 sp381

value: male


title: Schizophrenia ped123 sp380-50K Xba

description:
sp380-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped123 sp380

value: mother

value: healthy


title: Schizophrenia ped122 sp377-50K Xba

description:
sp377-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped122 sp377


title: Schizophrenia ped121 sp373-50K Xba

description:
sp373-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped121 sp373

value: father


title: Schizophrenia ped122 sp378-50K Xba

description:
sp378-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped122 sp378


title: Schizophrenia ped123 sp379-50K Xba

description:
sp379-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped123 sp379


title: Schizophrenia ped125 sp386-50K Xba

description:
sp386-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped125 sp386


title: Schizophrenia ped126 sp390-50K Xba

description:
sp390-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped126 sp390


title: Schizophrenia ped120 sp371-50K Xba

description:
sp371-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped120 sp371


title: Schizophrenia ped122 sp376-50K Xba

description:
sp376-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped122 sp376


title: Schizophrenia ped121 sp375-50K Xba

description:
sp375-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped121 sp375


title: Schizophrenia ped119 sp367-50K Xba

description:
sp367-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped119 sp367


title: Schizophrenia ped124 sp383-50K Xba

description:
sp383-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped124 sp383


title: Schizophrenia ped119 sp368-50K Xba

description:
sp368-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped119 sp368


title: Schizophrenia ped118 sp366-50K Xba

description:
sp366-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped118 sp366


title: Schizophrenia ped120 sp372-50K Xba

description:
sp372-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped120 sp372


title: Schizophrenia ped120 sp370-50K Xba

description:
sp370-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped120 sp370


title: Schizophrenia ped118 sp364-50K Xba

description:
sp364-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped118 sp364


title: Schizophrenia ped112 sp348-50K Xba

description:
sp348-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped112 sp348


title: Schizophrenia ped132 sp403-50K Xba

description:
sp403-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped132 sp403


title: Schizophrenia ped117 sp363-50K Xba

description:
sp363-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped117 sp363


title: Schizophrenia ped117 sp361-50K Xba

description:
sp361-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped117 sp361


title: Schizophrenia ped112 sp347-50K Xba

description:
sp347-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped112 sp347


title: Schizophrenia ped117 sp362-50K Xba

description:
sp362-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped117 sp362


title: Schizophrenia ped116 sp359-50K Xba

description:
sp359-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped116 sp359


title: Schizophrenia ped112 sp346-50K Xba

description:
sp346-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped112 sp346


title: Schizophrenia ped121 sp374-50K Xba

description:
sp374-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped121 sp374


title: Schizophrenia ped111 sp343-50K Xba

description:
sp343-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped111 sp343


title: Schizophrenia ped111 sp345-50K Xba

description:
sp345-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped111 sp345


title: Schizophrenia ped110 sp341-50K Xba

description:
sp341-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped110 sp341


title: Schizophrenia ped110 sp340-50K Xba

description:
sp340-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped110 sp340


title: Schizophrenia ped110 sp342-50K Xba

description:
sp342-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped110 sp342


title: Schizophrenia ped109 sp339-50K Xba

description:
sp339-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped109 sp339


title: Schizophrenia ped111 sp344-50K Xba

description:
sp344-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped111 sp344


title: Schizophrenia ped108 sp335-50K Xba

description:
sp335-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped108 sp335


title: Schizophrenia ped109 sp337-50K Xba

description:
sp337-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped109 sp337


title: Schizophrenia ped116 sp360-50K Xba

description:
sp360-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped116 sp360


title: Schizophrenia ped107 sp333-50K Xba

description:
sp333-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped107 sp333


title: Schizophrenia ped109 sp338-50K Xba

description:
sp338-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped109 sp338


title: Schizophrenia ped107 sp331-50K Xba

description:
sp331-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped107 sp331


title: Schizophrenia ped118 sp365-50K Xba

description:
sp365-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped118 sp365


title: 13970182 - ga1_penta-della DARK2 vs Wt dark 1.2

type: RNA

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: Identification of DELLA-dependent downstream targets in darkness

hyb_protocol: Wt dark 1.2 Cy5 / ga1_penta-della DARK2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

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

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

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Wt dark 1.2

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

growth_protocol: whole plant - Media: MS agar for 5days  hygrometry: 55%  Temperature: 22°c  Light: continuous dark

extract_protocol: Wt dark 1.2:60ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: genotype/variation

value: Wt

tag: growth condition

value: dark

tag: cultivar

value: arabidopsis thaliana (landsberg erecta)

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

source_name: ga1_penta-della DARK2

growth_protocol: whole plant - Media: MS agar for 5days  hygrometry: 55%  Temperature: 22°c  Light: dark

value: DARK

value: mutant (ga1-3_rga_gai_rgl1_rgl2_rgl3)


title: Schizophrenia ped108 sp336-50K Xba

description:
sp336-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped108 sp336


title: 13970181 - Wt dark 1.2 vs ga1_penta-della DARK2

hyb_protocol: ga1_penta-della DARK2 Cy5 / Wt dark 1.2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Schizophrenia ped107 sp332-50K Xba

description:
sp332-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped107 sp332


title: Schizophrenia ped106 sp330-50K Xba

description:
sp330-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped106 sp330


title: Schizophrenia ped108 sp334-50K Xba

description:
sp334-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped108 sp334


title: 13970184 - ga1_penta-della DARK3 vs Wt dark 1.3

hyb_protocol: Wt dark 1.3 Cy5 / ga1_penta-della DARK3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt dark 1.3

extract_protocol: Wt dark 1.3:60ug. (Qiagen_RNeasy.pdf)

source_name: ga1_penta-della DARK3


title: 13970183 - Wt dark 1.3 vs ga1_penta-della DARK3

hyb_protocol: ga1_penta-della DARK3 Cy5 / Wt dark 1.3 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: Schizophrenia ped105 sp326-50K Xba

description:
sp326-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped105 sp326


title: 13970170 - Wt dark 1.2 vs Wt light 2

hyb_protocol: Wt light 2 Cy5 / Wt dark 1.2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt light 2

growth_protocol: whole plant - Media: MS agar for 5days  hygrometry: 55%  Temperature: 22°c  Light: continuous light

extract_protocol: Wt light 2:60ug. (Qiagen_RNeasy.pdf)

value: light


title: Schizophrenia ped103 sp321-50K Xba

description:
sp321-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped103 sp321


title: Schizophrenia ped106 sp329-50K Xba

description:
sp329-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped106 sp329


title: Schizophrenia ped105 sp327-50K Xba

description:
sp327-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped105 sp327


title: 13970178 - Wt dark 1.1 vs ga1_penta-della DARK1

hyb_protocol: ga1_penta-della DARK1 Cy5 / Wt dark 1.1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ga1_penta-della DARK1

source_name: Wt dark 1.1

extract_protocol: Wt dark 1.1:60ug. (Qiagen_RNeasy.pdf)


title: Schizophrenia ped105 sp325-50K Xba

description:
sp325-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped105 sp325


title: 13970177 - Wt light 3 vs Wt dark 1.3

hyb_protocol: Wt dark 1.3 Cy5 / Wt light 3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt light 3

extract_protocol: Wt light 3:60ug. (Qiagen_RNeasy.pdf)


