title: HsO4E-042_359423

description:
M5 VEGFB vs Control
Date: 2009/09/29


title: PBC_MMTV-MYC_validation_11

status: Public on Mar 01 2011

type: RNA

city: Durham

first: Erich

last: Huang

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

country: USA

institute: Duke University

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.

scan_protocol: GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).

data_processing:
Data processing was performed in a pilot revision control system entitled Quality-Auditable Data Repository and Analysis (QUADRA). For fully versioned and annotated source code and data objects, please see http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project.
Data were RMA normalized according to the source code found at http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project/human-dataprep.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

label_protocol:
Purified total RNA (200 ng) was amplified using NuGEN Ovation™ RNA Amplification System (NuGEN Technologies, Inc., San Carlos, CA).
Biotinylated cRNA were prepared according to the standard Affymetrix IVT 1-cycle protocol from 2.5 ug total RNA.

extract_protocol:
Samples were collected using the submandibular (cheekpouch) method. Briefly, the vein that drains the face and cheek area was punctured by a lancet (GoldenRod animal lancet, MEDIpoint, Inc., Mineola, NY) and blood was captured in BD Microtainer™ tubes with potassium-EDTA anticoagulant (Becton Dickinson, Franklin Lakes, NJ). Tubes were immediately inverted 10-12 times and placed on ice.
Following erythrocyte lysis, total RNA was isolated from the leukocyte pellet using the QIAamp RNA Blood Mini Kit (Qiagen, Valencia, CA). Alternatively, the leukocyte pellet was immediately lysed, homogenized and stored at -80°C. RNA was isolated at a later date using the protocol described above or the adapted protocol associated with the QIAamp RNA Blood Mini Kit for use in the QIAcube (Qiagen, Valencia, CA).

tag: strain

value: FVB/NJ

tag: genotype/variation

value: MMTV/c-MYC transgenic

tag: phenotype

value: tumor-bearing transgenic mouse

tag: tissue

value: total white blood cells (WBCs)

tag: data set

value: validation


title: PBC_MMTV-MYC_validation_10


title: FT_1h_4

city: Salisbury

first: Jonathan

last: David

address: Porton Down

department: Biomedical Sciences

country: United Kingdom

institute: Dstl

hyb_protocol: Test and control RNA was resuspended in 250ul of hybridisation buffer supplied by the microarray slide manufacturer (MWG Biotech, Ebersberg, Germany). Slides were hybridised overnight in hybridisation chambers (Qiagen, Crawley, West Sussex) for 16 hours at 42C in the dark and then washed in 3 different wash buffers for 5 minutes each wash. Wash buffer 1 consisted of 2 x SSC (buffered solution of sodium chloride and trisodium citrate), 0.1% SDS (Sigma, Poole), wash buffer 2 consisted of 1 x SSC and wash buffer 3 consisted of 0.5% SSC. All wash buffers were filter sterilised to prevent contaminating debris. The slides were dried by centrifugation at 500 x g for 5 minutes.

scan_protocol: Scanning was performed using a 428 nm scanner (GenePix 4000B, Axon, US) using the appropriate gain settings and filters for the Cy3 and Cy5 dyes (Cy3 = 532nm, 17mW, Cy5 = 635nm, 10mW).

data_processing: Image analysis was carried out using BlueFuse image analysis software (BlueGnome, Cambridge, UK). Statistical analysis of the array data was performed using GeneSpring software, version GX7.3 (Agilent Technologies, Berks, UK). Data were normalised using a Lowess curve fit to log-intensity versus log ratio plot, where 20% of the data were used for the Lowess normalisation. Agent data were then normalised to the respective sham time-matched control expression level for every spot on the chip (1509) using the “normalise to specific sample” algorithm within GeneSpring version GX7.3 (e.g. 24 hour agent normalised to 24 hour sham).

label_protocol: RNA was labelled using the LabelStar Array Kit (Qiagen, Crawley, West Sussex, UK). 3mg of test RNA (ricin or sham exposed) was labelled with Cyanine 3-dNTP (Cy3) (Ambion, Cambridgeshire, UK) and 3mg of universal mouse reference RNA (Stratagene Europe, Netherlands) labelled with Cyanine 5-dNTP (Cy5) (Ambion, Cambridgeshire, UK).

extract_protocol: Total RNA was extracted from each of the 10 lung tissue samples, after homogenisation with a rotor stator homogeniser, using the RNeasy Mini Kit (Qiagen, Crawley, West Sussex, UK) following the manufacturer’s protocol.

treatment_protocol: Francisella tularensis or culture media aerosol exposure

tag: agent

value: aerosolised Francisella tularensis

tag: time point

value: Balb/c

tag: gender

value: Female

value: Lung

source_name: Stratagene Universal Reference RNA

value: Mixture of 11 cell lines


title: FT_1h_6


title: FT_1h_3


title: PBC_MMTV-MYC_validation_12


title: PBC_MMTV-MYC_validation_8


title: HsO4E-022_359495

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/30

hyb_protocol: Agilent : 80 pmol at 60 degree_C during 17 hours

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

data_processing: Lowess non linear normalization

organism: Homo sapiens

source_name: M5 LPS2

label_protocol: Amino Allyl MessageAmp aRNA Amplification Kit of Ambion, which incorporates amino allyl incorporation and aRNA amplification, as well as the Cy dyes.

extract_protocol: Qiagen

tag: patient

value: LPS

value: M5 LPS

value: Trizol

value: Macro

source_name: M5 VEGFB+LPS 2

value: VEGFB+LPS

value: M5 VEGFB+LPS


title: 13912513 - ss4-phs1 N2 vs WS N2

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

description: What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves.

hyb_protocol: WS N2 Cy5 / ss4-phs1 N2 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,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

