title: Spleen_LPS_day2

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 4.

source_name: spleen, LPS priming, 2day

value: female

value: BALB/c


title: wild-type Mef2GAL4 / + IFM replicate 3

status: Public on Mar 01 2011

type: RNA

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.

molecule: total RNA

organism: Drosophila melanogaster

source_name: wild-type Mef2GAL4 / + IFM replicate 3

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.

tag: genotype/variation

value: wild-type Mef2GAL4 / + IFM

source_name: Common Reference Sample-Pool from each Sample

tag: reference


title: wild-type Mef2GAL4 / + IFM technical replicate 3

value: Common Reference Sample-Pool from each Sample


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

value: wild-type Mef2GAL4 / + leg muslce


title: wild-type Mef2GAL4 / + IFM replicate 4

source_name: wild-type Mef2GAL4 / + IFM replicate 4


title: Aorta_FK with LPS_day2

city: Fukuoka

first: Hisanori

last: Nishio

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

department: Pediatrics

country: Japan

institute: Kyushu University

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 2.

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.).

organism: Mus musculus

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

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 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

tag: strain

tag: age

value: 5 week old

tag: tissue

value: aorta


title: 13832685 - Col0 N1 vs ss3-ss4 N1

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: ss3-ss4 N1 Cy5 / Col0 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.

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: ss3-ss4 N1

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

source_name: Col0 N1

extract_protocol: Col0 N1:11ug.

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


title: PBC_MMTV-MYC_training_9

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

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).

value: FVB/NJ

value: MMTV/c-MYC transgenic

tag: phenotype

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

tag: data set

value: training


title: Aorta_FK with LPS_day4

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 4.

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


title: salmIR(TF3029) / Mef2GAL4 technical replicate 1

source_name: salmIR(TF3029) / Mef2GAL4 replicate 1

value: salmIR(TF3029) / Mef2GAL4


title: salmIR(TF10152) / Mef2GAL4 technical replicate 1

value: salmIR(TF10152) / Mef2GAL4


title: salmIR(TF10152) / Mef2GAL4 replicate 2

source_name: salmIR(TF10152) / Mef2GAL4 replicate 2


title: Spleen_not stimulated

description: This sample is of spleen of mice(BALB/c) which was not stimulated.

source_name: spleen, no stimulation

value: spleen


title: 13832684 - ss3 N3 vs Col0 N3

hyb_protocol: Col0 N3 Cy5 / ss3 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.

source_name: ss3 N3

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


title: PBC_MMTV-MYC_training_7


title: salmIR(TF3029) / Mef2GAL4 replicate 2

source_name: salmIR(TF3029) / Mef2GAL4 replicate 2


title: PBC_MMTV-MYC_training_3


title: Aorta_FK_day4

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

source_name: aorta, FK stimulation, 4day

value: female

value: BALB/c


title: PBC_MMTV-MYC_training_4


title: Aorta_LPS_day2

description: This sample is of aorta of mice(BALB/c) which was intraperitoneally injected with 20 ug of LPS priming (day0). Aortic valve were collected at day 4.

source_name: aorta, LPS priming, 2day


title: PBC_MMTV-MYC_training_5


title: PBC_MMTV-MYC_training_8


title: 13832683 - Col0 N3 vs ss3 N3

hyb_protocol: ss3 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_6


title: 13832676 - ss4c N2 vs Col0 N2

hyb_protocol: Col0 N2 Cy5 / ss4c 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: ss4c N2

extract_protocol: ss4c N2:20ug.

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


title: Aorta_FK_day2

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

source_name: aorta, FK stimulation, 2day


title: 13832678 - ss4c N3 vs Col0 N3

hyb_protocol: Col0 N3 Cy5 / ss4c 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: ss4c N3


title: Aorta_FK_day7

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

source_name: aorta, FK stimulation, 7day


title: PBC_MMTV-MYC_training_2


title: 13832673 - Col0 N1 vs ss4c N1

hyb_protocol: ss4c N1 Cy5 / Col0 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: ss4c N1


title: wild-type Mef2GAL4 / + IFM technical replicate 1

value: wild-type Mef2GAL4 / + IFM

source_name: Common Reference Sample-Pool from each Sample


title: 13832667 - ss4c D3 vs Col0 D3

hyb_protocol: Col0 D3 Cy5 / ss4c 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: Col0 D3

source_name: ss4c D3


title: Pulmonary artery_FK with LPS_day7

description: This sample is of pulmonary artery 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: pulmonary artery, FK stimulation with LPS priming, 7day

value: 5 week old

value: pulmonary artery


title: salmIR(TF10152) / Mef2GAL4 replicate 1

source_name: salmIR(TF10152) / Mef2GAL4 replicate 1

value: Common Reference Sample-Pool from each Sample


title: 13832674 - ss4c N1 vs Col0 N1

hyb_protocol: Col0 N1 Cy5 / ss4c 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