title: 13970180 - ga1_penta-della DARK1 vs Wt dark 1.1

hyb_protocol: Wt dark 1.1 Cy5 / ga1_penta-della DARK1 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: Schizophrenia ped116 sp358-50K Xba

description:
sp358-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped116 sp358


title: Schizophrenia ped101 sp312-50K Xba

description:
sp312-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped101 sp312


title: 13970173 - Wt dark 1.3 vs Wt light 3

hyb_protocol: Wt light 3 Cy5 / Wt dark 1.3 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: 13969380 - Wt dark 1.1 vs Wt light 1

hyb_protocol: Wt light 1 Cy5 / Wt dark 1.1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt light 1

extract_protocol: Wt light 1:60ug. (Qiagen_RNeasy.pdf)


title: Schizophrenia ped103 sp320-50K Xba

description:
sp320-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped103 sp320


title: Schizophrenia ped101 sp313-50K Xba

description:
sp313-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped101 sp313


title: Schizophrenia ped100 sp310-50K Xba

description:
sp310-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped100 sp310


title: Schizophrenia ped103 sp322-50K Xba

description:
sp322-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped103 sp322


title: Schizophrenia ped119 sp369-50K Xba

description:
sp369-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped119 sp369


title: Schizophrenia ped106 sp328-50K Xba

description:
sp328-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped106 sp328


title: 13969184 - ga1 DARK2 vs Wt dark 2.2

hyb_protocol: Wt dark 2.2 Cy5 / ga1 DARK2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt dark 2.2

extract_protocol: Wt dark 2.2:60ug. (Qiagen_RNeasy.pdf)

source_name: ga1 DARK2

growth_protocol: whole plant - Media: MS agar for 5days  hygrometry: 55%  Temperature: 22°c  Light:  dark

extract_protocol: ga1 DARK2:60ug. (Qiagen_RNeasy.pdf)

value: mutant (ga1-3)


title: Schizophrenia ped101 sp314-50K Xba

description:
sp314-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped101 sp314


title: Schizophrenia ped100 sp311-50K Xba

description:
sp311-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped100 sp311


title: 13969187 - Wt dark 2.3 vs ga1 DARK3

hyb_protocol: ga1 DARK3 Cy5 / Wt dark 2.3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ga1 DARK3

extract_protocol: ga1 DARK3:60ug. (Qiagen_RNeasy.pdf)

source_name: Wt dark 2.3

extract_protocol: Wt dark 2.3:60ug. (Qiagen_RNeasy.pdf)


title: 13969381 - Wt light 1 vs Wt dark 1.1

hyb_protocol: Wt dark 1.1 Cy5 / Wt light 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt dark 1.1


title: Gastric cancer  tissue samples (FFPE) 10

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: A pool of DNA from blood of normal individuals

hyb_protocol: As described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Bluefuse software version 3.4 (BlueGnome, Cambridge, UK) was used for automatic feature extraction. Spots were excluded when the quality flag was below 1 or the confidence value was below 0.1. Log2 tumor to normal ratio was calculated for each clone and median block normalization was used to normalize the data.

source_name: Gastric cancer

label_protocol: Labeling was done by random priming (Bioprime DNA Labeling System, Invitrogen, Breda, The Netherlands)

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51

value: Gastric cancer

tag: site

value: Stomach

tag: tumor site

value: Antrum

tag: tnm

tag: age

value: F

tag: platform_id type

value: bac

source_name: male reference DNA

value: Pooled DNA from the blood of 18 normal male individuals


title: Gastric cancer  tissue samples (FFPE) 8

value: Cardia

value: M

source_name: female reference DNA

value: Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer  tissue samples (FFPE) 7


title: Gastric cancer  tissue samples (FFPE) 9


title: 13969186 - ga1 DARK3 vs Wt dark 2.3

hyb_protocol: Wt dark 2.3 Cy5 / ga1 DARK3 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: 13969185 - Wt dark 2.2 vs ga1 DARK2

hyb_protocol: ga1 DARK2 Cy5 / Wt dark 2.2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: qRT-PCR on Staphylococcus aureus strain US300 in neutophil

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

country: USA

institute: J Craig Venter Institute

hyb_protocol: RNA samples were reverse transcribed to produce cDNA using SuperScript III (Invitrogen) and then subjected to qRT-PCR using Roche Sybr Green 2x matermix on the Roche 480 Light Cycler in 384-well format.  Genes for each sample were represented in duplicates.  Reactions were carried out at 10ul final volume. Each reaction contained 10ng of total RNA.  PCR activation at 95°C for 10 min was followed by 70 cycles of 15 s at 95°C, 10 s at 55°C and 10 s at 70°C. Sybr green fluorescence was captured in each cycle following 70°C extension.

scan_protocol: Expression levels were reported in Cp values.

data_processing: Data was produced in duplicates. The internal controls set was selected and included all genes present in all samples from the same organ with Cp value below 40. The average of the control set for the sample was extracted from the minimum of 2 duplicates. All the data were done in duplicate. We selected the lowest Cp value among two to represent the true Cp value because we had some evaporation problems on some plates that gave unreasonably high Cp values for the number of wells. We did not have designated internal controls on our PCR plates. So we selected all the genes with the Cp values below 40 that present in all samples serve as an internal control set. From our experience Cp values below 40 are more precise and have better reproducibility. We took the average Cp value of the control set Cp(control)for each sample. This Cp(control) is a reflection of how much of the sample total RNA was used in the reaction. Then we normalize (shifted) each Cp value for the sample on that sample Cp(control): Cp- Cp(control).

label: Sybr Green

organism: Staphylococcus aureus

source_name: Staphylococcus aureus strain USA300 during human neutrophil infection

extract_protocol: Ambion mirVana RNA extraction

treatment_protocol: Human neutrophils were purified from blood donors in accordance with a protocol approved by the Institutional Review Board for Human Subject, Indiana University School of Medicine. The donor blood were heparinized and the neutrophils were purified using the Vacutainer CPT (BD) method. After discarding the upper phase containing plasma and peripheral blood macrophages, the lower phase containing the erythrocyte/neutrophil mixture were collected by a syringe. After lysing the erythrocytes with erythrocyte lysis buffer (EL buffer), the neutrophils were suspended in RPMI 1640 medium containing 10% fetal bovine serum. Trypan blue exclusion method were used to assess the viability of the purified cells. More than 95% of the purified cells should be viable; otherwise, the cells were discarded. The cell numbers were counted by hemocytometer. The strains TB15 and US300 were grown in TSB to early log phase (OD600 = 0.5), washed in Dulbecco’s PBS (DPBS), and then opsonized with 50% normal human serum. The opsonized bacterial cells (108 colony forming unit (CFU)) were mixed with human neutrophils  in all the wells of three 12-well tissue culture plates. After being centrifuged to synchronize phagocytosis, the plates were incubated in a 37 C incubator with 5% CO2. After incubation of 30min, 60 min and 120 min, RNAprotect solution were added, and neutrophils were lysed by 0.1% saponin treatment. The remaining staphylococcal cells were collected and combined. Then total RNA were purified.