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

organism: Arabidopsis thaliana

source_name: WS N2

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 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: rosette - Media: peat-based compost Hygrometry: approximately 60% during the day Temperature: 22°C during the day/ 17°C during the night Light: 16h light

treatment_protocol: no treatment

tag: genotype

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: ss4-phs1 N2

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4- phs1-); age:5 week


title: HsO4E-023_359496

description:
M5 VEGFB+LPS vs LPS
Date: 2009/09/30


title: 13912874 - WS N1 vs phs1 N1

hyb_protocol: phs1 N1 Cy5 / WS N1 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.

source_name: phs1 N1

value: Arabidopsis thaliana (wassilewskija)  mutant (phs1-); age:5 week

source_name: WS N1


title: PBC_MMTV-MYC_validation_7

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse


title: FT_1h_2

value: aerosolised Francisella tularensis


title: FT_1h_1

value: Balb/c


title: 13912883 - WS N2 vs ss4-phs1 N2

hyb_protocol: ss4-phs1 N2 Cy5 / WS N2 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: PBC_MMTV-MYC_validation_4

value: total white blood cells (WBCs)

value: validation


title: 13912504 - ss4w N3 vs WS N3

hyb_protocol: WS N3 Cy5 / ss4w N3 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.

source_name: WS N3

extract_protocol: WS N3:6ug.

source_name: ss4w N3

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4-); age:5 week


title: PBC_MMTV-MYC_validation_9


title: PBC_MMTV-MYC_validation_5


title: HsO4E-021_359449

description:
M5 VEGFB vs Control
Date: 2009/09/30

source_name: M5 C2

value: Control

value: M5 Control

source_name: M5 VEGFB2

value: VEGFB

value: M5 VEGFB


title: PBC_MMTV-MYC_validation_6


title: 13912502 - WS N3 vs ss4w N3

hyb_protocol: ss4w N3 Cy5 / WS N3 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: 13912506 - adg1 N1 vs WS N1

hyb_protocol: WS N1 Cy5 / adg1 N1 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.

source_name: adg1 N1

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1-); age:5 week


title: 13912505 - WS N1 vs adg1 N1

hyb_protocol: adg1 N1 Cy5 / WS N1 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: PBC_MMTV-MYC_validation_3


title: FT_1h_5

value: Female

value: Lung

value: Mixture of 11 cell lines


title: Manduca sexta larval midgut, animal 30-34

city: Jena

first: Heiko

last: Vogel

address: Hans-Knoell-Strasse 8

department: Dpt. of Entomology

country: Germany

description: pooled from 5 animals

hyb_protocol: 1,600 ng of cyanine 3 labeled cRNA was used for each array and hybridization was carried out at 65oC for 17 hours. Slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

scan_protocol: As per manufacturers instruction, using an Agilent Microarray Scanner

data_processing: data was extracted from TIFF images with Agilent Feature Extraction software version 9.1. Raw data output files were analyzed using the GeneSpring GX11 and GeneSifter microarray analysis softwares. The data points were normalized between arrays to the median intensity and log base 2-transformation of the normalized data was performed.

organism: Manduca sexta

label_protocol: Agilent Technologies spike-in RNA was added to 500 ng of total RNA and labeled using a combination of the QuickAmp Amplification kit (Agilent Technologies) and the Kreatech ULS Fluorescent Labeling Kit with cyanine 3-CTP dye following the manufacturer´s instructions. Labeled amplified cRNA samples were purified using Qiagen RNeasy MinElute columns and analyzed on a Nanodrop ND-1000 spectrophotometer using the microarray function. Amplified cRNA samples were used for microarray hybridisation only if the yield was >825 ng and the specific activity >8.0 pmol Cy3 per ug cRNA

growth_protocol: Animals were taken from a culture maintained at the Max Planck Institute for Chemical Ecology, Jena, Germany. For breeding, adults were kept in a flight cage containing a Nicotiana attenuata plant for oviposition, with artifical flowers providing a sugar solution for nutrition. Three times a week eggs were collected transferred to small boxes with artificial diet (46 g agar, 144 g wheat germ, 140 g corn meal, 76 g soz flour, 75 g casein, 24 g salt, 36 g sugar, 5 g cholesterol, 12 g ascorbic acid, 6 g sorbic acid, 3 g methyl paraben, 9 ml linseed oil, 60 ml 37% formalin, 30 mg nicotinic acid, 15 mg riboflavin, 7 mg thiamine, 7 mg pyridoxine, 7 mg folic acid and 0.6 mg biotin per 1.8 ml water). Eggs and emerging larvae were kept inside a climate controlled chamber at 27°C and 70% humidity. Hatched larvae were transferred into new boxes with artifical diet on metal lattices. On onset of wandering   (fifth instar) larvae were allowed to pupaete separately in small plastic boxes filled with paper. Pupae were kept inside climate chambers until 1 week before likely emergence.

extract_protocol: Tissues were cooled over liquid nitrogen. The frozen tissue was transferred to a liquid nitrogen cooled mortar and ground. The homogenate was covered with 1 ml Trizol reagent (Sigma-Aldrich, St. Louis, MIS). Further steps were performed according to the manufacturers instruction, replacing choloroform with 1-bromo-3-chloro-propane. Also, an additional DNAse (Turbo DNAse, Ambion, Austin, TX) treatment was included to eliminate any contaminating DNA. TotalRNA was dissolved in RNA Storage Solution (Ambion) and RNA content and quality was measured photometrically.

tag: Sex

value: both

value: larval midgut


title: Manduca sexta larval midgut, animal 35-39

institute: Max Planck Institute for Chemical Ecology

description: pooled from 5 animals


title: tissue_nonresponders_rep7

city: Chongqing

first: chunyan

last: Xiao

address: No.1 Youyi Road, Yuzhong District

department: Department of Infectious Diseases

country: China

institute: The First Affiliated Hospital, Chongqing Medical University

description: Gene expression in percutaneous needle liver biopsy specimens taken before IFN-α therapy

hyb_protocol: 875ng of labeled cRNA were used per GeneChip array. Hybridization was performed at 65℃ with 10rpm rotation for 17hours.After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G265BA),the scan resolution is 5um.Then Scaned automatically by Agilent DNA Microarray Scanner in 100% and 10% PMT each time.

data_processing: These two scanning results could combine automatically by Agilent Feature Extraction Software, and the normalization method was quantile.

