title: 13372764 - PI2 vs I2

hyb_protocol: I2 Cy5 / PI2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13372768 - PI2 vs PP2

status: Public on Mar 12 2008

type: RNA

city: Evry

first: Frederique

last: Bitton

address: 2 rue Gaston Cremieux

country: France

institute: INRA

description: Does Stifenia elicitor pretreatment prime defense genes?

hyb_protocol: PP2 Cy5 / PI2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

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

molecule: total RNA

organism: Arabidopsis thaliana

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

growth_protocol: leaf - 10 days on agar, 4°C, 8h then 20 days on soil, 22°C, 8h

treatment_protocol: Name:Stifeniax2 - compound based treatment - compound addition,stifenia:. Stifenia sprayed and another Stifenia sprayed one day later at 10 g/L.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

treatment_protocol: Name:Stifenia+Fusarium - compound+pathogen - elicitor+pathogen infection,stifenia+fusarium:. Stifenia sprayed at 10 g/L. Fusarium oxysporum infection: 10^6 spores/ml one day later.


title: 13372766 - PI2 vs P2

hyb_protocol: P2 Cy5 / PI2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Stifenia - compound based treatment - compound addition,stifenia:. Stifenia sprayed at 10 g/L.


title: 13372763 - I2 vs PI2

hyb_protocol: PI2 Cy5 / I2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Fusarium - compound+pathogen,pathogen - elicitor+pathogen infection,pathogen infection,fusarium:. Fusarium oxysporum pv rafani sprayed at 10^6 spores/ml.


title: 13372744 - P1 vs PI1

hyb_protocol: PI1 Cy5 / P1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13555933 - atnar2_6S2 vs WT_6S2

description: Does the ko of AtNAR2.1 leads to a differential expression in comparison to the WT when grown under high nitrate condition and transfered onto low nitrate concentration?

hyb_protocol: WT_6S2 Cy5 / atnar2_6S2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: aerial - Media 		6 mM nitrate hygrometry 	70% Temperature 	21/17°C day/night Light 		8h light 150 uE /16h dark

treatment_protocol: Name:6mM_nitrate - environmental treatment - azote concentration,nitrate:quantity 6mM time 24hour . Plants were transfered in new fresh solution containing 6 mM nitrate for 24hours before harvesting.

tag: Arabidopsis thaliana (wassilewskija)  - dev.stage (Boyes et al. Plant Cell 2001):boyes

tag: Arabidopsis thaliana (wassilewskija)  mutant (atnar2.1) - dev.stage (Boyes et al. Plant Cell 2001):boyes


title: Hela-2

city: Pamplona

first: Rafael

last: Aldabe

state: Navarra

address: Av Pio XII 55

department: Hepatology and Gene Therapy

country: Spain

institute: FIMA

description: The Hela cells were cultured in a 94/16 mm plate for 56 hours before harvesting them.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: The data were condensed with Affymetrix GCOS 1.2 software. The normalization target was set to 200.

label: biotin

organism: Homo sapiens

source_name: Tissue culture experiment without treatment

label_protocol: The cDNA was prepared from 5 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

tag: Hela cells


title: 13372751 - PI1 vs PP1

hyb_protocol: PP1 Cy5 / PI1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13372749 - PP1 vs PI1

hyb_protocol: PI1 Cy5 / PP1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Hela AS350-1

description: The Hela cells were cultured in a 94/16 mm plate and infected with adenovirus AdAS350 for 56 hours before harvesting them. This adenovirus expresses a siRNA control.

source_name: Tissue culture experiment with Adenovirus infection expressing siRNA 350


title: L.interrogans 56601 and IPAV-37°C Replicate 3

city: shanghai

first: xiaokui

last: guo

state: shanghai

address: ChongQing nan Road 280

department: Department of Microbiology and Parasitology

country: China

institute: Shanghai Jiao Tong University

description: Biological replicate 3 of 3

hyb_protocol: Samples were hybridized at 42°C for 16h, and then washed as described in the manual.

scan_protocol: The hybridized slides were scanned and analyzed by Tiffsplit (Agilent) to calculate the signal intensities and to determine the presence or absence of each CDS.

data_processing: The data were then normalized, and their backgrounds were defined using GeneSpring 4.0 (Silicon Genetics). The GeneSpring software was used to further analyze the transcription patterns.

organism: Leptospira interrogans serovar Lai str. 56601

label_protocol: Three expression profiling experiments were performed via reverse transcription using Superscript (Invitrogen) and with one experiment having the cDNA of IPAV labeled by Cy3 and of 56601 labeled by Cy5, while the other two having the cDNA of 56601 labeled by Cy3 and of IPAV labeled by Cy5.

growth_protocol: The virulent strain 56601 and the avirulent variant strain IPAV of L. interrogans serogroup Icterohaemorrhagiae serovar lai were grown in EMJH liquid medium 37°C , a temperature similar to that encountered during invasion of mammalian hosts under aerobic conditions. Only mid-log-phase cultures of 100 ml eachwere used for gene expression profiling.

extract_protocol: total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer's protocol.

tag: 56601, mid-phase, 37°C

organism: Leptospira interrogans serovar Lai

source_name: IPAV, 37°C

tag: IPAV strain, mid-phase, 37°C


title: Hela AS2-1

description: The Hela cells were cultured in a 94/16 mm plate and infected with adenovirus AdAS2 for 56 hours before harvesting them. This adenovirus expresses a siRNA that inhibits the expression of the protein hNat5/hNat3.

source_name: Tissue culture experiment with Adenovirus infection expressing siRNA 2 against hNat5/hNat3


title: 13555932 - WT_6S2 vs atnar2_6S2

hyb_protocol: atnar2_6S2 Cy5 / WT_6S2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L.interrogans 56601 and IPAV-37°C Replicate 2

description: Biological replicate 2 of 3


title: Hela-1


title: 13555935 - WT_6R2 vs atnar2_6R2

hyb_protocol: atnar2_6R2 Cy5 / WT_6R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: root - Media 		6 mM nitrate hygrometry 	70% Temperature 	21/17°C day/night Light 		8h light 150 uE /16h dark


title: 13501949 - atnar2_02R2 vs WT_02R2

hyb_protocol: WT_02R2 Cy5 / atnar2_02R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:0.2mM_nitrate - environmental treatment - azote concentration,nitrate:quantity 0.2mM time 24hour . Plants were transfered in new fresh solution containing 0.2 mM nitrate for 24hours before harvesting.