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


title: 13832675 - Col0 N2 vs ss4c N2

hyb_protocol: ss4c 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: Aorta_LPS_day7

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

source_name: aorta, LPS priming, 7day

value: aorta


title: salmIR(TF3029) / Mef2GAL4 replicate 1

source_name: salmIR(TF3029) / Mef2GAL4 replicate 1


title: PBC_control_training_14

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

value: FVB/NJ

value: wild type

value: tumor-free control


title: wild-type Mef2GAL4 / + IFM replicate 2

source_name: wild-type Mef2GAL4 / + IFM replicate 2


title: Aorta_not stimulated

description: This sample is of aorta of mice(BALB/c) which was not stimulated.

source_name: aorta, no stimulation


title: PBC_MMTV-MYC_training_1

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

value: MMTV/c-MYC transgenic

value: tumor-bearing transgenic mouse

value: total white blood cells (WBCs)

value: training


title: Aorta_LPS_day4

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

source_name: aorta, LPS priming, 4day


title: 13832677 - Col0 N3 vs ss4c N3

hyb_protocol: ss4c 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.

source_name: Col0 N3


title: Pulmonary artery_FK with LPS_day2

description: This sample is of pulmonary artery 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: pulmonary artery, FK stimulation with LPS priming, 2day


title: Pulmonary artery_FK_day7

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

source_name: pulmonary artery, FK stimulation, 7day


title: wild-type Mef2GAL4 / + IFM replicate 1

source_name: wild-type Mef2GAL4 / + IFM replicate 1


title: 13832666 - Col0 D3 vs ss4c D3

hyb_protocol: ss4c D3 Cy5 / Col0 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: 13832663 - Col0 D3 vs ss3-ss4 D3

hyb_protocol: ss3-ss4 D3 Cy5 / Col0 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: ss3-ss4 D3

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


title: PBC_control_training_8


title: PBC_control_training_11


title: PBC_control_training_13


title: 13832664 - ss3-ss4 D3 vs Col0 D3

hyb_protocol: Col0 D3 Cy5 / ss3-ss4 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: Col0 D3


title: PBC_control_training_12


title: Pulmonary artery_FK with LPS_day4

description: This sample is of pulmonary arterye 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: pulmonary artery, FK stimulation with LPS priming, 4day

value: female


title: 13832658 - Col0 D1 vs ss3-ss4 D1

hyb_protocol: ss3-ss4 D1 Cy5 / Col0 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: ss3-ss4 D1

source_name: Col0 D1


title: 13832659 - ss3-ss4 D1 vs Col0 D1

hyb_protocol: Col0 D1 Cy5 / ss3-ss4 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_training_10


title: Pulmonary artery_LPS_day7

description: This sample is of pulmonary artery of mice(BALB/c) which was intraperitoneally injected with 20 ug of LPS priming(day0). 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: pulmonary artery, LPS priming, 7day

value: BALB/c


title: PBC_control_training_9


title: Pulmonary artery_FK_day2

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

source_name: pulmonary artery, FK stimulation, 2day


title: Pulmonary artery_LPS_day4

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

source_name: pulmonary artery, LPS priming, 4day


title: Pulmonary artery_FK_day4

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

source_name: pulmonary artery, FK stimulation, 4day


title: Pulmonary artery_LPS_day2

description: This sample is of pulmonary artery of mice(BALB/c) which was intraperitoneally injected with 20 ug of LPS priming (day0). Aortic valve were collected at day 4.

source_name: pulmonary artery, LPS priming, 2day


title: low dose 18h, replicate 1

city: Helsinki

first: Massimiliano

last: Gentile

state: Finland

address: Haartmaninkatu 8

department: Biomedicum Bioinformatics Unit

country: Finland

institute: Biomedicum Helsinki

description: ATCC number CRL-1502

organism: Homo sapiens

source_name: WS1 human skin fibroblasts


title: 13832657 - ss3 D2 vs Col0 D2

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: Col0 D2 Cy5 / ss3 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: Col0 D2

source_name: ss3 D2

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


title: 13832660 - Col0 D2 vs ss3-ss4 D2

hyb_protocol: ss3-ss4 D2 Cy5 / Col0 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: ss3-ss4 D2


title: 13832670 - ss3-ss4 D2 vs Col0 D2

hyb_protocol: Col0 D2 Cy5 / ss3-ss4 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: 13832665 - ss4c D2 vs Col0 D2

hyb_protocol: Col0 D2 Cy5 / ss4c 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: ss4c D2

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


title: PBC_control_training_6

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.