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 7

label_protocol: The cRNA was purified and fluorochrome labeled with Cy3,followed by RNAeasy column purification (RNeasy Mini kit,Qiagen), and then fragmented for hybridization

extract_protocol: Total RNA was isolated from each liver biopsy specimen using the Qiagen RNeasy kit(Qiagen Canada). The concentration and quality of RNA were determined by spectrophotometry and by the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. The total RNA was further purified using an RNeasy Mini kit(Qiagen).

value: liver biopsy specimens

value: male

tag: age


title: tissue_nonresponders_rep6

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 6

value: female


title: 13912501 - ss4w N2 vs WS N2

hyb_protocol: WS N2 Cy5 / ss4w N2 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.

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: ss4w N2


title: 13912499 - ss4w N1 vs WS N1

hyb_protocol: WS N1 Cy5 / ss4w N1 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.

source_name: ss4w N1


title: tissue_responders_rep6

source_name: hepatic tissue,responders treat with IFN-α,replicate 6


title: 13912500 - WS N2 vs ss4w N2

hyb_protocol: ss4w N2 Cy5 / WS N2 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: Manduca sexta larval midgut, animal 40-44

description: pooled from 5 animals


title: tissue_responders_rep4

source_name: hepatic tissue,responders treat with IFN-α,replicate 4


title: tissue_responders_rep5

source_name: hepatic tissue,responders treat with IFN-α,replicate 5


title: PBC_MMTV-MYC_validation_1

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)


title: Manduca sexta larval midgut, animal 25-29

description: pooled from 5 animals


title: PBC_MMTV-MYC_validation_2

value: validation


title: Manduca sexta female antenna, animal 22-24

description: pooled from 3 animals

value: Adult antenna


title: tissue_responders_rep3

source_name: hepatic tissue,responders treat with IFN-α,replicate 3


title: PBC_control_validation_13

source_name: PBCs from tumor-free FVB/N mice matched for age and parity.

value: wild type

value: tumor-free control


title: PBC_control_validation_14


title: tissue_nonresponders_rep5

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 5


title: PBC_control_validation_11


title: 13912495 - WS D3 vs abb D3

hyb_protocol: abb D3 Cy5 / WS D3 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.

source_name: abb D3

extract_protocol: abb D3:9.8ug.

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1- be2- be3-); age:5 week

source_name: WS D3


title: tissue_nonresponders_rep4

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 4


title: Manduca sexta female antenna, animal 16-18

description: pooled from 3 animals


title: 13912498 - WS N1 vs ss4w N1

hyb_protocol: ss4w N1 Cy5 / WS N1 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.

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4-); age:5 week

source_name: WS N1


title: 13912496 - abb D3 vs WS D3

hyb_protocol: WS D3 Cy5 / abb D3 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: 13912494 - abb D2 vs WS D2

hyb_protocol: WS D2 Cy5 / abb D2 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.

source_name: WS D2

source_name: abb D2

extract_protocol: abb D2:9.1ug.


title: PBC_control_validation_12

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.


title: Manduca sexta female antenna, animal 13-15

description: pooled from 3 animals


title: tissue_nonresponders_rep3

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 3


title: tissue_responders_rep1

source_name: hepatic tissue,responders treat with IFN-α,replicate 1


title: CEMx174-DVV-2

city: Columbus

first: Amy

middle: M

last: Hayes

state: OH

address: 1925 Coffey Rd

department: Veterinary Biosciences

institute: Ohio State University

hyb_protocol: cDNA hybridized to arrays via HS4800 Hyb Station (Tecan), in 6x SSPE/30% formamide at 25 C for 18 hours

scan_protocol: Arrays scanned with Axon 4000B Scanner (Molecular Devices) at 635nm qred laser at 100% Power and 800 PMT

data_processing: GenePix Pro 6 image analysis software was used to quantify the signals detected by the array scanner. Background subtracted signal intensity was obtained for each spot on the chip and averaged over duplicate probe sets before log base 2 transformation. Quantile normalization was utilized to normalize experimental variation among chips.

source_name: CEMx174, DVV infected

label_protocol: RNA was denatured at 65ºC for 5 min and converted into cDNA with Sensiscript RT kit (Qiagen) by manufacturer protocol in the presence of biotinylated random hexamer primers.

growth_protocol: CEMx174 cells were cultured in RPMI medium with 10% FBS and 1x Antibiotic-Antimycotic (GIBCO).