title: Hela AS2-2


title: L.interrogans 56601 and IPAV-37°C Replicate 1

description: Biological replicate 1 of 3


title: 13501948 - WT_02R2 vs atnar2_02R2

hyb_protocol: atnar2_02R2 Cy5 / WT_02R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501947 - atnar2_02S2 vs WT_02S2

hyb_protocol: WT_02S2 Cy5 / atnar2_02S2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13555936 - atnar2_6R2 vs WT_6R2

hyb_protocol: WT_6R2 Cy5 / atnar2_6R2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501946 - WT_02S2 vs atnar2_02S2

hyb_protocol: atnar2_02S2 Cy5 / WT_02S2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13281045 - 100-10 vs 100-0

description: Effect of the Auxin/Cytokinin ratio on the transcriptome

hyb_protocol: 100-0 Cy5 / 100-10 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: cell culture - Medium = Gamborg+15g/l sucrose + 2,4-D and/or kinetin when required (see notes for each sample)

tag: Arabidopsis thaliana (columbia)  - harvest date:05-10-05


title: 13281046 - 100-0 vs 100-10

hyb_protocol: 100-10 Cy5 / 100-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501935 - atnar2_6S1 vs WT_6S1

hyb_protocol: WT_6S1 Cy5 / atnar2_6S1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13281040 - 50-0 vs 0-0

hyb_protocol: 0-0 Cy5 / 50-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: Arabidopsis thaliana (columbia)  - harvest date:21-09-05


title: 13281173 - 100-10 vs 200-20

hyb_protocol: 200-20 Cy5 / 100-10 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13278969 - 200-20 vs 100-10

hyb_protocol: 100-10 Cy5 / 200-20 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13278965 - 100-10 vs 100-20

hyb_protocol: 100-20 Cy5 / 100-10 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13281041 - 0-0 vs 50-0

hyb_protocol: 50-0 Cy5 / 0-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501934 - WT_6S1 vs atnar2_6S1

hyb_protocol: atnar2_6S1 Cy5 / WT_6S1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501929 - atnar2_02R1 vs WT_02R1

hyb_protocol: WT_02R1 Cy5 / atnar2_02R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: ER alpha localization in MCF7 (Whole Genome #6, Replicate #2)

status: Public on Mar 13 2008

type: genomic

city: Houston

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

country: USA

institute: MD Anderson Cancer Center

description: Chromatin immunoprecipitation on Affymetrix whole genome tiling arrays 2.0R for transcription factor ER alpha in MCF7 cells (ChIP).

hyb_protocol: According to standard Affymetrix protocols: Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

data_processing: Tiling array data were normalized and analyzed as described (Cawley et al, 2004).  Briefly, raw data were normalized within ChIP and control groups and for each genomic position a local dataset composed of intensities for all adjacent probes within a window of ¡À250 bp was generated.  A one-tailed Wilcoxon Rank Sum test was then applied to compare control and ChIP experiments and was performed in a sliding window across all tiled genomic regions.  Significantly enriched probes (p < 1e-5) were locally extended by merging adjacent enriched probes within 100 bp and these merged regions were defined as transcription factor bound regions.

molecule: genomic DNA

source_name: Chromatin Immunoprecipitated DNA

label_protocol: ChIPed DNA was amplified using linker-mediated PCR amplification method. 2mM dUTP was added to the 10mM dNTP mix during the amplification.

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were grown in phenol-free Dulbecco's modified Eagles's medium, 10% fetal bovine serum, with supplemental bovine insulin (0.01 mg/ml), 2 mM L-glutamine, and antibiotics at 37oC in a 5% CO2 humidified atmosphere.  Prior to hormone (E2 at 10 nM) or vehicle (100% EtOH) treatments, cells were changed to estrogen-depleted media for 72 hours by using 10% charcoal-stripped calf serum.

extract_protocol: According to the standard chromatin extraction protocol (Shang et al., 2000).

treatment_protocol: MCF7 Cells were E2-deprived for 3 days and then were treated with 10 nM E2 (45 minutes and 2 hours for mapping ER alpha and c-MYC binding sites, respectively) at 80% confluence.  ~5x10^6 cells per ChIP were cross-linked with 1% formaldehyde for 10 minutes at 37oC then quenched with 125 mM glycine.

tag: MCF7 cells. Anti-ER alpha antibodies were used for ChIP.


title: 13501441 - atnar2_6R1 vs WT_6R1

hyb_protocol: WT_6R1 Cy5 / atnar2_6R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501930 - WT_02R1 vs atnar2_02R1

hyb_protocol: atnar2_02R1 Cy5 / WT_02R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13278963 - 100-20 vs 100-10

hyb_protocol: 100-10 Cy5 / 100-20 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501928 - WT_02S1 vs atnar2_02S1

hyb_protocol: atnar2_02S1 Cy5 / WT_02S1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501939 - WT_6R1 vs atnar2_6R1

hyb_protocol: atnar2_6R1 Cy5 / WT_6R1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13275760 - 100-0 vs 200-0

hyb_protocol: 200-0 Cy5 / 100-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E. coli AcrB and EmrAB Multidrug Efflux Double Mutant

status: Public on Mar 11 2008

city: Jefferson

first: Christopher

middle: A

last: Elkins

state: AR

address: 3900 NCTR Drive

department: Microbiology

institute: FDA National Center for Toxicological Research

description: A total of five independent microarray data sets were generated for the pairing (AG102MB X AG102) from five independent cultures and associated RNA preparations. Each microarray slide contains three full copies of the array design giving a total of 15 data points (5x3) for each unique spot.

hyb_protocol: These differentially labeled cDNAs were hybridized together on Corning Epoxide slides containing the Operon E. coli Genome Oligo Set Version 1.0 printed by the Microarray and Proteomics Facility, Department of Biological Sciences, University of Alberta.  The hybridizations were performed in a hybridization cassette (ArrayIt) in a water bath at 45ºC for 18 hours.  The slides were then washed in pre-warmed washing buffer 2X SSC containing 0.1% SDS for 5 minutes, 1X SSC for 5 minutes, and 0.5X SSC for 5 minutes.

scan_protocol: The spun-dried hybridized slides were scanned with a GenePix 4000B scanner (Axon Instruments) at 10 µm resolution using appropriate photomultiplier tube gains to obtain the highest intensity with <0.1% saturated pixels.  The resulting images were analyzed by measuring the fluorescence of all features on the slides using the GenePix Pro 6.0 software (Axon Instruments).  The median fluorescence intensity of these pixels within each feature was taken as the intensity value for the whole feature.

data_processing: The analyzed data were imported to ArrayTrack (NCTR Center for Toxicoinformatics;http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/arraytrack_webaccess.htm). The raw data were normalized by using median channel (intensity) scaling with no background subtraction.

organism: Escherichia coli

source_name: AcrB- and EmrAB-Negative, Multidrug Efflux Mutant Strain

label_protocol: Total RNA was reverse transcribed with random primer mix and labeled with Cy3.

growth_protocol: Cultures were grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C.  Cells were cultured with 25 ug/ml chloramphenicol to maintain selection. However, this genomic mutation is stable and RNA was prepared from non-selectively grown cultures inoculated with overnight stocks (grown with selection) to eliminate any unrelated effects of exogenous drugs on gene expression.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kit.

tag: HNCE4 is an isogenic mutant derived from drug sensitive AG102MB (marR1, AcrB::kan). It contains an additional mutation at the emrAB locus (marR1, acrB::kan, emrAB::cat) resulting in a multidrug efflux negative phenotype.

source_name: Efflux Mutant Parent Strain

label_protocol: Total RNA was reverse transcribed with random primer mix and labeled with Cy5.

tag: The parent strain, AG102, was previously derived from AG100 (K-12).  AG102 is drug hyper-resistant due to a mutation in marR (marR1) which increases expression of MarA, a global regulator, which in turn results in overexpression of the AcrAB-TolC multidrug efflux system.