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


title: Pulmonary artery_not stimulated

description: This sample is of pulmonary artery of mice(BALB/c) which was not stimulated.

source_name: pulmonary artery, no stimulation

value: 5 week old


title: PBC_control_training_3


title: 13832653 - ss3 D1 vs Col0 D1

hyb_protocol: Col0 D1 Cy5 / ss3 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: ss3 D1

extract_protocol: ss3 D1:6ug.


title: Aortic root_FK with LPS_day7

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

source_name: aortic valve, FK stimulation with LPS priming, 7day

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. In vitro 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: aortic root


title: 13832656 - Col0 D2 vs ss3 D2

hyb_protocol: ss3 D2 Cy5 / Col0 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: Aortic root_FK with LPS_day2

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

source_name: aortic valve, FK stimulation with LPS priming, 2day


title: PBC_control_training_4


title: Aortic root_FK with LPS_day4

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

source_name: aortic root, FK stimulation with LPS priming, 4day


title: PBC_control_training_5


title: PBC_control_training_2


title: Aortic root_FK_day7

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

source_name: aortic valve, FK stimulation, 7day


title: 13832654 - Col0 D2 vs ss4c D2

hyb_protocol: ss4c D2 Cy5 / Col0 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_training_7


title: 13832652 - Col0 D1 vs ss3 D1

hyb_protocol: ss3 D1 Cy5 / Col0 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: Col0 D1


title: BM stroma Ep300+/-, biological rep4

city: San Antonio

first: Vivienne

last: Rebel

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSCSA

description: Gene expression data from primary bone marrow stroma derived from Ep300+/- mice

hyb_protocol: Followed standard Affymetrix protocols

scan_protocol: Followed standard Affymetrix protocols

data_processing: The data were normalized using the Bioconductor GCRMA package, generating log2 scale gene expression data. Probe sets with intensities below log2(100) in at least 25% of the samples were excluded, as well as those with variance so small that differential expression was undetectable (i.e., genes for which the interquartile range was <0.5).

source_name: Primary bone marrow stroma from Ep300+/- mice

label_protocol: Followed standard Affymetrix protocols

growth_protocol: Bone marrow was plated in M5300 media for 2 weeks to establish a stroma layer. The stroma layer was then irradiated with 1500 cGy and a complete media change was performed.

extract_protocol: Total RNA was isolated from primary bone marrow stroma cells using the RNeasy Midi Kit (Qiagen) according the manufacture's instruction

value: Pimary bone marrow stroma

value: 3-4 months


title: BM stroma Ep300+/-, biological rep3


title: Aortic root_FK_day4

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

source_name: aortic root, FK stimulation, 4day


title: 13832651 - ss4c D1 vs Col0 D1

hyb_protocol: Col0 D1 Cy5 / ss4c 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 (col-0); age:5 week

source_name: ss4c D1


title: Aortic root_LPS_day7

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

source_name: aortic root, LPS priming, 7day


title: Aortic root_LPS_day4

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

source_name: aortic root, LPS priming, 5day


title: BM stroma Ep300+/-, biological rep2


title: BM stroma Ep300+/-, biological rep1


title: Aortic root_FK_day2

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

source_name: aortic root, FK stimulation, 2day


title: 13832650 - Col0 D1 vs ss4c D1

hyb_protocol: ss4c D1 Cy5 / Col0 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: Aortic root_LPS_day2

description: This sample is of aortic valve of mice(BALB/c) which was intraperitoneally injected with 20 ug of LPS priming (day0). Aortic valve were collected at day 4.

source_name: aortic root, LPS priming, 2day


title: PBC_control_training_1

value: FVB/NJ


title: BM stroma Crebbp+/-, biological rep4

description: Gene expression data from primary bone marrow stroma derived from Crebbp+/- mice

source_name: Primary bone marrow stroma from Crebbp+/- mice

value: Crebbp+/-


title: BM stroma Crebbp+/-, biological rep3


title: BM stroma Crebbp+/-, biological rep2


title: HPAEC_none

description: This sample is of HPAEC not stimulated.

hyb_protocol: Hybridization was performed for 19h at 42C to the human Nimblegen Gene Expression arrays　(090828_HG18_opt_expr_HX12, Roche NimbleGen, Madison, WI, USA) .