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen).

treatment_protocol: CEMx174 cells (1×10^6) were incubated with cell-free supernatant medium containing 3×10^8 pg/ml of Gag for 48 hours. Viable cells were isolated on Ficoll and co-cultured with naive CEMx174 at a ratio of 1:10. Progression of the infections was evaluated at regular intervals by FACS of intracellular Gag. The criteria established for harvest was ~80% infection, which typically was observed at 40-48 hours.

tag: cell type

value: lymphocyte

tag: cell line

tag: infection

value: DVV infected


title: tissue_responders_rep2

source_name: hepatic tissue,responders treat with IFN-α,replicate 2


title: 13912491 - WS D1 vs abb D1

hyb_protocol: abb D1 Cy5 / WS D1 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.

source_name: abb D1

extract_protocol: abb D1:8.4ug.

source_name: WS D1


title: Manduca sexta male antenna, animal 4-6

description: pooled from 3 animals

source_name: Manduca sexta male antenna, animal 4-6


title: PBC_control_validation_9


title: Manduca sexta female antenna, animal 19-21

description: pooled from 3 animals


title: 13912490 - ss4-phs1 D3 vs WS D3

hyb_protocol: WS D3 Cy5 / ss4-phs1 D3 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.

source_name: ss4-phs1 D3

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4- phs1-); age:5 week


title: Manduca sexta male antenna, animal 7-9

description: pooled from 3 animals

source_name: Manduca sexta male antenna, animal 7-9


title: 13912492 - abb D1 vs WS D1

hyb_protocol: WS D1 Cy5 / abb D1 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: PBC_control_validation_8

source_name: PBCs from tumor-free FVB/N mice matched for age and parity.


title: Manduca sexta male antenna, animal 1-3

description: pooled from 3 animals

source_name: Manduca sexta male antenna, animal 1-3


title: PBC_control_validation_10


title: CEMx174-DVV-1


title: tissue_nonresponders_rep2

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 2

value: liver biopsy specimens


title: 13912493 - WS D2 vs abb D2

hyb_protocol: abb D2 Cy5 / WS D2 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: PBC_control_validation_7


title: tissue_nonresponders_rep1

source_name: hepatic tissue,nonresponders treat with IFN-α,replicate 1

value: male


title: 13912489 - WS D3 vs ss4-phs1 D3

hyb_protocol: ss4-phs1 D3 Cy5 / WS D3 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.

source_name: WS D3


title: PBC_control_validation_5


title: CD4

city: Clermont Ferrand

first: Christiane

last: Forestier

address: 28 place H Dunant

department: Pharmacie

institute: Universite d'Auvergne Clermont 1

description: US83000163_251485026557_S01_GE2-v5_10_Apr08_1_2.txt

hyb_protocol: Procedure established by Agilent

scan_protocol: data were extracted from the scanned image using Feature Extraction version 10.2 (Agilent technologies)

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters.
Supplementary file processed_data.txt reports normalized data fold changes (control/test) data.

source_name: Dentritic cells exposed to Lactobacillus (MOI 10^4 CFU)

label_protocol: Cy5 (control) and Cy3 (10e3 or 10e7 CFU) were synthetised using the Quick Amp kit (Agilent) with 500 ng of total RNA as a matrix

growth_protocol: Dendritic cells were generated from peripheral blood mononuclear cells isolated from buffy-coat of healthy volunteers.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen) and quantification and qualification assessments were performed using a Qubit fluorometer (Quant-iT RNA assay kit,Invitrogen)

treatment_protocol: Dendritic cells were incubated with either 10e4 or 10e7 CFU of Lactobacillus rhamnosus Lcr35 for 3 hours.

value: Dendritic cells

value: Lactobacillus rhamnosus Lcr35

tag: dose

value: MOI 10^4 CFU

source_name: Dentritic cells non exposed


title: PBC_control_validation_4

value: FVB/NJ


title: 13912487 - WS D2 vs ss4-phs1 D2

hyb_protocol: ss4-phs1 D2 Cy5 / WS D2 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.

source_name: ss4-phs1 D2

source_name: WS D2

value: Arabidopsis thaliana (wassilewskija); age:5 week


title: CEMx174-RSS-1

source_name: CEMx174, RSS infected

value: RSS infected


title: PBC_control_validation_2

value: total white blood cells (WBCs)

value: validation


title: PBC_control_validation_6

value: wild type


title: 13912488 - ss4-phs1 D2 vs WS D2

hyb_protocol: WS D2 Cy5 / ss4-phs1 D2 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: CEMx174-HIV-1-2

source_name: CEMx174, HIV-1 NL4-3 infected

value: HIV-1 NL4-3 infected


title: CEMx174-Mock-1

source_name: CEMx174, mock infected

value: mock infected


title: CEMx174-HIV-1-1


title: 13832811 - phs1 D3 vs WS D3

hyb_protocol: WS D3 Cy5 / phs1 D3 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.

source_name: phs1 D3

value: Arabidopsis thaliana (wassilewskija)  mutant (phs1-); age:5 week


title: 13912485 - WS D1 vs ss4-phs1 D1

hyb_protocol: ss4-phs1 D1 Cy5 / WS D1 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.

source_name: ss4-phs1 D1

source_name: WS D1


title: CEMx174-RSS-2

value: lymphocyte


title: CD7

description: US83000163_251485026557_S01_GE2-v5_10_Apr08_1_1.txt

source_name: Dentritic cells exposed to Lactobacillus (MOI 10^7 CFU)

value: MOI 10^7 CFU


title: TOM1 STI571 10uM + RI-BPI 20uM

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description:
Agilent Feature Extraction file 12_75_TOM1_S_B.txt linked below as supplementary file.
Gene expression after 24 hours of 10 μM STI571 and 20 μM RI-BPI in TOM1

hyb_protocol: Agilent Hyb Protocol. cRNA was fragmented to uniform size and verified on the Bioanalyzer. Agilent-014850 Whole Human Genome Microarrays 4x44K were hybridized with the cRNA target

scan_protocol: Agilent Technologies G2505C Scanner

data_processing: Data was processed by Agilent Feature Extraction and GeneSpring GX 10.0 softwares

source_name: TOM1 STI571 10uM + RI-BPI 20uM

label_protocol: Agilent Labeling Protocol. Biotinylated cRNA were prepared according to the standard Agilent protocol.

extract_protocol: Sample Extraction Protocol. Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

value: Ph+ ALL cell line TOM-1


title: PBC_MMTV-MYC_training_32

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse

value: training


title: PBC_control_validation_1

source_name: PBCs from tumor-free FVB/N mice matched for age and parity.

value: tumor-free control


title: CEMx174-Mock-2


title: 13912486 - ss4-phs1 D1 vs WS D1

hyb_protocol: WS D1 Cy5 / ss4-phs1 D1 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.