title: 13275759 - 200-0 vs 100-0

hyb_protocol: 100-0 Cy5 / 200-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13275758 - 50-0 vs 100-0

hyb_protocol: 100-0 Cy5 / 50-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501414 - atnar2_02S1 vs WT_02S1

hyb_protocol: WT_02S1 Cy5 / atnar2_02S1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 129X1/SvJ

city: Baltimore

first: Patrick

last: Cahan

state: MD

address: 733 North Broadway, MRB 653

department: ICE and Biomedical Engineering

institute: Johns Hopkins University School of Medicine

description: replicate

data_processing: normalization: qspline

organism: Mus musculus

extract_protocol: Phenol chloroform

tag: sex

value: female

tag: tissue

value: spleen

value: male


title: 129X1/SvJ 120839_SOM01GFG

description: 129X1/SvJ 120839_SOM01GFG

extract_protocol: Phenol chloroform. DNA pooled from 2-6 animals.

value: kidney


title: 13275757 - 100-0 vs 50-0

hyb_protocol: 50-0 Cy5 / 100-0 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: E. coli AcrB Multidrug Efflux Mutant

description: A total of five independent microarray data sets were generated for the pairing (AG102MB X AG102) from five independent cultures and associated RNA preparations.  Each microarray slide contains three full copies of the array design giving a total of 15 data points (5x3) for each unique spot.

source_name: AcrB-Negative, Multidrug Efflux Mutant Strain

growth_protocol: Cultures were grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C.  Cells were cultured with 25 ug/ml kanamycin to maintain selection.  However, this genomic mutation is stable and RNA was prepared from non-selectively grown cultures inoculated with overnight stocks (grown with selection) to eliminate any unrelated effects of exogenous drugs on gene expression.

tag: AG102MB is an isogenic mutant derived from hyper-resistant AG102 (marR1).  It contains a mutation at the acrB locus (marR1, acrB::kan) resulting in a multidrug efflux negative phenotype.


title: quail, long day condition at ZT22, biological rep2

city: Nagoya

first: Takashi

last: Yoshimura

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

description: gene expression data of MBH at long day condition ZT22

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

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

data_processing: The data were analyzed with GeneChip Operating Software version 1.2 (GCOS 1.2) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Coturnix japonica

source_name: mediobasal hypothalamus, long day condition (20h light:4h dark), 2week

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Eight week-old male quail kept under short day condition (6h light:18h dark) for 4 weeks were used.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

treatment_protocol: At the age of 8 weeks old, birds were devided into two groups. One group was continuously kept under short day condition (6h light:18h dark) for 2 weeks. And the other group was transferred to long day condition (20h light: 4h dark) for 2 weeks.

tag: male


title: quail, long day condition at ZT10, biological rep2

description: gene expression data of MBH at long day condition ZT10


title: quail, long day condition at ZT6, biological rep2

description: gene expression data of MBH at long day condition ZT6


title: E. coli AcrA Multidrug Efflux Mutant

description: A total of six independent microarray data sets were generated for the pairing (HNCE3 X AG102) from six independent cultures and associated RNA preparations. Each microarray slide contains three full copies of the array design giving a total of 18 data points (6x3) for each unique spot.  After quality control, one of the array slides was only partially useable (by one array copy) decreasing the total data points to 17.

source_name: AcrA-Negative, Multidrug Efflux Mutant Strain

growth_protocol: Cultures were grown to mid-log phase in Luria-Bertani (Miller) broth medium at 37C.

tag: HNCE3 is an isogenic mutant derived from hyper-resistant AG102 (marR1).  It contains a nonpolar mutation at the acrA locus which allows read-through for acrB expression and results in a multidrug efflux negative phenotype.


title: quail, long day condition at ZT14, biological rep1

description: gene expression data of MBH at long day condition ZT14


title: quail, long day condition at ZT22, biological rep1


title: quail, long day condition at ZT18, biological rep1

description: gene expression data of MBH at long day condition ZT18


title: quail, short day condition at ZT18, biological rep1

description: gene expression data of MBH at short day condition ZT18

source_name: mediobasal hypothalamus, short day condition (6h light:18h dark), 2week


title: quail, short day condition at ZT14, biological rep2

description: gene expression data of MBH at short day condition ZT14


title: quail, long day condition at ZT14, biological rep2


title: quail, long day condition at ZT18, biological rep2


title: Comparative genome hybridisation of an invasive and non-invasive C. albicans strain

city: Jena

first: Bernhard

last: Hube

address: Beutenbergstr. 11a

country: Germany

institute: Hans Knoell Institute

hyb_protocol: Labelled DNA-fragments from strain SC5314 and strain ATCC10231 were combined (final volume 25 µl), denatured for 5 min at 95°C and hybridisation and washing of C. albicans microarrays (Eurogentec) was carried out as described (Moran et al., 2004, Microbiology). Each strain was hybridised in duplicate including one dye swap.

scan_protocol: Immediately after washing, slides were scanned with an Axon 4000B scanner and data were extracted using GenePix 4.1 (Axon).

data_processing: Data were transferred into GeneSpring 7.2 (Agilent) and normalised using LOWESS. Genes were called as “absent/divergent” in strain ATCC10231 if the normalised signal intensity was at least 2-fold lower compared to the intensity of strain SC5314.

organism: Candida albicans

source_name: C. albicans strain SC5314, gDNA

label_protocol: Labelling of genomic DNA was done as described (Moran et al., 2004, Microbiology). Briefly, 1.5 µg DNA of strain SC5314 were fragmented by restriction endonuclease digestion with Tru1l and RsaI (1 µg each). These digests were then heat inactivated, extracted once with a mixture of phenol/chloroform/isoamyl alcohol (25:24:1) and ethanol precipitated. The two digest were combined and labelling reaction was carried out using the RadPrime DNA Labelling Kit (Invitrogen) incorporating Cy3 dUTP. After labelling, reaction products were purified and concentrated.

extract_protocol: High-molecular-mass total genomic DNA was recovered from C. albicans strains by organic extraction following digestion of the cell wall with Zymolyase 20T (Seikagaku) and proteinase K treatment (Roche Diagnostics) as described (Gallagher PJ, Bennett DE, Henman MC, Russell RJ, Flint SR, Shanley DB, Coleman DC: Reduced azole susceptibility of oral isolates of Candida albicans from HIV-positive patients and a derivative exhibiting colony morphology variation. J Gen Microbiol 1992, 138:1901-1911).

tag: C. albicans strain SC5314

source_name: C. albicans strain ATCC10231, gDNA

label_protocol: Labelling of genomic DNA was done as described (Moran et al., 2004, Microbiology). Briefly, 1.5 µg DNA of strain ATCC10231 were fragmented by restriction endonuclease digestion with Tru1l and RsaI (1 µg each). These digests were then heat inactivated, extracted once with a mixture of phenol/chloroform/isoamyl alcohol (25:24:1) and ethanol precipitated. The two digest were combined and labelling reaction was carried out using the RadPrime DNA Labelling Kit (Invitrogen) incorporating Cy5 dUTP. After labelling, reaction products were purified and concentrated.

tag: C. albicans strain ATCC10231


title: HNSCC cell line UM-SCC46

city: Bethesda

first: Bin

last: Yan

address: 10 Center Dr. Bldg 10, Rm 5D55

department: NIDCD

institute: National Institute of Health

hyb_protocol: After denaturation, labeled cDNAs were added to processed cDNA array chips, which were then placed in hybridization chambers and incubated overnight (10-16 hours) at 65oC.  The next day, slides were washed for 1 minute in 1X SSC, 1 minute in 0.2X SSC, 10 seconds in 0.05X SSC, and then spin dry.