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: HPAEC, no stimulation, 24hours

growth_protocol: HCAEC and HPAEC were cultured in EBM-2 medium with EGM-2MV and EGM-2 (Lonza), respectively, in a CO2 (5%) incubator at 37°C. These cells were used for experiments between passages 6 and 10.

treatment_protocol: HCAEC and HPAEC were stimulated with FK565 (10mg/mL) or LipidA(100ng/mL) for 24 hour in 12-well plates (1×104 cells/cm2)

tag: cell type

value: pulmonary artery endothelial cell

tag: treatment


title: Aortic root_not stimulated

description: This sample is of aortic root of mice(BALB/c) which was not stimulated.

source_name: aortic root, no stimulation

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. In vitro study, each tissue of aortic root, pulmonary artery and aortic arch  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.


title: SMC-4_WT_EMB_rep2_BP-82

type: genomic

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

hyb_protocol: Hybridization protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

scan_protocol: Sample scan protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

data_processing: Log base 2 ratios of experimental/input were determined using SignalMap v2.5. No normalization.

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: wild type N2 XX embryo

label_protocol: Sample labeling protocol provided and performed by the FHCRC Genomics Facility using standard NimbleGen protocol

growth_protocol: Worms grown on NG agar with E. coli HB101

extract_protocol: Extracts from wild type N2 XX, sdc-2mut (y93,RNAi) XX, sdc-2mut TY2222 XO, sdc-3mut TY2205 XO, dpy-27mut TY2470 XO, dpy-30mut TY1119 XX, and X:V fusion ypT28 XX embryos were created as published in Pferdehirt et al.  Briefly, gravid hermaphrodites were bleached and crosslinked with 2% formaldehyde in M9 at room temperature for 30 minutes.  Crosslinking was quenched with 100mM Tris-HCl (pH 7.5).  Embryos were resuspended and frozen in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF).  Samples were sheared with a sonicator.  Samples were then sheared using a sonicator.  Immunoprecipitations were performed with the appropriate antibody (as displayed in the beginning of each sample name) and were washed and processed as described in Pferdehirt et al.

value: wild type N2

value: XX

tag: developmental stage

value: embryo

tag: sample type

value: input

value: ChIP fraction

tag: chip antibody

tag: chip antibody provider

value: Meyer Lab polyclonal rb2655


title: BM stroma Crebbp+/-, biological rep1


title: DPY-27_WT_EMB_rep 1

data_processing: Log base 2 ratios of experimental/input were determined using SignalMap v2.5.  For comparison with gene expression, the dynamic range of embryo and fed L1 ChIP- chip experimental values were normalized using STATA SE 9.2 (StataCorp LP).

extract_protocol: Extracts from wild type N2 XX embryos were created as published in Pferdehirt et al.  Briefly, gravid hermaphrodites were bleached and crosslinked with 2% formaldehyde in M9 at room temperature for 30 minutes.  Crosslinking was quenched with 100mM Tris-HCl (pH 7.5).  Embryos were resuspended and frozen in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF).  Samples were sheared with a sonicator. To collect fed L1 worms for ChIP-chip, gravid hermaphrodites were bleached and embryos were synchronized in M9 for 24 hours at 20 degrees celcius.  Synchronous L1s were fed for 3 hours with HB101 in liquid culture.  They were then crosslinked in 2% formaldehyde in M9 for 30 minutes at 20 degrees celcius and quenched with 100mM Tris-HCl. They were washed in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF, PI inhibitor cocktail (EMD Biosciences)) and frozen.  Samples were then ground by mortar and pestle under liquid nitrogen and were resuspended in Homogenization buffer and snap frozen.  Samples were then sheared using a sonicator.  Immunoprecipitations were performed with the appropriate antibody (as displayed in the beginning of each sample name) and were washed and processed as described in Pferdehirt et al.

value: Meyer Lab polyclonal rb699


title: HCAEC_none

description: This sample is of HCAEC not stimulated.