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4- phs1-); age:5 week


title: PBC_control_validation_3

value: FVB/NJ


title: SUP-B15 STI571 10uM + RI-BPI 20uM

description:
Agilent Feature Extraction file 9_62_SUPB15_S_B.txt linked below as supplementary file.
Gene expression after 24 hours of 10 μM STI571 and 20 μM RI-BPI in SUP-B15

source_name: SUP-B15 STI571 10uM + RI-BPI 20uM

value: Ph+ ALL cell line SUP-B15


title: TOM1 Control

description:
Agilent Feature Extraction file 10_75_TOM1_C.txt linked below as supplementary file.
Gene expression in absence of STI157 and RI-BPI in TOM1

source_name: TOM1 Control

value: control


title: 13832810 - WS D3 vs phs1 D3

hyb_protocol: phs1 D3 Cy5 / WS D3 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.

source_name: WS D3

value: Arabidopsis thaliana (wassilewskija); age:5 week


title: PBC_MMTV-MYC_training_29

value: total white blood cells (WBCs)


title: PBC_MMTV-MYC_training_30


title: SUP-B15 STI571 10uM

description:
Agilent Feature Extraction file 8_64_SUPB15_S.txt linked below as supplementary file.
Gene expression after 24 hours of 10 μM STI571 in SUP-B15

source_name: SUP-B15 STI571 10uM


title: SUP-B15 Control

description:
Agilent Feature Extraction file 7_64_SUPB15_C.txt linked below as supplementary file.
Gene expression in absence of STI157 and RI-BPI in SUP-B15

source_name: SUP-B15 Control


title: TOM1 STI571 10uM

description:
Agilent Feature Extraction file 11_75_TOM1_S.txt linked below as supplementary file.
Gene expression after 24 hours of 10 μM STI571 in TOM1

source_name: TOM1 STI571 10uM


title: PBC_MMTV-MYC_training_27


title: BV173 STI571 10uM + RI-BPI 20uM

description:
Agilent Feature Extraction file 3_62_BV173_S_B.txt linked below as supplementary file.
Gene expression after 24 hours of 10 μM STI571 and 20 μM RI-BPI in BV173

source_name: BV173 STI571 10uM + RI-BPI 20uM

value: Ph+ ALL cell line BV-173


title: PBC_MMTV-MYC_training_31


title: 13832807 - phs1 D1 vs WS D1

hyb_protocol: WS D1 Cy5 / phs1 D1 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.

source_name: phs1 D1


title: 13832806 - WS D1 vs phs1 D1

hyb_protocol: phs1 D1 Cy5 / WS D1 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: PBC_MMTV-MYC_training_28

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.


title: 13832808 - WS D2 vs phs1 D2

hyb_protocol: phs1 D2 Cy5 / WS D2 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.

source_name: phs1 D2

extract_protocol: phs1 D2:18ug.

source_name: WS D2


title: 13832805 - ss4w D3 vs WS D3

hyb_protocol: WS D3 Cy5 / ss4w D3 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.

source_name: ss4w D3

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4-); age:5 week


title: PBC_MMTV-MYC_training_26


title: Aorta_no stimulation_ex vivo

city: Fukuoka

first: Hisanori

last: Nishio

address: Maidashi 3-1-1, Higashi-ku

department: Pediatrics

country: Japan

institute: Kyushu University

description: Aorta, no stimulation, 24hours, ex vivo

hyb_protocol: Hybridization was performed for 19h at 42C to the mouse Nimblegen Gene Expression arrays　(090901_MM9_EXP_HX12, Roche NimbleGen, Madison, WI, USA) .

scan_protocol: GeneChips were scanned using the Gene Pix 4000B (Molecular Devices Corporation) .

data_processing: The raw data (tif.) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.5. (Roche NimbleGen, Inc.).

source_name: Aorta, no stimulation, 24hours, ex vivo

label_protocol: Nimblegen one-color cy3 labeling

extract_protocol: Total RNA was extracted using the RNeasy Fibrous Tissue (Qiagen Inc., Valencia, CA, USA) and amplified using Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Austin, TX, USA). RNA quality and concentration was determined by analysis with NanoDrop at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: In vivo study, aortic root, pulmonary artery, aorta and spleen were isolated from mice in 3 groups: 1) intraperitoneal injection of 20mg of LPS priming only, 2) oral administration of FK565 (100mg) for consecutive days 3) oral administration of FK565 (100mg) for consecutive days 1 day after LPS priming, at day 2, 4, and 7. Ex vivo study, each tissue of aortic root, pulmonary artery and aorta sterilely isolated from mice (BALB/c) was cultured in a 96-well plate with EBM-2 medium and EGM-2 (Lonza) in the presence of   FK565 (10μg/mL, N=6) or none (N=6) in a CO2 (5%) incubator at 37°C for 24 hours.

value: female

value: BALB/c

value: 5 week old

value: Aorta


title: PBC_MMTV-MYC_training_25


title: BV173 STI571 10uM

description:
Agilent Feature Extraction file 2_62_BV173_S.txt linked below as supplementary file.
Gene expression after 24 hours of 10 μM STI571 in BV173


title: Manduca sexta male antenna, animal 10-12

description: pooled from 3 animals

hyb_protocol: 1,600 ng of cyanine 3 labeled cRNA was used for each array and hybridization was carried out at 65oC for 17 hours. Slides were washed in GE Wash Buffers according to the manufacturer´s instructions (Agilent Technologies). Slides were treated in Stabilization and Drying Solution and scanned.