scan_protocol: Fluorescence images were captured by GenePix 4000 microarray scanner  with GenePix Pro software (Axon Instruments, Union City, CA). The PMT voltage for both channels was adjusted between 750V to 890V range to give same overall intensity between both channels, and the raw image was saved in TIFF format.

data_processing: Raw images were analyzed using the ArraySuite 2.1 extensions in the IPLab program (Scanalytics, Inc., Fairfax, VA) to calibrate relative ratios and develop confidence intervals of significance. Background subtracted fluorescence intensities of each individual spot were obtained for both dyes (Cy3 and Cy5). Spots quality was filtered based on RQuality score provided by the software as well as visual checking. The software assigns an RQuality score to each ratio measurement between 0 (the lowest) and 1 (the highest) for measurement quality. Any spots with less than 0.5 were excluded. For each spot, the calibrated ratio (the median of the pixel-by-pixel ratios of pixel intensities that have the median background intensity subtracted) was used in subsequent analysis. Expression outliners were determined using +3.0 SD and a 99% confidence interval as cutoff. The resulting gene list was further filtered to exclude EST and hypothetical clones and genes with expression value from less than three human normal keratinocyte and seven tumor cell lines, resulting in a total of 9273 genes.

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC46

label_protocol: 50-100 µg total RNA was incubated in a cocktail containing Cy3 or Cy5-dUTP and SuperScript II reverse transcriptase (Invitrogen).  Labeled cDNAs were purified using a Microcon column.  The appropriate Cy3 or Cy5 labeled cDNAs were combined, along with 2 µl (20 µg) human COT-1 DNA (Invitrogen), 1 µl (8-10 µg) polyA (Amersham), 2.6 µl 20X SSC and 0.45 µl 10% SDS in a final volume of 15 µl.

growth_protocol: UM-SCC cell lines were maintained in Eagle's minimal essential media supplemented with 10% heat inactivated fetal bovine serum and penicillin/streptomycin/glutamine. Human normal keratinocytes were maintained in keratinocyte serum-free medium 154CF containing 0.08mM of calcium chloride and supplemented with human keratinocyte growth supplements (HKGS, Cascade Biologics Inc., Portland, OR).

extract_protocol: Total RNA was isolated from cultured UM-SCC cells and human normal keratinocytes at their log growth phase using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol and stored at -80°C. Common reference total RNA was provided by Stratagene, see http://www.stratagene.com/products/showProduct.aspx?pid=439. Catalog # 740000

treatment_protocol: untreated

tag: Female, 57 years, Primary sites

value: Suprglottic Larynx, stage III, radiation and chemotherapy, survival 6 months, died with disease

source_name: common reference

tag: 10 human cell lines from adenocarcinoma (mammary gland), melanoma, hepatoblastoma (liver), liposarcoma, adenocarcinoma (cervix), histiocytic lymphoma (macrophage, histocyte),  embryonal carcinoma (testis), lymphoblastic leukemia (T lymphoblast), glioblastoma (brain), plasmacytoma myeloma (B lymphocyte).

tag: human universal reference RNA


title: quail, long day condition at ZT6, biological rep1


title: quail, short day condition at ZT22, biological rep2

description: gene expression data of MBH at short day condition ZT22


title: quail, long day condition at ZT2, biological rep2

description: gene expression data of MBH at long day condition ZT2


title: quail, short day condition at ZT10, biological rep1

description: gene expression data of MBH at short day condition ZT10


title: quail, long day condition at ZT10, biological rep1


title: quail, short day condition at ZT2, biological rep2

description: gene expression data of MBH at short day condition ZT2


title: quail, time70, biological rep2

description: gene expression data of MBH at time 70

source_name: Japanese quail mediobasal hypothalamus, time70

treatment_protocol: Animals were transferred from short day condition (6h light: 18h dark) to long day conditions (20h light: 4h dark) (1 short day and 2 long days).


title: quail, short day condition at ZT2, biological rep1


title: quail, long day condition at ZT2, biological rep1


title: quail, short day condition at ZT22, biological rep1


title: quail, short day condition at ZT18, biological rep2


title: quail, short day condition at ZT14, biological rep1


title: HNSCC cell line UM-SCC22A

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC22A

tag: Female, 59 years, Primary sites

value: Hypopharynx, T2N1M0, none therapy, survival 10 months, died with disease


title: Transcriptional profiling of invasive and non-invasive C. albicans strains

hyb_protocol: For transcriptional profiling C. albicans microarrays (Eurogentec) were prehybridised for 45 min at 42°C in 5x SSC, 1% SDS and 1% BSA. Prehybridised microarrays were washed 5x with water, once with isopropanol and the washed arrays were air dried. Before hybridisation, Cy3- and Cy5-labeled cDNA was mixed, filled up to 25 µl with water and denatured for 5 min at 95°C. Twenty-five microliter hybridisation buffer (50% formamide, 10x SSC, 0.2% SDS) were added. The mixture was applied on the prehybridised microarrays, covered with a LifterSlip (25x44 inch; Erie Scientific Company), and hybridisation took place over night in a humidified chamber (Corning) in a water bath at 42°C. Hybridised microarrays were washed for 15 min in 2x SSC, 1% SDS, for 8 min in 1x SSC, 0.2% SDS, and for 5 min in 0.1x SSC, 0.2% SDS. Hybridisation for each strain was done in triplicate including one dye swap.

scan_protocol: After washing, the microarrays were immediately scanned with an Axon 4000B scanner at a resolution of 10 µm and data were extracted using the GenePix 4.1 software package (Axon).

data_processing: Extracted data were normalised (LOWESS) and analysed in GeneSpring 7.2 (Agilent). Genes were identified as differentially expressed using Student’s t-test with P ≤ 0.05.

source_name: C. albicans strain SC5314, SD-medium, 37°C, OD600=0.15

label_protocol: Labeled cDNA for transcriptional profiling was produced by incubating 30 µg (22 µl) total RNA  of each strain with 1 µg oligo-d(T)-primer (Invitrogen) at 70°C for 10 min. After adding 30 µl of labelling master mix (1x reverse transcriptase buffer, 1 mM dithiotreithol, 500 µM dATP, 500 µM dCTP, 500 µM dGTP, 100 µM dTTP; Invitrogen), 3 µl Cy3-dUTP (Amersham) and 40 U RNaseOutTM (Invitrogen), labelling occurred after addition of 200 U SuperScriptTM II reverse transcriptase (Invitrogen) for 2 h at 42°C. After 1 h of incubation 200 U of fresh reverse transcriptase were added. The reaction was stopped by adding 3 µl EDTA (20 µM) and RNA was degraded by addition of 3 µl NaOH (500 mM) following an incubation at 70°C for 10 min. The reaction was neutralised by adding 3 µl HCl (500 mM). Labelled cDNA was washed and concentrated and stored at –20°C until further use.

growth_protocol: For transcriptional profiling strain SC5314 was grown up to OD600 of 0.15 in SD medium at 37°C. Cells were centrifuged and the resulting pellet was immediately frozen in liquid nitrogen and stored at –80°C until further use.