tag: sample source

value: human neutrophil infection

tag: strain


title: qRT-PCR on Staphylococcus aureus strain TB-15 in neutophil

source_name: Staphylococcus aureus strain TB-15 during human neutrophil infection


title: Schizophrenia ped100 sp309-50K Xba

description:
sp309-50K Xba
Hybridized to 50K_Xba

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

source_name: Schizophrenia ped100 sp309

value: peripheral blood

value: father

value: male

value: healthy


title: 13969182 - ga1 DARK1 vs Wt dark 2.1

hyb_protocol: Wt dark 2.1 Cy5 / ga1 DARK1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt dark 2.1

extract_protocol: Wt dark 2.1:60ug. (Qiagen_RNeasy.pdf)

value: Wt

value: dark

value: arabidopsis thaliana (landsberg erecta)

source_name: ga1 DARK1

growth_protocol: whole plant - Media: MS agar for 5days  hygrometry: 55%  Temperature: 22°c  Light:  continuous dark

extract_protocol: ga1 DARK1:60ug. (Qiagen_RNeasy.pdf)

value: DARK


title: Gastric cancer  tissue samples (FFPE) 4

value: Gastric cancer

value: Stomach


title: Gastric cancer  tissue samples (FFPE) 1

value: Body


title: Gastric cancer  tissue samples (FFPE) 3

value: bac


title: qRT-PCR on Staphylococcus aureus strain US300 in kidney

source_name: Staphylococcus aureus strain US300 during mouse kidney infection

treatment_protocol: The murine kidney model experiment were carried out by following the procedures reported.  Strain  US300 was grown overnight in 3 ml TSB and then diluted 1:100 into fresh TSB in 50ml TSB in a 500 ml flask to OD660 = 0.5. The bacterial cells were collected by centrifugation, washed once with 10ml PBS and then suspended in 1.25 ml PBS. In this volume, the bacterial concentration were 2× 108 CFU per 30 l volume. Six week-old BALB/c mice (10 mice per strain) were anesthetized with Avertin and then inoculated with 30 µl of the cell suspension. After being held upright for 1 minute, the mice were placed into the cage in a supine position. At 72 hr post-infection, the mice were euthanized by CO2 asphyxiation and the kidneys were harvested. The harvested kidnesy were homogenized and the bacterial numbers were measured by diluting and spreading of the lung homogenate on TSA agar plates. We recovered 106 – 108 CFU from the kidney homogenate.

value: mouse kidney infection


title: Gastric cancer  tissue samples (FFPE) 5

value: F

value: Pooled DNA from the blood of 18 normal male individuals


title: qRT-PCR on Staphylococcus aureus strain TB15 in skin

source_name: Staphylococcus aureus strain TB15 during mouse skin infection

treatment_protocol: The experiment for the soft tissue infection model were carried out by following the procedures reported by Horsburgh M. J.  (Horsburgh, M. J., J. L. Aish, I. J. White, L. Shaw, J. K. Lithgow, and S. J. Foster. 2002. sigmaB modulates virulence determinant expression and stress resistance: characterization of a functional rsbU strain derived from Staphylococcus aureus 8325-4. J Bacteriol 184:5457-67) with minor modifications.  The strains TB15 and USA300 were grown in  50ml TSB in a 500 ml flask to early log phase (OD600 = 0.5) and the cells were collected by centrifugation. The collected cells were washed once with 10ml PBS and then suspended in 10ml PBS. After adjusting the cell suspension to OD600 = 4, which corresponds to 109 CFU/ml, 100 ul of the cell suspension were subcutaneously injected in the right flank of 10 Crl:SKH1-hrBR hairless mice (6 – 8 week-old). Seven days after injection, the mice were euthanized, and the lesions produced were removed and homogenized. The bacteria number were measured by CFU on TSA plates. We recovered approximately 107 - 108 CFU from each mouse.  If, compared with USA300 a significantly lower number of bacteria are recovered from  the phage-deletion mutant TB15, a higher inoculum (e.g., 5X108 CFU, 109 CFU etc) were injected into the mice for the mutants; then the optimal inoculum that allows growth of the mutant equivalent to that of USA300 were determined.

value: mouse skin infection


title: qRT-PCR on Staphylococcus aureus strain TB15 in kidney

source_name: Staphylococcus aureus strain TB-15 during mouse kidney infection

treatment_protocol: The murine kidney model experiment were carried out by following the procedures reported.  Strain  TB15 was grown overnight in 3 ml TSB and then diluted 1:100 into fresh TSB in 50ml TSB in a 500 ml flask to OD660 = 0.5. The bacterial cells were collected by centrifugation, washed once with 10ml PBS and then suspended in 1.25 ml PBS. In this volume, the bacterial concentration were 2× 108 CFU per 30 l volume. Six week-old BALB/c mice (10 mice per strain) were anesthetized with Avertin and then inoculated with 30 µl of the cell suspension. After being held upright for 1 minute, the mice were placed into the cage in a supine position. At 72 hr post-infection, the mice were euthanized by CO2 asphyxiation and the kidneys were harvested. The harvested kidnesy were homogenized and the bacterial numbers were measured by diluting and spreading of the lung homogenate on TSA agar plates. We recovered 106 – 108 CFU from the kidney homogenate.


title: MCF7 vs. Human fibroblast GAPF_G

city: Seattle

first: Jamie

last: Guenthoer

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: MCF7 whole genome GAPF profile, Array G

hyb_protocol: Seven and a half micrograms of biotin-labeled DNA was hybridized to the appropriate Affymetrix Human Tiling 2.0R Array for 16 hours at 45°C at 60 rpm in an Affymetrix hybridization oven per manufacturer’s protocol.

scan_protocol: The arrays were scanned on an Affymetrix Scanner 3700 7G.

data_processing:
Affymetrix Human Tiling 2.0R Arrays were analyzed using Tiling Array Software (v 1.1.02 Affymetrix). Probe locations were mapped using the NCBI36/hg18 genome build from March 2006. Raw-intensity data were scaled to a target intensity of 100 and normalized by quantile normalization. Normalized probe intensities were analyzed by Wilcoxon rank sum one-sided test, detecting probes with intensities significantly different between the cancer and normal reference samples. The probe analysis for determining signal ratios and p-values was performed using a bandwidth of 500 bp.
pvalue.bar and signal.bar files were generated using the Tiling Array Software (Affymetrix) as described in the data processing protocol. The pvalue.bar files contain -10log10 pvalues calculated form a Wilcoxon one-sided test. The signal.bar files contain Log2 signal intensity (test/control).

label: biotin

source_name: MCF7 WG GAPF assay G

label_protocol: Seven and a half micrograms of DNA were fragmented using 0.016 U of DNaseI (NEB) and 10x DNaseI buffer in a 50 μL reaction. The reaction was incubated at 37°C for 25 minutes followed by heat inactivation at 95°C for 15 minutes. The fragmented samples were enzymatically biotinylated using the GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) per manufacturer’s protocol.