value: male

value: Adult antenna


title: PBC_MMTV-MYC_training_24

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse


title: HaCaT_edelfosine_Block_B

city: Berlin

first: Geo

last: Semini

address: Oudenarderstrasse 16

department: Institute for Biochemie

institute: Charité - Universitätmedizin

description: Gene expression after 24h in 5µM edelfosine stimulated HaCaT cells

hyb_protocol: All samples were hybridized to Agilent whole human genome microarray kit 44K (G4112A) according to the manufacturer´s instructions (One-Color Microarray-Based Gene Expression Analysis; Version 5.7).

scan_protocol: Arrays were scanned with the use of a GenePix 4000A Scanner (Axon Instruments-Molecular Devices, Sunnyvale, USA).

data_processing: The scanned images were analyzed with Feature Extraction Software (version 9.5.3) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Data files from Feature Extraction were imported into GeneSpring® GX software version 10 (Agilent Technologies) and analyzed using GeneSpring® default settings.

source_name: HaCaT cells, with edelfosine, 24h, replicate B

label_protocol: 200 ng of total RNA were used for production of fluorescent (Cyanine-3) cRNA as described in the Agilent analysis instruction manual for One-Color Microarray-Based Gene Expression Analysis (Agilent Technologies, Palo Alto, USA). Amplified cRNA was purificated using RNAeasy mini spin columns and subsequently quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: HaCaT cells were grown in RPMI medium supplemented with heat-inactivated fetal bovine serum (10 %), penicillin (100 U/ml), streptomycin (0.1 mg/ml) and L-glutamine (440 mg/l). One day prior to experimentation, cells were adapted to defined keratinocyte serum-free medium with growth supplement (including insulin, EGF, and FGF).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit in accordance to the manufacturer instructions (Qiagen Hilden, Germany). The integrity of RNA was verified by the presence of the 28S and 18S rRNA on agarose gels and an A260/280 ratio in the range of 1.9–2.1.

treatment_protocol: The assay was performed in defined keratinocytes serum-free medium without growth supplement. Cells were treated with respectively 5 µM Ino-C2-PAF, GlcPAF and edelfosine or left untreated (control) 24 h.

value: HaCaT

value: edelfosine


title: Pulmonary artery_no stimulation_ex vivo

description: pulmonary artery, no stimulation, 24hours, ex vivo

value: pulmonary artery


title: HaCaT_edelfosine_Block_C

source_name: HaCaT cells, with edelfosine 24h, replicate C


title: 13832809 - phs1 D2 vs WS D2

hyb_protocol: WS D2 Cy5 / phs1 D2 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.

value: Arabidopsis thaliana (wassilewskija)  mutant (phs1-); age:5 week


title: HaCaT_edelfosine_Block_A

source_name: HaCaT cells, with edelfosine, 24h, replicate A


title: PBC_MMTV-MYC_training_23

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

value: FVB/NJ

value: training


title: BV173 Control

description:
Agilent Feature Extraction file 1_62_BV173_C.txt.txt linked below as supplementary file.
Gene expression in absence of STI157 and RI-BPI in BV173

source_name: BV173 Control

value: control


title: 13832802 - WS D2 vs ss4w D2

hyb_protocol: ss4w D2 Cy5 / WS D2 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.

source_name: ss4w D2

extract_protocol: ss4w D2:7ug.

value: Arabidopsis thaliana (wassilewskija); age:5 week


title: Pulmonary artery_FK_ex vivo

description: pulmonary artery, FK stimulation, 24hours, ex vivo


title: Aorta_FK_ex vivo

description: Aorta, FK stimulation, 24hours, ex vivo

source_name: Aorta, FK stimulation, 24hours, in vitro


title: NB1 5mC

type: genomic

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: 5mC profile in NB1 sample

hyb_protocol: standard NimbleGen Protocol

scan_protocol: standard NimbleGen Protocol

data_processing: Loess normalization was applied exclusing top 5% probes with the largest original Cy5/Cy3 log2 ratio

molecule: genomic DNA

source_name: NB1  5mC (MIRA) enriched samples

label_protocol: standard NimbleGen Protocol

extract_protocol: DNeasy Blood and Tissue kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).

treatment_protocol: No Treatment

value: Frontal Lobe

tag: enrichment procedure

value: 5mC (MIRA)

tag: purification method

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: brain frontal lobe

source_name: NB1 input DNA

treatment_protocol: No treatment

tag: sample type

value: input DNA


title: 13832803 - ss4w D2 vs WS D2

hyb_protocol: WS D2 Cy5 / ss4w D2 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.