extract_protocol: Total RNA was extracted as described (Fradin C, De Groot P, MacCallum D, Schaller M, Klis F, Odds FC, Hube B: Granulocytes govern the transcriptional response, morphology and proliferation of Candida albicans in human blood. Mol Microbiol 2005, 56:397-415).

source_name: C. albicans strain ATCC10231, SD-medium, 37°C, OD600=0.15

label_protocol: Labeled cDNA for transcriptional profiling was produced by incubating 30 µg (22 µl) total RNA  of each strain with 1 µg oligo-d(T)-primer (Invitrogen) at 70°C for 10 min. After adding 30 µl of labelling master mix (1x reverse transcriptase buffer, 1 mM dithiotreithol, 500 µM dATP, 500 µM dCTP, 500 µM dGTP, 100 µM dTTP; Invitrogen), 3 µl Cy5-dUTP (Amersham) and 40 U RNaseOutTM (Invitrogen), labelling occurred after addition of 200 U SuperScriptTM II reverse transcriptase (Invitrogen) for 2 h at 42°C. After 1 h of incubation 200 U of fresh reverse transcriptase were added. The reaction was stopped by adding 3 µl EDTA (20 µM) and RNA was degraded by addition of 3 µl NaOH (500 mM) following an incubation at 70°C for 10 min. The reaction was neutralised by adding 3 µl HCl (500 mM). Labelled cDNA was washed and concentrated and stored at –20°C until further use.

growth_protocol: For transcriptional profiling strain ATCC10231 was grown up to OD600 of 0.15 in SD medium at 37°C. Cells were centrifuged and the resulting pellet was immediately frozen in liquid nitrogen and stored at –80°C until further use.


title: quail, time66, biological rep2

description: gene expression data of MBH at time 66

source_name: Japanese quail mediobasal hypothalamus, time66


title: quail, time66, biological rep1

description: gene expression data of MBH at time 66


title: HNSCC cell line UM-SCC11B

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC11B

tag: Male, 65 years, Primary sites

value: Hypopharynx, T2N2aM0,  chemotherapy, survival 14 months, died with disease


title: quail, time70, biological rep1

description: gene expression data of MBH at time 70


title: HNSCC cell line UM-SCC22B

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC22B

value: Hypopharynx, T2N1M0, lymph nodes metastasis, survival 10 months, died with disease


title: quail, time62, biological rep1

description: gene expression data of MBH at time 62

source_name: Japanese quail mediobasal hypothalamus, time62


title: quail, short day condition at ZT6, biological rep2

description: gene expression data of MBH at short day condition ZT6


title: quail, time58, biological rep1

description: gene expression data of MBH at time 58

source_name: Japanese quail mediobasal hypothalamus, time58


title: HNSCC cell line UM-SCC9

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC9

tag: Female, 72 years, Primary sites

value: Tonsil/base of tongue, T2N0M0, radiation therapy, survival 15 months, died with disease


title: quail, short day condition at ZT10, biological rep2


title: quail, time58, biological rep2

description: gene expression data of MBH at time 58


title: 129X1/SvJ

description: replicate

value: tail


title: quail, short day condition at ZT6, biological rep1


title: HNSCC cell line UM-SCC6

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC6

tag: Male, 37 years, Primary sites:Anterior tongue, T2N0M0, none therapy, Lost to follow-up


title: HNSCC cell line UM-SCC38

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC38

tag: Male, 60 years, Primary sites

value: Tonsil/base of tongue, T2N2aM0, none therapy, survival 11 months, died with disease


title: HNSCC cell line UM-SCC11A

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC11A

value: Hypopharynx, T2N2aM0, none therapy, survival 14 months, died with disease


title: HNSCC cell line UM-SCC5

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC5

tag: Male, 59 years, Primary sites:Supraglottic Larynx, T2N1M0, surgery therapy, survival 8 months, died with disease


title: HNSCC cell line UM-SCC1

source_name: head and neck Squamous Cell Carcinoma cell line UM-SCC1

tag: Male, 72 years, Primary sites

value: floor of mouth, T1N0M0, radiation therapy, survival 15 months, died without disease


title: Human normal keratinocyte 4 rep-1

source_name: Human normal keratinocytes

tag: from skin (Cascade Biologics Inc., Portland, OR)


title: quail, time62, biological rep2

description: gene expression data of MBH at time 62


title: quail, time50, biological rep2

description: gene expression data of MBH at time 50

source_name: Japanese quail mediobasal hypothalamus, time50


title: Human normal keratinocyte 3 rep-1

source_name: common reference


title: quail, time44, biological rep2

description: gene expression data of MBH at time 44

source_name: Japanese quail mediobasal hypothalamus, time44


title: quail, time46, biological rep1

description: gene expression data of MBH at time 46

source_name: Japanese quail mediobasal hypothalamus, time46


title: quail, time44, biological rep1

description: gene expression data of MBH at time 44


title: quail, time54, biological rep1

description: gene expression data of MBH at time 54

source_name: Japanese quail mediobasal hypothalamus, time54


title: quail, time50, biological rep1

description: gene expression data of MBH at time 50


title: quail, time36, biological rep2

description: gene expression data of MBH at time 36

source_name: Japanese quail mediobasal hypothalamus, time36


title: quail, time46, biological rep2

description: gene expression data of MBH at time 46


title: quail, time42, biological rep1

description: gene expression data of MBH at time 42

source_name: Japanese quail mediobasal hypothalamus, time42


title: quail, time38, biological rep1

description: gene expression data of MBH at time 38

source_name: Japanese quail mediobasal hypothalamus, time38


title: quail, time36, biological rep1

description: gene expression data of MBH at time 36


title: quail, time26, biological rep2

description: gene expression data of MBH at time 26

source_name: Japanese quail mediobasal hypothalamus, time26


title: quail, time54, biological rep2

description: gene expression data of MBH at time 54


title: quail, time42, biological rep2

description: gene expression data of MBH at time 42


title: quail, time18, biological rep1

description: gene expression data of MBH at time 18

source_name: Japanese quail mediobasal hypothalamus, time18


title: quail, time40, biological rep2

description: gene expression data of MBH at time 40

source_name: Japanese quail mediobasal hypothalamus, time40


title: quail, time18, biological rep2

description: gene expression data of MBH at time 18


title: quail, time40, biological rep1

description: gene expression data of MBH at time 40


title: Human normal keratinocyte 2 rep-1


title: quail, time22, biological rep1

description: gene expression data of MBH at time 22

source_name: Japanese quail mediobasal hypothalamus, time22


title: Human normal keratinocyte 1 rep-1


title: quail, time38, biological rep2

description: gene expression data of MBH at time 38


title: quail, time34, biological rep2

description: gene expression data of MBH at time 34

source_name: Japanese quail mediobasal hypothalamus, time34


title: quail, time30, biological rep2

description: gene expression data of MBH at time 30

source_name: Japanese quail mediobasal hypothalamus, time30


title: quail, time6, biological rep1

description: gene expression data of MBH at time 6

source_name: Japanese quail mediobasal hypothalamus, time6


title: quail, time22, biological rep2

description: gene expression data of MBH at time 22


title: quail, time26, biological rep1

description: gene expression data of MBH at time 26


title: quail, time30, biological rep1

description: gene expression data of MBH at time 30


title: quail, time34, biological rep1

description: gene expression data of MBH at time 34


title: chicken DNA, biological rep1

description: data of genomic DNA hybridization

hyb_protocol: Ten ug of labelled DNA  were hybridized for 16 h at 45 C on Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Gallus gallus

source_name: liver

label_protocol: Biotinylated DNA were labelled by BioPrime DNA labelling system (Invitrogen) according to manufacturer's protocol from 0.3 ug genomic DNA.