extract_protocol: Genomic DNA was extracted from the cell lines and human tumor tissue with the QIAamp DNA Micro kit (QIAGEN) per manufacturer’s protocol. The genomic DNA used to analyze copy number alterations on the SNP6.0 arrays was processed per manufacterer's instructions. The GAPF assay was performed with 50% formamide as described (Diede et al. 2010a). Two micrograms of genomic DNA from cells were split evenly and digested with 10 U of SbfI, KpnI or PmeI (NEB) for at least eight hours at 37°C in a volume of 20 μL. The restriction enzymes were heat inactivated by incubation at 65°C for 20 minutes. The digests were then combined into one tube. To the mixture was added 3 μL of 3 M NaCl (final concentration of 100 mM), 45 μL of formamide (final concentration of 50%), and 2 μL of water. This mixture was heated to 99°C in a thermocycler for 7 minutes to denature the DNA, and then rapidly cooled in a ice-water bath for 3 minutes leading to the formation of “snap-back” DNA. S1 digestion was performed by adding 100 U of S1 nuclease (2 μL of 100 U/μL solution; Invitrogen), 12 μL of 10x S1 nuclease buffer, and 8 μL of 3 M NaCl. The sample was incubated at 37°C for 60 minutes. S1 nuclease was extracted with phenol:chloroform, and the DNA was ethanol precipitated in the presence of 20 ug glycogen. The DNA pellet was resuspended in 80 μL of 1/10 TE. The DNA was split equally between two tubes and digested with 40 U of MseI (NEB) or 40 U of MspI (NEB) for at least 8 hours at 37°C in a reaction volume of 50 μL. The restriction enzymes were heat inactivated by incubation at 65°C for 20 minutes. For the ligation-mediated PCR, linkers were generated by creating a 100 pM equimolar solution of each linker oligo in 10 mM TE supplemented with NaCl for a final salt concentration of 100 mM. This solution was incubated in a boiling water bath for 7 minutes and then allowed to cool to 25°C to permit annealing. Linkers were recovered by ethanol precipitation and resuspended in 500 μL of water. The linkers were ligated to the MseI- or MspI-digested DNA by adding 5 μL of appropriate linker, 10x T4 DNA ligase buffer, water and 400 U of T4 DNA ligase (NEB) in a 50 μL reaction volume. This reaction was incubated at 16°C for at least 8 hoursm, and the ligase was heat inactivated at 65°C for 10 minutes. Free linkers were removed using a YM-50 spin column (Microcon) by adding the ligation reaction and 160 μL of 1/10 TE to the column and spinning at 12,000xg for 5 minutes or until the membrane is almost dry. The sample was recovered by adding 20 μL of 1/10 TE to the membrane, incubating at room temperature for 5 minutes, and spinning at 1000xg for 3 minutes per manufacturer’s instructions. The PCR was performed with the FastStart High Fidelity PCR System (Roche) with the following reaction reagents: 4 μL of linker-ligated DNA, 10 μL of 10x FastStart PCR buffer, 10 μL of 2mM dNTPs, 12 μL of 10 pM linker-specific primer, 20 μL of 5x GC-rich solution, 1 μL of FastStart Taq Polymerase, and 43 μL of water. The PCR conditions were as follows: 96°C for 6 minutes; 30 cycles of 96°C for 30 seconds, 55°C for 30 seconds, and 72°C for 30 seconds; 72°C for 7 minutes. Three microliters of the PCR product were run on a 1.5% agarose gel for quality control. The products shoμLd range from 200 bp to 600 bp. The MseI and MspI PCR products were combined and concentrated in a YM-30 spin column (Microcon). The combined PCR products (~200 μL) and 300 μL of 1/10 TE were added to the membrane and spun at 14,000xg 40 to 60 minutes, checking every 15 minutes until the volume is approximately 25 μL. The DNA was recovered per manufacturer’s instruction. The DNA was quantitated using the NanoDrop system (Thermo Scientific).

tag: cell line

tag: cell type

value: breast cancer cell line

tag: estrogen receptor status

value: positive

tag: erbb2 status

value: not amplified

source_name: HF GAPF assay G

value: primary cultured fibroblast cells


title: qRT-PCR on Staphylococcus aureus strain US300 in liver

source_name: Staphylococcus aureus strain US300 during mouse liver infection

treatment_protocol: The murine liver model experiment were carried out by following the procedures reported.  Strain  US300 was grown overnight in 3 ml TSB and then diluted 1:100 into fresh TSB in 50ml TSB in a 500 ml flask to OD660 = 0.5. The bacterial cells were collected by centrifugation, washed once with 10ml PBS and then suspended in 1.25 ml PBS. In this volume, the bacterial concentration were 2× 108 CFU per 30 ul volume. Six week-old BALB/c mice (10 mice per strain) were anesthetized with Avertin and then inoculated with 30 µl of the cell suspension. After being held upright for 1 minute, the mice were placed into the cage in a supine position. At 72 hr post-infection, the mice were euthanized by CO2 asphyxiation and the livers were harvested. The harvested kidnesy were homogenized and the bacterial numbers were measured by diluting and spreading of the lung homogenate on TSA agar plates. We  recovered 106 – 108 CFU from the liver homogenate.

value: mouse liver infection


title: MCF7 vs. Human fibroblast GAPF_E

description: MCF7 whole genome GAPF profile, Array E

source_name: MCF7 WG GAPF assay E

source_name: HF GAPF assay E


title: qRT-PCR on Staphylococcus aureus strain US300 in skin

source_name: Staphylococcus aureus strain US300 during mouse skin infection


title: Gastric cancer  tissue samples (FFPE) 6

source_name: Gastric cancer

tag: tissue

value: Antrum

tag: gender

value: M

value: Pooled DNA from the blood of 18 normal female individuals


title: qRT-PCR on Staphylococcus aureus strain TB15

source_name: Staphylococcus aureus strain TB15 during mouse lung infection

treatment_protocol: The murine pneumonica model experiment was carried out by following the procedures reported by Wardenburg, J.B. et al  (Nat Med 13:1405-6 2007). Strain  TB15 was grown overnight in 3 ml TSB and then diluted 1:100 into fresh TSB in 50ml TSB in a 500 ml flask to OD660 = 0.5. The bacterial cells were collected by centrifugation, washed once with 10ml PBS and then suspended in 1.25 ml PBS. In this volume, the bacterial concentration was  2× 108 CFU per 30 ul volume . Six week-old BALB/c mice (10 mice per strain) were anesthetized with Avertin and then inoculated with 30 µl of the cell suspension into the left nare. After being held upright for 1 minute, the mice were placed into the cage in a supine position. At 72 hr post-infection, the mice were euthanized by CO2 asphyxiation and the lungs were harvested. The harvested lungs were homogenized and the bacterial number measured by diluting and spreading of the lung homogenate on TSA agar plates. We recovered 106 – 108 CFU from the lung homogenate.

value: mouse lung infection


title: qRT-PCR on Staphylococcus aureus strain TB15 in liver

source_name: Staphylococcus aureus strain TB15 during mouse liver infection

treatment_protocol: The murine liver model experiment were carried out by following the procedures reported.  Strain  TB15 was grown overnight in 3 ml TSB and then diluted 1:100 into fresh TSB in 50ml TSB in a 500 ml flask to OD660 = 0.5. The bacterial cells were collected by centrifugation, washed once with 10ml PBS and then suspended in 1.25 ml PBS. In this volume, the bacterial concentration were 2× 108 CFU per 30 ul volume. Six week-old BALB/c mice (10 mice per strain) were anesthetized with Avertin and then inoculated with 30 µl of the cell suspension. After being held upright for 1 minute, the mice were placed into the cage in a supine position. At 72 hr post-infection, the mice were euthanized by CO2 asphyxiation and the livers were harvested. The harvested kidnesy were homogenized and the bacterial numbers were measured by diluting and spreading of the lung homogenate on TSA agar plates. We  recovered 106 – 108 CFU from the liver homogenate.