source_name: HCAEC, no stimulation, 24hours

value: coronary artery endothelial cell


title: HPAEC_LipidA

description: This sample is of HPAEC stimulated by FK565 (10μg/mL) for 24 hours.

source_name: HPAEC, LipidA stimulation, 24hours

value: LipidA (100ng/mL)


title: SMC-4_WT_EMB_rep1_BP-10

treatment_protocol: Briefly, gravid hermaphrodites were bleached and crosslinked with 2% formaldehyde in M9 at room temperature for 30 minutes.  Crosslinking was quenched with 100mM Tris-HCl (pH 7.5).  Embryos were resuspended and frozen in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF).  Samples were sheared with a sonicator.


title: SDC-3_dpy30mut_TY1119_rep2

source_name: dpy-30 mutant TY1119 XX embryo

value: dpy-30 mutant TY1119

value: Meyer Lab polyclonal rb1079


title: BM stroma Wildtype, biological rep3

description: Gene expression data from primary bone marrow stroma derived from Wildtype mice

source_name: Primary bone marrow stroma from Wild-type mice

value: Pimary bone marrow stroma

value: Wild-type


title: BM stroma Wildtype, biological rep4

value: 3-4 months


title: HPAEC_FK

description: This sample is of HPAEC stimulated by LipidA (100ng/mL) for 24 hours.

source_name: HPAEC, FK stimulation, 24hours


title: HCAEC_LipidA

description: This sample is of HCAEC stimulated by FK565 (10μg/mL) for 24 hours.

source_name: HCAEC, LipidA stimulation, 24hours


title: SDC-3_sdc2mut_TY2222_EMB_rep2

source_name: sdc-2 mutant TY2222 XO hermaphrodite embryo

value: sdc-2 mutant TY2222

value: XO


title: SDC-3_WT_EMB_rep1


title: HCAEC_FK

description: This sample is of HCAEC stimulated by LipidA (100ng/mL) for 24 hours.

source_name: HCAEC, FK stimulation, 24hours


title: SDC-3_sdc2mut_TY2222_EMB_rep1


title: SDC-3_dpy30mut_TY1119_rep1


title: BM stroma Wildtype, biological rep1


title: BM stroma Wildtype, biological rep2


title: NK1

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression values were obtained from flow-sorted lymphocytes.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml (6 ul per reaction).

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

data_processing: Gene expression values were normalized with the RMA algorithm in the Affy BioConductor package for the R environment (R version 2.10, Bioconductor version 2.5). The data were analyzed with a custom CDF environment created by the MBNI, University of Michigan. The version 12 Entrez Gene ID CDF was used.

source_name: NKTL (extranasal)

label_protocol: After cleanup of the double-stranded cDNA using the Affymetrix GeneChip Sample Cleanup Module (Part # 900371), 10 ug of sample cDNA was biotin-labeled with the Affymetrix IVT Labeling Kit (Part # 900449) for 16 hrs at 37 °C.  The biotin-labeled sample was then cleaned again with the Affymetrix GeneChip Sample Cleanup Module (Part # 900371), and 20 ug of the cleaned, biotin-labeled cDNA was fragmented at 94°C for 35 minutes prior to hybridization on the Affymetrix GeneChip Human Genome U133 Plus 2.0 array chip (Part # 900467).

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

tag: cell line

value: cultured cell line from a xenograft tumor derived from a primary NKTL lymphoma

tag: subtype

value: NKTL (extranasal)


title: PolII_S2_WT_EMB

tag: genotype/variation

value: wild type N2

value: XX

value: PolII

value: BethylLab

tag: chip antibody catalog#


title: SDC-3_WT_EMB_rep2

tag: gender

value: embryo

value: input

value: ChIP fraction


title: 9221 AITL

source_name: AITL

value: lymphoma

value: AITL


title: RmxA180_2:1PNA4.101

city: Chicago

first: Justin

last: Borevitz

state: IL

department: Ecology and Evolution

institute: University of Chicago

description: total RNA followed by poly A-RNA purification and double-stranded cDNA synthesis, labelled products were hybridized to the array in a total amount of 20ug

hyb_protocol: Standard hybridization protocol for tiling array from Affymetrix

scan_protocol: Affymetrix Scanner 7G, GeneChip Operating Software Version 1.4 (GCOS)