growth_protocol: Eight week-old female quail and chicken (WL-G) kept under long day condition (18 h light: 6h dark) were used.

extract_protocol: Genomic DNA was extracted using DNeasy tissue kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: female


title: Glioblastoma 3 rep 1

status: Public on Mar 10 2008

city: Sao Paulo

first: Oswaldo

middle: Keith

last: Okamoto

state: SP

address: R. Botucatu, 862.

department: Neurology

country: Brazil

institute: UNIFESP

hyb_protocol: As described in the manufacturer's protocol.

scan_protocol: Fluorescence was measured using an Axon GenePix 4000B Scanner (Axon Instruments Inc, Sunnyvale, CA).

data_processing: Data were normalized with the CodeLink Software v.2.3 (GE Healthcare, Piscataway, NJ).

source_name: Brain tumor

extract_protocol: All tissues were microdissected and RNA was extracted with trizol.

treatment_protocol: Tumor specimens were obtained from patients with CNS tumors treated by the Neurosurgery Group of the Department of Neurology at Hospital das Clínicas, School of Medicine, University of São Paulo, São Paulo, Brazil, between 2000 and 2005. The tissues were categorized according to the WHO grading system (PMID: 11895036, PMID: 8047695) by neuropathologists from the Division of Pathological Anatomy of the same institution. Informed consent was obtained from each patient. Fresh surgical samples of different grades and non-neoplastic tissues of the CNS (temporal lobectomy from epilepsy surgeries) were macrodissected and immediately snap-frozen in liquid nitrogen upon surgical removal.

tag: CNS tumor


title: quail, time14, biological rep2

description: gene expression data of MBH at time 14

source_name: Japanese quail mediobasal hypothalamus, time14

tag: male


title: Glioblastoma 5 rep 1

label_protocol: As described in the manufacturer's protocol.


title: quail DNA, biological rep2

description: data of genomic DNA hybridization


title: quail, time14, biological rep1

description: gene expression data of MBH at time 14


title: Glioblastoma 1 rep 1


title: quail, time6, biological rep2

description: gene expression data of MBH at time 6


title: quail, time2, biological rep2

description: gene expression data of MBH at time 2

source_name: Japanese quail mediobasal hypothalamus, time2


title: Glioblastoma 1 rep 2


title: Glioblastoma 2 rep 1


title: Glioblastoma 6 rep 1


title: Pilocytic astrocytoma 2 rep 2


title: Pilocytic astrocytoma 2 rep 1


title: quail, time10, biological rep2

description: gene expression data of MBH at time 10

source_name: Japanese quail mediobasal hypothalamus, time10


title: Glioblastoma 4 rep 1


title: quail, time10, biological rep1

description: gene expression data of MBH at time 10


title: Pilocytic astrocytoma 3 rep 2

source_name: Brain sample


title: Glioblastoma 2 rep 2


title: quail, time2, biological rep1

description: gene expression data of MBH at time 2


title: quail DNA, biological rep3

description: data of genomic DNA hybridization


title: hGRa dexamethasone vs. N363S dexamethasone (Replicate 2, Hyb 2)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: U-2 OS cells were transfected with the BD Clontech pTET-OFF regulatory plasmid to establish the U-OFF parental cell line.  MluI and EcoRV ends were generated onto the coding region of hGRa using PCR amplification of the pCMVhGRa plasmid.  The pTRE2hyg vector was digested with MluI and EcoRV and the two DNAs were ligated to form the pTRE2hGRa plasmid (Lu and Cidlowski).  Site-directed mutagenesis was then performed to make pTRE2N363S.  The wild type hGR and the N363S mutant were individually transfected into the U-OFF cells and clones were selected which stably expressed either hGRa or N363S using 200 mg/ml of geneticin and 500 mg/ml of hygromycin. Several clones were obtained for each receptor, and the receptor levels were compared using western blot analyses. In these cell lines, the expression of hGR can be repressed by the addition of tetracycline or the derivative doxycycline to the media. U-2 OS (human osteosarcoma) cells were maintained in DMEM/F-12 supplemented with 10% FCS:CS, 2 mM glutamine and pen-strep and selected clones were maintained in the same media with the addition of 200 mg/ml Geneticin and 200 mg/ml hygromycin. All cells were maintained in a humidified, 5% CO2 atmosphere.  For the Microarray:  U-2 OS cells stably expressing either wild type hGR or N363S were treated for six hours with 10 nM dexamethasone or vehicle, and total RNA was isolated using the Qiagen RNeasy midi kit (Qiagen, Valencia, CA).

data_processing: Gene expression analysis was conducted using Agilent Human1Av2 arrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer?s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters.

source_name: N363S dexamethasone (Cy3)

tag: N363S dexamethasone

source_name: hGRa dexamethasone (Cy5)

tag: hGRa dexamethasone


title: hGRa dexamethasone vs. N363S dexamethasone (Replicate 2, Hyb 1)

source_name: hGRa dexamethasone (Cy3)

source_name: N363S dexamethasone (Cy5)


title: hGRa vehicle vs. hGRa dexamethasone (Replicate 2, Hyb 1)

source_name: hGRa vehicle (Cy3)

tag: hGRa vehicle


title: hGRa vehicle vs. hGRa dexamethasone (Replicate 1, Hyb 1)


title: N363S vehicle vs. N363S dexamethasone (Replicate 2, Hyb 2)

source_name: N363S vehicle (Cy5)

tag: N363S vehicle


title: N363S vehicle vs. N363S dexamethasone (Replicate 1, Hyb 1)

source_name: N363S vehicle (Cy3)


title: SAS1-HA vs WT, Replica 6

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

description: RNA was extracted from plants that overexpress SAS1 and from non-transformed plants. Plants were grown for 3 weeks under long day conditions. Hybridization was performed on an array from Arabidopsis Keck Resource Lab Array (Yale University) containing 12K Arabidopsis ESTs. Data in this platform contains 6 repetitions including 2 independent biological experiments.

hyb_protocol: For each biological repetition, two hybridizations with swapped dye labeling were preformed.

scan_protocol: Separate images for each fluorescence were acquired using ScanArray 4000 software (Packard BioScience, Meridan, CT) at a resolution of 10 mm per pixel, adjusting the photomultiplier and laser power to achieve an optimal distribution of signals without minimal saturation.

data_processing:
Data analysis was performed applying per-spot
and per-chip normalization (GeneSpring 5.1; Silicon Genetics, Redwood
City, CA).

source_name: untransformed plants

extract_protocol: Total RNA was isolated from 3-4 weeks old rosettes using the RNAeasy plant mini kit (Qiagen) and subjected to reverse transcription and amplified by in vitro transcription with t7 polymerase (Ambion).

tag: Total RNA was extracted from 3 weeks old leaves of WT Arabidopsis thaliana Col-0

label_protocol: Amplified RNA products were subjected to reverse transcription and then labeled with Cy3 and Cy5 by indirect amino-allyl method.