title: Gastric cancer  tissue samples (FFPE) 2

value: Gastric cancer

value: Whole Stomach

source_name: male reference DNA


title: qRT-PCR on Staphylococcus aureus strain US300

source_name: Staphylococcus aureus strain USA300 during mouse lung infection

treatment_protocol: The murine pneumonica model experiment was carried out by following the procedures reported by Wardenburg, J.B. et al  (Nat Med 13:1405-6 2007). Strain  USA300 was grown overnight in 3 ml TSB and then diluted 1:100 into fresh TSB in 50ml TSB in a 500 ml flask to OD660 = 0.5. The bacterial cells were collected by centrifugation, washed once with 10ml PBS and then suspended in 1.25 ml PBS. In this volume, the bacterial concentration was  2× 108 CFU per 30 ul volume. Six week-old BALB/c mice (10 mice per strain) were anesthetized with Avertin and then inoculated with 30 µl of the cell suspension into the left nare. After being held upright for 1 minute, the mice were placed into the cage in a supine position. At 72 hr post-infection, the mice were euthanized by CO2 asphyxiation and the lungs were harvested. The harvested lungs were homogenized and the bacterial number measured by diluting and spreading of the lung homogenate on TSA agar plates. We recovered 106 – 108 CFU from the lung homogenate.


title: MCF7 vs. Human fibroblast GAPF_D

description: MCF7 whole genome GAPF profile, Array D

source_name: MCF7 WG GAPF assay D

source_name: HF GAPF assay D


title: Colorectal cancer  tissue samples (FFPE) 27_control

source_name: Colorectal cancer

value: Colorectal cancer

value: control

value: oligo

source_name: female reference DNA


title: Colo320DM vs. Human fibroblast GAPF_E

description: Colo320DM whole genome GAPF profile, Array E

source_name: Colo320DM GAPF assay E

value: colon cancer cell line


title: Colo320DM vs. Human fibroblast GAPF_C

description: Colo320DM whole genome GAPF profile, Array C

source_name: Colo320DM GAPF assay C

source_name: HF GAPF assay C


title: Colo320DM vs. Human fibroblast GAPF_G

description: Colo320DM whole genome GAPF profile, Array G

source_name: Colo320DM GAPF assay G

source_name: HF GAPF assay G


title: Colo320DM vs. Human fibroblast GAPF_D

description: Colo320DM whole genome GAPF profile, Array D

source_name: Colo320DM GAPF assay D


title: MCF7 vs. Human fibroblast GAPF_C

description: MCF7 whole genome GAPF profile, Array C

source_name: MCF7 WG GAPF assay C


title: D22C20BH

city: Los Angeles

first: Juyong

middle: Brian

last: Kim

state: CA

address: 675 Charles Young Dr.

department: Department of Medicine

institute: UCLA School of Medicine

description:
Gene expression data from HAEC
31406
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using median invariant normalization with Microarray Suite 5.0 software.

source_name: HAEC treated with 20ug/ml OxPAPC

label_protocol: Double stranded cDNA were prepared with the Invitrogen reverse transcription kit. Biotin-labeled cRNA was generated and used to probe Affymetrix arrays

growth_protocol: Human aortic endothelial cells were isolated from aortic samples retrieved at the time of organ harvest for cardiac transplantation and used at passages 4–7

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

treatment_protocol: Cells were treated with PAPC or oxPAPC (10–50 μg/ml), in medium containing 1% FBS.

tag: individual identifier

value: human aortic endothelial cell (HAEC) cell line

tag: agent

value: OxPAPC

tag: dose


title: D22C0A_

description:
Gene expression data from HAEC
31403
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml PAPC

value: PAPC (control)


title: D22C40AH

description:
Gene expression data from HAEC
31407
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml OxPAPC


title: D22C0B_

description:
Gene expression data from HAEC
31404
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D17C40AL

description:
Gene expression data from HAEC
31392
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D22C40BH

description:
Gene expression data from HAEC
31408
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D17C20BL

description:
Gene expression data from HAEC
31391
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D17C20AL

description:
Gene expression data from HAEC
31390
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped171 sp527-50K Xba

description:
sp527-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped171 sp527

extract_protocol: Genomic DNA was extracted from peripheral blood using standard phenol/chloroform extraction. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel.electrophoresis.

value: peripheral blood

tag: individual

value: father

value: male

tag: affection _status

value: healthy


title: D17C40BL

description:
Gene expression data from HAEC
31393
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D12C40AL

description:
Gene expression data from HAEC
31377
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: 13970172 - Wt light 2 vs Wt dark 1.2

hyb_protocol: Wt dark 1.2 Cy5 / Wt light 2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Wt dark 1.2

extract_protocol: Wt dark 1.2:60ug. (Qiagen_RNeasy.pdf)

tag: genotype/variation

value: Wt

tag: growth condition

value: dark

tag: cultivar

value: arabidopsis thaliana (landsberg erecta)

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

source_name: Wt light 2

value: light


title: D22C20AH

description:
Gene expression data from HAEC
31405
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped155 sp478-50K Xba

description:
sp478-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped155 sp478


title: Schizophrenia ped171 sp529-50K Xba

description:
sp529-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped171 sp529

value: patient

value: schizophrenia


title: D17C0A_

description:
Gene expression data from HAEC
31388
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped155 sp480-50K Xba

description:
sp480-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped155 sp480


title: D17C0B_

description:
Gene expression data from HAEC
31389
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped171 sp528-50K Xba

description:
sp528-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped171 sp528

value: mother

value: female


title: D12C40BL

description:
Gene expression data from HAEC
31378
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D12C20AL

description:
Gene expression data from HAEC
31375
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D12C0B_

description:
Gene expression data from HAEC
31374
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: 13969183 - Wt dark 2.1 vs ga1 DARK1

description: Identification of DELLA-dependent downstream targets in darkness

hyb_protocol: ga1 DARK1 Cy5 / Wt dark 2.1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: ga1 DARK1

value: DARK

value: mutant (ga1-3)

source_name: Wt dark 2.1


title: D12C20BL

description:
Gene expression data from HAEC
31376
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line


title: Schizophrenia ped138 sp423-50K Xba

description:
sp423-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped138 sp423


title: Schizophrenia ped160 sp493-50K Xba

description:
sp493-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped160 sp493


title: Schizophrenia ped140 sp430-50K Xba

description:
sp430-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped140 sp430


title: Schizophrenia ped126 sp389-50K Xba

description:
sp389-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped126 sp389


title: Schizophrenia ped148 sp458-50K Xba

description:
sp458-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped148 sp458


title: D12C0A_

description:
Gene expression data from HAEC
31373
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: ERP3 vs. Peripheral blood lymphocyte GAPF_F

description: ERP3 GAPF profile, Array F

source_name: ERP3 GAPF assay F

value: primary breast cancer

tag: histology

value: invasive ductal carcinoma

value: positive

value: not amplified

source_name: PBL GAPF assay F

value: peripheral blood lymphocytes


title: ERP1 vs. Peripheral blood lymphocyte GAPF_F

description: ERP1 GAPF profile, Array F

source_name: ERP1 GAPF assay F


title: D11C20BH

description:
Gene expression data from HAEC
31354
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 20ug/ml OxPAPC

value: OxPAPC


title: ERN3 vs. Peripheral blood lymphocyte GAPF_F

description: ERN3 GAPF profile, Array F

source_name: ERN3 GAPF assay F

value: negative


title: D11C20AH

description:
Gene expression data from HAEC
31353
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D11C40BH

description:
Gene expression data from HAEC
31356
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml OxPAPC


title: Schizophrenia ped066 sp206-50K Xba

description:
sp206-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped066 sp206

value: peripheral blood

value: male


title: D11C0B_

description:
Gene expression data from HAEC
31352
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml PAPC

value: PAPC (control)