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4-); age:5 week


title: Aortic root_no stimulation_ex vivo

description: aortic root, no stimulation, 24hours, ex vivo

value: female

tag: strain

value: BALB/c

value: 5 week old

value: aortic root


title: HaCaT_GlcPAF_Block_B

description: Gene expression after 24h in 5µM GlcPAF stimulated HaCaT cells

source_name: HaCaT cells, with GlcPAF, 24h, replicate B

value: HaCaT

value: GlcPAF


title: HaCaT_GlcPAF_Block_C

source_name: HaCaT cells, with GlcPAF, 24h, replicate C


title: 13832804 - WS D3 vs ss4w D3

description: What is the impact of the absence of different genes related to the starch metabolism on the global gene expression in Arabidopsis leaves.

hyb_protocol: ss4w D3 Cy5 / WS D3 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.

source_name: WS D3


title: 13832801 - ss4w D1 vs WS D1

hyb_protocol: WS D1 Cy5 / ss4w D1 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.

source_name: WS D1

source_name: ss4w D1


title: NB2 5hmC

description: 5hmC profile in NB2 sample

source_name: NB2 5hmC enriched samples

tag: tissue

tag: antibodies/kit  information

value: polyclonal anti-5hmC antibody from Active Motif (Carlsbad, CA)

tag: chip antibody

value: polyclonal anti-5hmC antibody

tag: antibody manufacturer

value: Active Motif (Carlsbad, CA)

tag: antibody catalog #

tag: antibody lot #

source_name: NB2 input DNA


title: PBC_MMTV-MYC_training_22

extract_protocol:
Samples were collected using the submandibular (cheekpouch) method. Briefly, the vein that drains the face and cheek area was punctured by a lancet (GoldenRod animal lancet, MEDIpoint, Inc., Mineola, NY) and blood was captured in BD Microtainer™ tubes with potassium-EDTA anticoagulant (Becton Dickinson, Franklin Lakes, NJ). Tubes were immediately inverted 10-12 times and placed on ice.
Following erythrocyte lysis, total RNA was isolated from the leukocyte pellet using the QIAamp RNA Blood Mini Kit (Qiagen, Valencia, CA). Alternatively, the leukocyte pellet was immediately lysed, homogenized and stored at -80°C. RNA was isolated at a later date using the protocol described above or the adapted protocol associated with the QIAamp RNA Blood Mini Kit for use in the QIAcube (Qiagen, Valencia, CA).

value: FVB/NJ

tag: genotype/variation

value: MMTV/c-MYC transgenic

tag: phenotype

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

tag: data set

value: training


title: NB2 5mC

description: 5mC profile in NB2 sample

source_name: NB2  5mC (MIRA) enriched samples

value: Frontal Lobe

value: 5mC (MIRA)

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: brain frontal lobe


title: PBC_MMTV-MYC_training_20


title: Spleen_FK with LPS_day4

description: This sample is of  spleen of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days 1 day after LPS priming. Aortic valve were collected at day 4.

source_name: spleen, FK stimulation with LPS priming, 4day

treatment_protocol: In vivo study, aortic valve, pulmonary artery, aorta and spleen were isolated from mice in 3 groups: 1) intraperitoneal injection of 20mg of LPS priming only, 2) oral administration of FK565 (100mg) for consecutive days 3) oral administration of FK565 (100mg) for consecutive days 1 day after LPS priming, at day 2, 4, and 7. In vitro study, each tissue of aortic valve, pulmonary artery, aortic arch, and abdominal aorta (between roots of right and left renal arteries) sterilely isolated from mice (BALB/c) was cultured in a 96-well plate with EBM-2 medium and EGM-2 (Lonza) in the presence of   FK565 (10μg/mL, N=6) or none (N=6) in a CO2 (5%) incubator at 37°C for 24 hours.

tag: gender

value: female

value: BALB/c

tag: age

value: spleen


title: Spleen_FK with LPS_day7

description: This sample is of  spleen of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days 1 day after LPS priming. Aortic valve were collected at day 7.

source_name: spleen, FK stimulation with LPS priming, 7day

value: 5 week old


title: HaCaT_InoPAF_Block_B

description: Gene expression after 24h in 5µM InoPAF stimulated HaCaT cells

source_name: HaCaT cells, with InoPAF, 24h, replicate B

tag: cell line

value: HaCaT

tag: agent

value: InoPAF


title: HaCaT_InoPAF_Block_A

source_name: HaCaT cells, with InoPAF, 24h, replicate A


title: PBC_MMTV-MYC_training_21

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.


title: 13832697 - adg1 D3 vs WS D3

hyb_protocol: WS D3 Cy5 / adg1 D3 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: genotype

value: Arabidopsis thaliana (wassilewskija); age:5 week

source_name: adg1 D3

value: Arabidopsis thaliana (wassilewskija)  mutant (adg1-); age:5 week


title: Aortic root_FK_ex vivo

description: aortic root, FK stimulation, 24hours, ex vivo

value: aortic root


title: 13832694 - WS D2 vs adg1 D2

hyb_protocol: adg1 D2 Cy5 / WS D2 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.

source_name: adg1 D2

source_name: WS D2


title: 13832696 - WS D3 vs adg1 D3

hyb_protocol: adg1 D3 Cy5 / WS D3 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: HaCaT_GlcPAF_Block_A

source_name: HaCaT cells, with GlcPAF, 24h, replicate A

value: GlcPAF


title: HaCaT_InoPAF_Block_C

source_name: HaCaT cells, with InoPAF, 24h, replicate C


title: PBC_MMTV-MYC_training_17

value: FVB/NJ

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse


title: Spleen_FK with LPS_day2

description: This sample is of  spleen of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days 1 day after LPS priming. Aortic valve were collected at day 2.

source_name: spleen, FK stimulation with LPS priming, 2day


title: PBC_MMTV-MYC_training_18

value: total white blood cells (WBCs)

value: training


title: 13832693 - adg1 D1 vs WS D1

hyb_protocol: WS D1 Cy5 / adg1 D1 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.

source_name: adg1 D1


title: PBC_MMTV-MYC_training_19


title: 13832695 - adg1 D2 vs WS D2

hyb_protocol: WS D2 Cy5 / adg1 D2 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: Spleen_FK_day7

description: This sample is of  spleen of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days. Aortic valve were collected at day 7.

source_name: spleen, FK stimulation, 7day


title: 13832692 - WS D1 vs adg1 D1

hyb_protocol: adg1 D1 Cy5 / WS D1 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.