tag: Total RNA was extracted from 3 weeks old leaves of SAS1-HA over expression line in Arabidopsis thaliana Col-0


title: hGRa dexamethasone vs. N363S dexamethasone (Replicate 1, Hyb 2)


title: SAS1-HA vs WT, Replica 4

label_protocol: Amplified RNA products were subjected to reverse transcription and then labeled with Cy3 and Cy5 by indirect amino-allyl method


title: hGRa vehicle vs. N363S vehicle (Replicate 2, Hyb 1)


title: SAS1-HA vs WT, Replica 2


title: hGRa vehicle vs. N363S vehicle (Replicate 1, Hyb 1)


title: female FSHD #9_U133A_S2

status: Public on Mar 08 2008

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: female FSHD #9_U133A_S2

hyb_protocol: Hybridization, washing, and staining with phycoerythrin-streptavidin were done with an Affymetrix hybridization oven and fluidics station as recommended by Affymetrix

scan_protocol: Arrays were scanned with an Affymetrix scanner after signal enhancement with biotinylated anti-streptavidin antibody

data_processing: GCRMA normalization was done using Bioconductor package

source_name: vastus lateralis muscle, after (S2) antibody enhancement, FSHD, U133A

label_protocol: Biotinylated cRNA was prepared from 5 ug total RNA using the BioArray kit (Enzo Life Sciences) according to manufacturer's instructions

growth_protocol: not applicable

extract_protocol: RNA was extracted from frozen biopsy specimens in Tri-Reagent according to the manufacturer's recommended protocol

treatment_protocol: not applicable

tag: female, FSHD #9


title: female FSHD #3_U133A_S2

description: female FSHD #3_U133A_S2

tag: female, FSHD #3


title: female FSHD #4_U133A_S2

description: female FSHD #4_U133A_S2

tag: female, FSHD #4


title: female FSHD #6_U133A_S2

description: female FSHD #6_U133A_S2

tag: female, FSHD #6


title: male FSHD #7_U133A_S2

description: male FSHD #7_U133A_S2

tag: male, FSHD #7


title: chicken DNA, biological rep3

description: data of genomic DNA hybridization


title: quail DNA, biological rep1

description: data of genomic DNA hybridization


title: Glioblastoma 3 rep 2


title: chicken DNA, biological rep2

description: data of genomic DNA hybridization


title: Pilocytic astrocytoma 3 rep 1


title: male FSHD #5_U133A_S2

description: male FSHD #5_U133A_S2

tag: male, FSHD #5


title: Pilocytic astrocytoma 1 rep 2

source_name: brain tumor


title: Pilocytic astrocytoma 1 rep 1


title: male FSHD #2_U133A_S2

description: male FSHD #2_U133A_S2

tag: male, FSHD #2


title: hGRa vehicle vs. N363S vehicle (Replicate 2, Hyb 2)

source_name: hGRa vehicle (Cy5)


title: hGRa vehicle vs. hGRa dexamethasone (Replicate 2, Hyb 2)


title: female 67.3 yr_U133A_S2

description: female 67.3 yr_U133A_S2

source_name: vastus lateralis muscle, after (S2) antibody enhancement, normal, U133A

tag: female, 67.3 yr, normal


title: female 65.9 yr_U133A_S2

description: female 65.9 yr_U133A_S2

tag: female, 65.9 yr, normal


title: hGRa vehicle vs. hGRa dexamethasone (Replicate 1, Hyb 2)


title: female 65.1 yr_U133A_S2

description: female 65.1 yr_U133A_S2

tag: female, 65.1 yr, normal


title: N363S vehicle vs. N363S dexamethasone (Replicate 1, Hyb 2)


title: female 68.4 yr_U133A_S2

description: female 68.4 yr_U133A_S2

tag: female, 68.4 yr, normal


title: SAS1-HA vs WT, Replica 5


title: N363S vehicle vs. N363S dexamethasone (Replicate 2, Hyb 1)

tag: N363S dexamethasone


title: Control rep 2

source_name: Brain tissue

tag: A pool of three non-neoplastic brain tissues (mean age of 47 yo) corresponding to temporal lobectomy samples from epilepsy surgeries.


title: female 29.8 yr_U133A_S2

description: female 29.8 yr_U133A_S2

tag: female, 29.8 yr, normal


title: female 20.1 yr_U133A_S2

description: female 20.1 yr_U133A_S2

tag: female, 20.1 yr, normal


title: female 26.5 yr_U133A_S2

description: female 26.5 yr_U133A_S2

tag: female, 26.5 yr, normal


title: SAS1-HA vs WT, Replica 3

tag: Total RNA was extracted from 3 weeks old leaves of WT Arabidopsis thaliana Col-0

tag: Total RNA was extracted from 3 weeks old leaves of SAS1-HA over expression line in Arabidopsis thaliana Col-0


title: hGRa dexamethasone vs. N363S dexamethasone (Replicate 1, Hyb 1)

tag: hGRa dexamethasone


title: female 24.4 yr_U133A_S2

description: female 24.4 yr_U133A_S2

tag: female, 24.4 yr, normal


title: Control rep 1


title: female FSHD #5_U133A_S2

description: female FSHD #5_U133A_S2

tag: female, FSHD #5


title: female FSHD #7_U133A_S2

description: female FSHD #7_U133A_S2

tag: female, FSHD #7


title: SAS1-HA vs WT. Replica 1


title: female FSHD #2_U133A_S2

description: female FSHD #2_U133A_S2

tag: female, FSHD #2


title: female FSHD #8_U133A_S2

description: female FSHD #8_U133A_S2

tag: female, FSHD #8


title: male 71.2 yr_U133A_S2

description: male 71.2 yr_U133A_S2

tag: male, 71.2 yr, normal


title: hGRa vehicle vs. N363S vehicle (Replicate 1, Hyb 2)

tag: N363S vehicle

tag: hGRa vehicle


title: female FSHD #1_U133A_S2

description: female FSHD #1_U133A_S2

tag: female, FSHD #1


title: male FSHD #8_U133A_S2

description: male FSHD #8_U133A_S2

tag: male, FSHD #8


title: male FSHD #9_U133A_S2

description: male FSHD #9_U133A_S2

tag: male, FSHD #9


title: male FSHD #10_U133A_S2

description: male FSHD #10_U133A_S2

tag: male, FSHD #10


title: male 24.2 yr_U133A_S2

description: male 24.2 yr_U133A_S2

tag: male, 24.2 yr, normal


title: male FSHD #6_U133A_S2

description: male FSHD #6_U133A_S2

tag: male, FSHD #6


title: male FSHD #4_U133A_S2

description: male FSHD #4_U133A_S2

tag: male, FSHD #4


title: male FSHD #3_U133A_S2

description: male FSHD #3_U133A_S2

tag: male, FSHD #3


title: female FSHD #9_U133A_S1

description: female FSHD #9_U133A_S1

source_name: vastus lateralis muscle, before (S1) antibody enhancement, FSHD, U133A