title: D10C40BL

description:
Gene expression data from HAEC
28580
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped005 sp017-50K Xba

description:
sp017-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped005 sp017

value: healthy


title: D10C40AL

description:
Gene expression data from HAEC
28579
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D11C40AH

description:
Gene expression data from HAEC
31355
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D11C0A_

description:
Gene expression data from HAEC
31351
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: ERN1 vs. Peripheral blood lymphocyte GAPF_F

description: ERN1 GAPF profile, Array F

source_name: ERN1 GAPF assay F


title: ERN2 vs. Peripheral blood lymphocyte GAPF_F

description: ERN2 GAPF profile, Array F

source_name: ERN2 GAPF assay F


title: Schizophrenia ped005 sp016-50K Xba

description:
sp016-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped005 sp016

value: father


title: Schizophrenia ped004 sp015-50K Xba

description:
sp015-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped004 sp015

value: patient

value: schizophrenia


title: D9C40AL

description:
Gene expression data from HAEC
31903
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D10C20BL

description:
Gene expression data from HAEC
28578
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D10C20AL

description:
Gene expression data from HAEC
28577
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped084 sp261-50K Xba

description:
sp261-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped084 sp261

value: female


title: D10C0A_

description:
Gene expression data from HAEC
28575
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D10C0B_

description:
Gene expression data from HAEC
28576
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped001 sp003-50K Xba

description:
sp003-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped001 sp003


title: MDA231 vs. Peripheral blood lymphocyte GAPF_F

description: MDA231 GAPF profile, Array F

source_name: MDA231 GAPF assay F

value: breast cancer cell line


title: ERP2 vs. Peripheral blood lymphocyte GAPF_F

description: ERP2 GAPF profile, Array F

source_name: ERP2 GAPF assay F


title: D9C40BL

description:
Gene expression data from HAEC
29489
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line


title: D9C20AL

description:
Gene expression data from HAEC
29486
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: MCF7 vs. Peripheral blood lymphocyte GAPF_F

description: MCF7 GAPF profile, Array F

source_name: MCF7 GAPF assay F


title: Schizophrenia ped001 sp002-50K Xba

description:
sp002-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped001 sp002

value: mother


title: D9C20BL

description:
Gene expression data from HAEC
29487
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D9C0A_

description:
Gene expression data from HAEC
29484
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: BT474 vs. Peripheral blood lymphocyte GAPF_F

description: BT474 GAPF profile, Array F

source_name: BT474 GAPF assay F

value: amplified

source_name: PBL GAPF assay F


title: D9C0B_

description:
Gene expression data from HAEC
29485
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped171 sp529-50K Hind

description:
sp529-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped171 sp529


title: D8C40BL

description:
Gene expression data from HAEC
29474
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml OxPAPC


title: Colo320DM vs. Human fibroblast GAPF_F

description: Colo320DM whole genome GAPF profile, Array F

source_name: Colo320DM GAPF assay F

value: colon cancer cell line

source_name: HF GAPF assay F

value: primary cultured fibroblast cells


title: D8C40AL

description:
Gene expression data from HAEC
29473
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: MCF7 vs. Human fibroblast GAPF_F

description: MCF7 whole genome GAPF profile, Array F

source_name: MCF7 WG GAPF assay F

value: positive

value: not amplified


title: Schizophrenia ped001 sp001-50K Xba

description:
sp001-50K Xba
Hybridized to 50K_Xba

source_name: Schizophrenia ped001 sp001


title: D8C20AL

description:
Gene expression data from HAEC
29471
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 20ug/ml OxPAPC

value: OxPAPC


title: D8C20BL

description:
Gene expression data from HAEC
29472
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: ERN3 CopyNumber

description: ERN3 Copy Number profile, SNP6.0

source_name: ERN3 SNP6.0 assay

value: primary breast cancer

value: invasive ductal carcinoma

value: negative


title: Schizophrenia ped171 sp528-50K Hind

description:
sp528-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped171 sp528

value: peripheral blood

value: healthy


title: Schizophrenia ped171 sp527-50K Hind

description:
sp527-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped171 sp527

value: father

value: male


title: Colo320DM CopyNumber

description: Colo320DM Copy Number profile, SNP6.0

source_name: Colo320DM SNP6.0 assay


title: D8C0B_

description:
Gene expression data from HAEC
31876
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml PAPC

value: PAPC (control)


title: D8C0A_

description:
Gene expression data from HAEC
29469
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped165 sp511-50K Hind

description:
sp511-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped165 sp511

value: patient

value: schizophrenia


title: D5C40BH

description:
Gene expression data from HAEC
29433
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line


title: ERP1 CopyNumber

description: ERP1 Copy Number profile, SNP6.0

source_name: ERP1 SNP6.0 assay


title: D5C20BH

description:
Gene expression data from HAEC
29431
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: UACC893 vs. Peripheral blood lymphocyte GAPF_F

description: UACC893 GAPF profile, Array F

source_name: UACC893 GAPF assay F

value: breast cancer cell line

value: amplified

value: peripheral blood lymphocytes


title: D5C40AH

description:
Gene expression data from HAEC
29432
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped163 sp504-50K Hind

description:
sp504-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped163 sp504

value: mother

value: female


title: ERP3 CopyNumber

description: ERP3 Copy Number profile, SNP6.0

source_name: ERP3 SNP6.0 assay

value: positive

value: not amplified


title: ERP2 CopyNumber

description: ERP2 Copy Number profile, SNP6.0

source_name: ERP2 SNP6.0 assay

value: primary breast cancer

value: invasive ductal carcinoma


title: ERN2 CopyNumber

description: ERN2 Copy Number profile, SNP6.0

source_name: ERN2 SNP6.0 assay

value: negative


title: Small bowel cancer  tissue samples (FFPE) 33_control

description: A pool of DNA from blood of normal individuals

source_name: Small bowel cancer

value: Small bowel cancer

tag: site

value: control

tag: tumor site

tag: tnm

tag: age

tag: platform_id type

value: bac

source_name: female reference DNA

value: Pooled DNA from the blood of 18 normal female individuals


title: Small bowel cancer  tissue samples (FFPE) 25_control

tag: tissue

source_name: male reference DNA

value: Pooled DNA from the blood of 18 normal male individuals


title: ERN1 CopyNumber

description: ERN1 Copy Number profile, SNP6.0

source_name: ERN1 SNP6.0 assay

tag: cell line

tag: cell type

tag: estrogen receptor status

tag: erbb2 status


title: Gastric cancer  tissue samples (FFPE) 28_control

source_name: Gastric cancer

value: Gastric cancer

tag: gender

value: oligo


title: D4C20BH

description:
Gene expression data from HAEC
29416
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 20ug/ml OxPAPC

tag: individual identifier

value: human aortic endothelial cell (HAEC) cell line

tag: agent

value: OxPAPC

tag: dose


title: Schizophrenia ped138 sp421-50K Hind

description:
sp421-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped138 sp421

value: peripheral blood

tag: individual

value: father

value: male

tag: affection _status

value: healthy


title: D4C40AH

description:
Gene expression data from HAEC
29417
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml OxPAPC


title: D5C0A_

description:
Gene expression data from HAEC
29428
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: PAPC (control)


title: Gastric cancer  tissue samples (FFPE) 27

value: Stomach

value: Cardia

value: F


title: D4C0B_

description:
Gene expression data from HAEC
29414
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped136 sp414-50K Hind

description:
sp414-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped136 sp414


title: D4C40BH

description:
Gene expression data from HAEC
29418
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped138 sp423-50K Hind

description:
sp423-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped138 sp423

value: patient

value: female

value: schizophrenia


title: Gastric cancer  tissue samples (FFPE) 29

value: Body

value: bac


title: Gastric cancer  tissue samples (FFPE) 28

value: Gastric cancer

value: Unknown

value: Pooled DNA from the blood of 18 normal male individuals


title: D5C20AH

description:
Gene expression data from HAEC
29430
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line

value: OxPAPC


title: D4C0A_

description:
Gene expression data from HAEC
29413
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml PAPC


title: Tetrahymena_C-18

city: Toronto

first: Ronald

last: Pearlman

state: Ontario

address: 4700 Keele St

department: Core Molecular Biology Facility

country: China

institute: York University

description: references: Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

hyb_protocol: Sample Hybridization protocol provided and performed by NimbleGen.