source_name: WS D1


title: Spleen_LPS_day7

description: This sample is of  spleen of mice(BALB/c) which was intraperitoneally injected with 20 ug of LPS priming(day0). Aortic valve were collected at day 7.

source_name: spleen, LPS priming, 7day


title: PBC_MMTV-MYC_training_16

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on Mouse Genome M430 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.


title: HaCaT_Control_Block_C

description: Gene expression after 24h in unstimulated HaCaT cells

source_name: HaCaT cells, unstimulated, 24h, replicate C

value: control


title: PBC_MMTV-MYC_training_15


title: HaCaT_Control_Block_A

source_name: HaCaT cells, unstimulated, 24h, replicate A


title: Spleen_FK_day4

description: This sample is of  spleen of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days. Aortic valve were collected at day 4.

source_name: spleen, FK stimulation, 4day


title: NB1 5hmC

description: 5hmC profile in NB1 sample

source_name: NB1 5hmC enriched samples

value: Frontal Lobe

tag: enrichment procedure

value: polyclonal anti-5hmC antibody from Active Motif (Carlsbad, CA)

value: polyclonal anti-5hmC antibody

value: Active Motif (Carlsbad, CA)

value: brain frontal lobe

source_name: NB1 input DNA

value: input DNA


title: PBC_MMTV-MYC_training_14


title: Spleen_FK_day2

description: This sample is of  spleen of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days. Aortic valve were collected at day 2.

source_name: spleen, FK stimulation, 2day

value: female

value: BALB/c

value: 5 week old

value: spleen


title: Spleen_LPS_day4

description: This sample is of  spleen of mice(BALB/c) which was intraperitoneally injected with 20 ug of LPS priming(day0). Aortic valve were collected at day 2.

source_name: spleen, LPS priming, 4day


title: 13832691 - ss3-ss4 N3 vs Col0 N3

hyb_protocol: Col0 N3 Cy5 / ss3-ss4 N3 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.

source_name: Col0 N3

extract_protocol: Col0 N3:18ug.

value: Arabidopsis thaliana (col-0); age:5 week

source_name: ss3-ss4 N3

value: Arabidopsis thaliana (col-0)  mutant (ss3- ss4-); age:5 week


title: PBC_MMTV-MYC_training_11

source_name: PBCs from MMTV/c-MYC mice with advanced mammary tumors.

value: FVB/NJ

value: MMTV/c-MYC transgenic


title: 13832800 - WS D1 vs ss4w D1

hyb_protocol: ss4w D1 Cy5 / WS D1 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.

source_name: ss4w D1

value: Arabidopsis thaliana (wassilewskija)  mutant (ss4-); age:5 week

value: Arabidopsis thaliana (wassilewskija); age:5 week


title: HaCaT_Control_Block_B

source_name: HaCaT cells, unstimulated, 24h, replicate B

value: HaCaT

value: control


title: Aorta_FK with LPS_day7

description: This sample is of aorta of mice(BALB/c) which was oral administrated of FK565 (100ug) for consecutive days 1 day after LPS priming. Aortic valve were collected at day 7.

hyb_protocol: Hybridization was performed for 19h at 42C to the mouse Nimblegen Gene Expression arrays　(090901_MM9_EXP_HX12, Roche NimbleGen, Madison, WI, USA) .

source_name: aorta, FK stimulation with LPS priming, 7day

value: aorta


title: wild-type Mef2GAL4 / + leg muslce technical replicate 1

city: Vienna

first: Martin

last: Radolf

address: Dr.Bohrgasse 7

country: Austria

institute: IMP

hyb_protocol: Quick Amp Labeling Kit from Agilent according to provided protocol, using 825 ng labeled sample, hybridization with Agilent gasket sliedes in an Agilent Hybridization oven at 65°C

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1), scanned with Agilent Scanner G2505C at 5µm resolution,

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

organism: Drosophila melanogaster

label_protocol: Quick Amp Labeling Kit from Agilent according to provided protocol, 500 ng total RNA where amplified and labeled according manufactureres protocol

growth_protocol: Drosophila strains were crossed and grown under standard conditions at 27 ºC

extract_protocol: Total RNA was extracted using TriPure (Roche) according to the manufaturer

treatment_protocol: For indirect flight muscle isolation the thorax of 30 males (wild-type) or 60 males (salmIR) were bissected and the IFMs isolated with fine forceceps and stored for less than an hour in PBS on ice. For leg muscle isolation 360 legs from male flies were cut from the thorax and leg muscles dissect with forceps and stored for less than an hour in PBS on ice.

value: wild-type Mef2GAL4 / + leg muslce

source_name: Common Reference Sample-Pool from each Sample

tag: reference


title: PBC_MMTV-MYC_training_13

tag: strain

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

value: training


title: 13832690 - Col0 N3 vs ss3-ss4 N3

hyb_protocol: ss3-ss4 N3 Cy5 / Col0 N3 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: PBC_MMTV-MYC_training_10

tag: tissue


title: PBC_MMTV-MYC_training_12


title: wild-type Mef2GAL4 / + leg muslce replicate 2

value: Common Reference Sample-Pool from each Sample


title: 13832688 - ss3-ss4 N2 vs Col0 N2

hyb_protocol: Col0 N2 Cy5 / ss3-ss4 N2 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.

source_name: Col0 N2

source_name: ss3-ss4 N2


title: 13832687 - Col0 N2 vs ss3-ss4 N2

hyb_protocol: ss3-ss4 N2 Cy5 / Col0 N2 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: 13832686 - ss3-ss4 N1 vs Col0 N1

hyb_protocol: Col0 N1 Cy5 / ss3-ss4 N1 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.

source_name: Col0 N1

extract_protocol: Col0 N1:11ug.

source_name: ss3-ss4 N1