tag: female, FSHD #9


title: male 21.5 yr_U133A_S2

description: male 21.5 yr_U133A_S2

tag: male, 21.5 yr, normal


title: female FSHD #8_U133A_S1

description: female FSHD #8_U133A_S1


title: female 67.9 yr_U133A_S2

description: female 67.9 yr_U133A_S2

tag: female, 67.9 yr, normal


title: male FSHD #1_U133A_S2

description: male FSHD #1_U133A_S2

tag: male, FSHD #1


title: female 66.6 yr_U133A_S2

description: female 66.6 yr_U133A_S2

tag: female, 66.6 yr, normal


title: female 71.4 yr_U133A_S2

description: female 71.4 yr_U133A_S2

tag: female, 71.4 yr, normal


title: female 70.7 yr_U133A_S2

description: female 70.7 yr_U133A_S2

tag: female, 70.7 yr, normal


title: female FSHD #2_U133A_S1

description: female FSHD #2_U133A_S1

tag: female, FSHD #2


title: male FSHD #10_U133A_S1

description: male FSHD #10_U133A_S1


title: male FSHD #9_U133A_S1

description: male FSHD #9_U133A_S1


title: male FSHD #8_U133A_S1

description: male FSHD #8_U133A_S1


title: female 22.5 yr_U133A_S2

description: female 22.5 yr_U133A_S2

tag: female, 22.5 yr, normal


title: female 21.5 yr_U133A_S2

description: female 21.5 yr_U133A_S2

tag: female, 21.5 yr, normal


title: male FSHD #6_U133A_S1

description: male FSHD #6_U133A_S1


title: female 23.5 yr_U133A_S2

description: female 23.5 yr_U133A_S2

tag: female, 23.5 yr, normal


title: male FSHD #4_U133A_S1

description: male FSHD #4_U133A_S1


title: male 74.5 yr_U133A_S2

description: male 74.5 yr_U133A_S2

tag: male, 74.5 yr, normal


title: male 75.1 yr_U133A_S2

description: male 75.1 yr_U133A_S2

tag: male, 75.1 yr, normal


title: male 25.2 yr_U133A_S2

description: male 25.2 yr_U133A_S2

tag: male, 25.2 yr, normal


title: female FSHD #1_U133A_S1

description: female FSHD #1_U133A_S1

tag: female, FSHD #1


title: male 67.2 yr_U133A_S2

description: male 67.2 yr_U133A_S2

tag: male, 67.2 yr, normal


title: female FSHD #5_U133A_S1

description: female FSHD #5_U133A_S1

tag: female, FSHD #5


title: female FSHD #6_U133A_S1

description: female FSHD #6_U133A_S1

tag: female, FSHD #6


title: male 27.1 yr_U133A_S2

description: male 27.1 yr_U133A_S2

tag: male, 27.1 yr, normal


title: male 69.6 yr_U133A_S2

description: male 69.6 yr_U133A_S2

tag: male, 69.6 yr, normal


title: male 69.2 yr_U133A_S2

description: male 69.2 yr_U133A_S2

tag: male, 69.2 yr, normal


title: male 73.5 yr_U133A_S2

description: male 73.5 yr_U133A_S2

tag: male, 73.5 yr, normal


title: female FSHD #4_U133A_S1

description: female FSHD #4_U133A_S1

tag: female, FSHD #4


title: male FSHD #1_U133A_S1

description: male FSHD #1_U133A_S1

tag: male, FSHD #1


title: female FSHD #3_U133A_S1

description: female FSHD #3_U133A_S1

tag: female, FSHD #3


title: male FSHD #7_U133A_S1

description: male FSHD #7_U133A_S1

tag: male, FSHD #7


title: male 23.4 yr_U133A_S2

description: male 23.4 yr_U133A_S2

tag: male, 23.4 yr, normal


title: male 26.2 yr_U133A_S2

description: male 26.2 yr_U133A_S2

tag: male, 26.2 yr, normal


title: male FSHD #3_U133A_S1

description: male FSHD #3_U133A_S1

tag: male, FSHD #3


title: female 67.3 yr_U133A_S1

description: female 67.3 yr_U133A_S1

source_name: vastus lateralis muscle, before (S1) antibody enhancement, normal, U133A

tag: female, 67.3 yr, normal


title: female 70.7 yr_U133A_S1

description: female 70.7 yr_U133A_S1

tag: female, 70.7 yr, normal


title: male FSHD #5_U133A_S1

description: male FSHD #5_U133A_S1

tag: male, FSHD #5


title: male 25.1 yr_U133A_S2

description: male 25.1 yr_U133A_S2

tag: male, 25.1 yr, normal


title: male 68.4 yr_U133A_S2

description: male 68.4 yr_U133A_S2

tag: male, 68.4 yr, normal


title: female 71.4 yr_U133A_S1

description: female 71.4 yr_U133A_S1

tag: female, 71.4 yr, normal


title: female 67.9 yr_U133A_S1

description: female 67.9 yr_U133A_S1

tag: female, 67.9 yr, normal


title: male FSHD #2_U133A_S1

description: male FSHD #2_U133A_S1

tag: male, FSHD #2


title: female FSHD #7_U133A_S1

description: female FSHD #7_U133A_S1

tag: female, FSHD #7


title: female 65.1 yr_U133A_S1

description: female 65.1 yr_U133A_S1

tag: female, 65.1 yr, normal


title: female 20.1 yr_U133A_S1

description: female 20.1 yr_U133A_S1

tag: female, 20.1 yr, normal


title: female 66.6 yr_U133A_S1

description: female 66.6 yr_U133A_S1

tag: female, 66.6 yr, normal


title: female 22.5 yr_U133A_S1

description: female 22.5 yr_U133A_S1

tag: female, 22.5 yr, normal


title: female 26.5 yr_U133A_S1

description: female 26.5 yr_U133A_S1

tag: female, 26.5 yr, normal


title: female 29.8 yr_U133A_S1

description: female 29.8 yr_U133A_S1

tag: female, 29.8 yr, normal


title: female 68.4 yr_U133A_S1

description: female 68.4 yr_U133A_S1

tag: female, 68.4 yr, normal


title: female 65.9 yr_U133A_S1

description: female 65.9 yr_U133A_S1

tag: female, 65.9 yr, normal


title: female 21.5 yr_U133A_S1

description: female 21.5 yr_U133A_S1

tag: female, 21.5 yr, normal


title: male 75.1 yr_U133A_S1

description: male 75.1 yr_U133A_S1

tag: male, 75.1 yr, normal


title: male 71.2 yr_U133A_S1

description: male 71.2 yr_U133A_S1

tag: male, 71.2 yr, normal


title: male 67.2 yr_U133A_S1

description: male 67.2 yr_U133A_S1

tag: male, 67.2 yr, normal


title: female FSHD #9_U133B_S1

description: female FSHD #9_U133B_S1

source_name: vastus lateralis muscle, before (S1) antibody enhancement, FSHD, U133B

tag: female,  FSHD #9


title: female FSHD #8_U133B_S1

description: female FSHD #8_U133B_S1

tag: female,  FSHD #8


title: female FSHD #3_U133B_S1

description: female FSHD #3_U133B_S1

tag: female,  FSHD #3


title: female 23.5 yr_U133A_S1

description: female 23.5 yr_U133A_S1

tag: female, 23.5 yr, normal


title: female 24.4 yr_U133A_S1

description: female 24.4 yr_U133A_S1

tag: female, 24.4 yr, normal


title: male 68.4 yr_U133A_S1

description: male 68.4 yr_U133A_S1

tag: male, 68.4 yr, normal