scan_protocol: Nimblegen. Sample scan protocol provided and performed by NimbleGen.

data_processing: Array normalization was performed using the quantile normalization method of Bolstad et al. (2003). Normalized expression values for the individual probes were used to obtain the expression values for a given open reading frame (ORF) by using the robust multiarray average (RMA) procedure as previously described by Irizarry et al. (2003).

organism: Tetrahymena thermophila

source_name: B2086 mate with CU428 cells at 18 hr postmixing

label_protocol: Sample labeling protocol provided and performed by NimbleGen.

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 18 hr without shaking. B2086 and CU428 cells were mixed, and samples were collected at 0 hr postmixing.

extract_protocol: Homogenization was done using a Qiashredder spin column and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instructions. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE) and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).

tag: conjugation time


title: Gastric cancer  tissue samples (FFPE) 26

tag: site

value: Antrum

value: M

value: Pooled DNA from the blood of 18 normal female individuals


title: Schizophrenia ped117 sp363-50K Hind

description:
sp363-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped117 sp363

value: peripheral blood


title: D5C0B_

description:
Gene expression data from HAEC
29429
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: PAPC (control)


title: D4C20AH

description:
Gene expression data from HAEC
29415
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped136 sp415-50K Hind

description:
sp415-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped136 sp415

value: mother

value: healthy


title: Schizophrenia ped138 sp422-50K Hind

description:
sp422-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped138 sp422


title: Gastric cancer  tissue samples (FFPE) 19_control

value: control

tag: tumor site

value: oligo


title: D3C40BH

description:
Gene expression data from HAEC
29403
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Gastric cancer  tissue samples (FFPE) 25

value: Stomach

tag: tnm


title: Gastric cancer  tissue samples (FFPE) 24

tag: age

value: F


title: Tetrahymena_C-16

source_name: B2086 mate with CU428 cells at 16 hr postmixing


title: Schizophrenia ped116 sp360-50K Hind

description:
sp360-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped116 sp360

value: patient

value: male

value: schizophrenia


title: Schizophrenia ped122 sp377-50K Hind

description:
sp377-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped122 sp377

value: female


title: D3C40AH

description:
Gene expression data from HAEC
29402
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line


title: Gastric cancer  tissue samples (FFPE) 21

value: Gastric cancer

value: Body

tag: platform_id type

value: bac

value: Pooled DNA from the blood of 18 normal male individuals


title: Gastric cancer  tissue samples (FFPE) 22

tag: tissue

value: Antrum

value: M

source_name: female reference DNA

value: Pooled DNA from the blood of 18 normal female individuals


title: Tetrahymena_C-12

source_name: B2086 mate with CU428 cells at 12 hr postmixing


title: Gastric cancer  tissue samples (FFPE) 20


title: Tetrahymena_C-8

source_name: B2086 mate with CU428 cells at 8 hr postmixing

value: 8 h


title: Schizophrenia ped118 sp366-50K Hind

description:
sp366-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped118 sp366

value: peripheral blood


title: Tetrahymena_C-14

source_name: B2086 mate with CU428 cells at 14 hr postmixing


title: Gastric cancer  tissue samples (FFPE) 19

source_name: Gastric cancer


title: D3C20BH

description:
Gene expression data from HAEC
29401
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 20ug/ml OxPAPC

tag: cell line

value: OxPAPC


title: Tetrahymena_C-4

source_name: B2086 mate with CU428 cells at 4 hr postmixing

value: 4 h


title: Schizophrenia ped116 sp359-50K Hind

description:
sp359-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped116 sp359

value: mother

value: healthy


title: D3C0A_

description:
Gene expression data from HAEC
29398
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml PAPC

value: PAPC (control)


title: D2C40BL

description:
Gene expression data from HAEC
29388
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml OxPAPC


title: Tetrahymena_C-10

source_name: B2086 mate with CU428 cells at 10 hr postmixing


title: Schizophrenia ped111 sp345-50K Hind

description:
sp345-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped111 sp345

value: patient

value: male

value: schizophrenia


title: D3C0B_

description:
Gene expression data from HAEC
29399
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line


title: Gastric cancer  tissue samples (FFPE) 18

description: A pool of DNA from blood of normal individuals

value: Gastric cancer

value: Stomach


title: Gastric cancer  tissue samples (FFPE) 16

value: Body

value: F

value: bac

source_name: male reference DNA

value: Pooled DNA from the blood of 18 normal male individuals


title: Schizophrenia ped109 sp339-50K Hind

description:
sp339-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped109 sp339


title: Tetrahymena_C-2

source_name: B2086 mate with CU428 cells at 0 hr postmixing

value: 2 h


title: Tetrahymena_C-6

source_name: B2086 mate with CU428 cells at 6 hr postmixing

value: 6 h


title: D2C40AL

description:
Gene expression data from HAEC
29387
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: OxPAPC


title: Schizophrenia ped111 sp344-50K Hind

description:
sp344-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped111 sp344

value: peripheral blood

value: female


title: Schizophrenia ped109 sp338-50K Hind

description:
sp338-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped109 sp338

value: mother

value: healthy


title: Schizophrenia ped101 sp314-50K Hind

description:
sp314-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped101 sp314

value: patient


title: Gastric cancer  tissue samples (FFPE) 15

value: Antrum

value: M

source_name: female reference DNA

value: Pooled DNA from the blood of 18 normal female individuals


title: Gastric cancer  tissue samples (FFPE) 14

value: Gastric cancer

value: Cardia


title: D2C20BL

description:
Gene expression data from HAEC
29386
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line


title: Schizophrenia ped091 sp278-50K Hind

description:
sp278-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped091 sp278

value: schizophrenia


title: Gastric cancer  tissue samples (FFPE) 12

source_name: Gastric cancer

value: Stomach

value: Body

value: bac


title: D2C0B_

description:
Gene expression data from HAEC
29384
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: PAPC (control)


title: Schizophrenia ped084 sp261-50K Hind

description:
sp261-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped084 sp261


title: Tetrahymena_C-0

value: 0 h


title: Tetrahymena_S-0,replicate 2

city: Ann Arbor

first: Yifan

last: Liu

state: MI

address: 500 S. State St

institute: University of Michigan

source_name: CU427 cells starved for 0 hr,replicate 2

growth_protocol: 1XSPP(1%PP), 30 degree, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix; starved at 200K cells/ml for 0 hr without shaking.

tag: cell type

value: CU427 cells

tag: stress

value: starvation

tag: time


title: D1C40BL

description:
Gene expression data from HAEC
29373
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: OxPAPC


title: D2C20AL

description:
Gene expression data from HAEC
29385
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 20ug/ml OxPAPC


title: D1C40AL

description:
Gene expression data from HAEC
29372
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: D3C20AH

description:
Gene expression data from HAEC
29400
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Tetrahymena_S-9,replicate 2

description: references: Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

source_name: CU427 cells starved for 9 hr,replicate 2

value: 9 h


title: Tetrahymena_S-9,replicate 1

source_name: CU427 cells starved for 9 hr,replicate 1


title: Schizophrenia ped078 sp242-50K Hind

description:
sp242-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped078 sp242

value: peripheral blood

value: mother

tag: gender

value: female

value: healthy


title: D2C0A_

description:
Gene expression data from HAEC
29383
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

source_name: HAEC treated with 40ug/ml PAPC

tag: individual identifier


title: slr1 (k1001)_ shoot_biological rep 1

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

institute: RIKEN

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

organism: Oryza sativa

source_name: Oryza sativa slr1 (k1001) mutant (Taichung 65 background)_shoot

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Grown in green house under natural condition

extract_protocol: Total RNA was prepared with the RNeasy plant Mini Kit (Qiagen).

tag: cultivar

value: Taichung 65

tag: genotype/variation

value: slr1 (k1001) mutant

value: shoot

value: five weeks after germination


title: slr1 (k1001)_ shoot_biological rep 3


title: Schizophrenia ped084 sp260-50K Hind

description:
sp260-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped084 sp260

tag: individual


title: Schizophrenia ped076 sp237-50K Hind

description:
sp237-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped076 sp237

value: patient

tag: affection _status

value: schizophrenia


title: Tetrahymena_C-15m

source_name: B2086 mate with CU428 cells at 15 min postmixing

tag: conjugation time

value: 15 min


title: Schizophrenia ped078 sp241-50K Hind

description:
sp241-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped078 sp241

value: father

value: male


title: D1C20BL

description:
Gene expression data from HAEC
29371
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

value: human aortic endothelial cell (HAEC) cell line

tag: agent

tag: dose


title: gid2-1_ shoot_biological rep 3

source_name: Oryza sativa gid2-1 mutant (Taichung 65 background)_shoot

value: gid2-1 mutant


title: Tetrahymena_S-24

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

description:
Expression level at 24 hour during starvation.
References:
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

hyb_protocol: Sample hybridization protocol provided and performed by NimbleGen.

scan_protocol: Sample scan protocol provided and performed by NimbleGen.

source_name: CU428 cells starved for 24 hr

growth_protocol: 1X SPP (1%PP), 30 degrees, 150 rpm shaking, 1/10 cell volume to flask size (2 L Erlenmeyer flasks for G and S, 1 L flasks for C), 200,000 cells/ml; washed with 10 mM tris (pH 7.4-7.5), 100X antibiotic- antimycotic mix.

extract_protocol: Homogenization was done using a Qiashredder spin column, and total RNA was extracted using the RNeasy Protect Cell Mini Kit (Qiagen, Valenica, CA) according to manufacturer's instructions. The concentration of total RNA was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE), and RNA integrity was verified using a Bioanalyzer 1000 (Agilent, Palo Alto, CA).

treatment_protocol: Starved at 200K cells/ml in 10 mM Tris (pH 7.5) for 24 hr without shaking.

tag: treatment

value: starvation

tag: treatment time

value: 24 hr


title: Schizophrenia ped075 sp234-50K Hind

description:
sp234-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped075 sp234

value: peripheral blood


title: Gastric cancer  tissue samples (FFPE) 23

value: Gastric cancer

tag: site

value: Stomach

tag: tumor site

value: Body

tag: tnm

tag: age

value: F

tag: platform_id type

value: bac

source_name: male reference DNA

value: Pooled DNA from the blood of 18 normal male individuals


title: slr1 (k1001)_ shoot_biological rep 2

value: Taichung 65

value: slr1 (k1001) mutant

tag: tissue

value: shoot

value: five weeks after germination


title: gid2-1_ shoot_biological rep 2


title: Schizophrenia ped078 sp243-50K Hind

description:
sp243-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped078 sp243

value: patient

tag: gender

value: schizophrenia


title: Tetrahymena_S-0,replicate 1

source_name: CU427 cells starved for 0 hr,replicate 1

tag: cell type

value: CU427 cells

tag: stress

tag: time

value: 0 h


title: Gastric cancer  tissue samples (FFPE) 17

source_name: Gastric cancer


title: gid2-1_ shoot_biological rep 1

tag: cultivar

tag: genotype/variation

value: gid2-1 mutant


title: Schizophrenia ped001 sp001-50K Hind

description:
sp001-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped001 sp001

tag: individual

value: father

value: male

tag: affection _status

value: healthy


title: D1C0A_

description:
Gene expression data from HAEC
29368
Supplementary file .TXT represents Expression Analysis: Metrics Tab.

tag: individual identifier

tag: cell line

value: human aortic endothelial cell (HAEC) cell line

tag: agent

value: PAPC (control)

tag: dose


title: D1C0B_

description:
Gene expression data from HAEC
29369
Supplementary file .TXT represents Expression Analysis: Metrics Tab.


title: Schizophrenia ped014 sp056-50K Hind

description:
sp056-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped014 sp056

value: peripheral blood

value: female


title: Tetrahymena_S-0

description:
Expression level at 0 hour during starvation.
References:
Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.

source_name: CU428 cells starved for 0 hr

treatment_protocol: Starved at 200K cells/ml in 10 mM Tris (pH 7.5) for 0 hr without shaking.

tag: treatment

value: starvation

tag: treatment time


title: Schizophrenia ped075 sp233-50K Hind

description:
sp233-50K Hind
Hybridized to 50K_Hind

source_name: Schizophrenia ped075 sp233

value: mother


title: MCF7 vs. Human fibroblast GAPF_A

description: MCF7 whole genome GAPF profile, Array A

source_name: MCF7 WG GAPF assay A

value: breast cancer cell line

tag: estrogen receptor status

value: positive

tag: erbb2 status

value: not amplified

source_name: HF GAPF assay A

value: primary cultured fibroblast cells


title: Gastric cancer  tissue samples (FFPE) 11

tag: tissue

value: Gastric cancer

tag: site

value: Stomach

tag: tumor site

value: Unknown

tag: tnm

tag: age

value: F

tag: platform_id type

value: bac

value: Pooled DNA from the blood of 18 normal male individuals


title: Colo320DM vs. Human fibroblast GAPF_A

description: Colo320DM whole genome GAPF profile, Array A

source_name: Colo320DM GAPF assay A

tag: cell type

value: colon cancer cell line


title: MCF7 vs. Human fibroblast GAPF_B

description: MCF7 whole genome GAPF profile, Array B

source_name: MCF7 WG GAPF assay B

source_name: HF GAPF assay B


title: Colo320DM vs. Human fibroblast GAPF_B

description: Colo320DM whole genome GAPF profile, Array B

source_name: Colo320DM GAPF assay B


title: Gastric cancer  tissue samples (FFPE) 13

description: A pool of DNA from blood of normal individuals

value: Cardia

tag: gender


title: gid1-3_ shoot_biological rep 3

source_name: Oryza sativa gid1-3 mutant (Taichung 65 background)_shoot

tag: cultivar

value: Taichung 65

tag: genotype/variation

value: gid1-3 mutant

value: shoot

value: five weeks after germination