data_processing: Bioconductor package Affy

source_name: total RNA

label_protocol: Invitrogen Bioprime random labeling

extract_protocol: Qiagen RNeasy Plant Mini kit

value: leaf

value: F1 hybrid between accession RmxA180_2 and 1PNA4.101

value: 5th or 6th true leaf

tag: growth condition

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: PolII_S5_sdc2RNAi_EMB

source_name: sdc-2 mutant (y93, RNAi) XX embryo

growth_protocol: sdc-2(y93) grown on NG plates suplimented with 100 µg/ml carbinicillin and 1 µg/ml IPTG seeded with E. coli HT115 (DE3) carrying an RNAi vector to sdc-2

value: sdc-2 mutant (y93, RNAi)


title: NKO

value: xenograft tumor derived from a primary NKTL lymphoma


title: SDC-3_dpy27mut_TY2470_EMB_rep2

source_name: dpy-27 mutant TY2470 XO hermaphrodite embryo

value: dpy-27 mutant TY2470

value: XO

value: Meyer Lab polyclonal rb1079


title: FR209MIB:Mrk-0

value: F1 hybrid between accession FR209MIB and Mrk-0

tag: age


title: PolII_8WG16_WT_EMB

value: wild type N2

value: XX

value: PolII

value: Covance


title: SDC-3_dpy27mut_TY2470_EMB_rep1

value: embryo

value: input

value: ChIP fraction


title: FR352TOU:DRAIV 1-7

tag: tissue

value: leaf

value: F1 hybrid between accession FR352TOU and DRAIV 1-7


title: PolII_8WG16_sdc2RNAi_EMB_rep1


title: CS28097:2ST-0

tag: genotype

value: F1 hybrid between accession CS28097 and 2ST-0

value: 5th or 6th true leaf


title: 8144_NK-T

value: lymphoma

value: NKTL (extranasal)


title: PolII_S2_sdc2RNAi_EMB

value: sdc-2 mutant (y93, RNAi)

value: BethylLab


title: PolII_S5_WT_EMB


title: 3168_NK-T

source_name: NKTL (nasal)

value: NKTL (nasal)


title: 28891 AITL

value: AITL


title: CS28140:2LIS-1

value: F1 hybrid between accession CS28140 and 2LIS-1

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: MIX-1_WT_EMB_rep2

value: wild type N2

value: XX

value: Meyer Lab polyclonal rb1822,rb1951


title: 2691 PTCL-U

source_name: PTCL-U

value: PTCL-U


title: UKKT06278:Fr234

value: F1 hybrid between accession UKKT06278 and Fr234


title: 24224 AITL


title: UKKT06466:2RSCH-4

value: leaf

value: F1 hybrid between accession UKKT06466 and 2RSCH-4


title: red1∆_rep2

city: Tsukuba

first: Tomoyasu

last: Sugiyama

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

description: This sample is of red1∆ S.pombe

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

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

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

organism: Schizosaccharomyces pombe

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

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA) at 30˚C.

extract_protocol: Total RNA was extracted using mirVana miRNA isolation kit (Applied Biosystems) according manufacturer's instructions.

tag: strain


title: Fei0B:An-1

value: F1 hybrid between accession Fei0B and An-1


title: 20441 AITL


title: red1∆_rep1

description: This sample is of red1∆ S.pombe


title: CS28513:Fr132

value: F1 hybrid between accession CS28513 and Fr132

value: 5th or 6th true leaf


title: 20288 AITL

value: lymphoma


title: MIX-1_WT_EMB_rep1

value: embryo

value: input

value: ChIP fraction


title: 17519 PTCL-U


title: PolII_8WG16_sdc2RNAi_EMB_rep2

value: sdc-2 mutant (y93, RNAi)

value: PolII

value: Covance


title: wild-type_rep1

description: This sample is of wild-type S.pombe.

value: wild-type


title: IgGmock_sdc2mut_TY2222_EMB

source_name: sdc-2 mutant TY2222 XO embryo

value: sdc-2 mutant TY2222

value: XO

value: IgGmock

value: SantaCruzBiotechnology


title: PolII_Bentley_WT_EMB

source_name: wild type N2 XX embryo

value: wild type N2

value: XX

value: Bentley Lab polyclonal


title: CS28779:FR154MIB

value: leaf

value: F1 hybrid between accession CS28779 and FR154MIB

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: wild-type_rep2

description: This sample is of wild-type S.pombe. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures.


title: 1650 PTCL-U

value: lymphoma

value: PTCL-U


title: CS28492:UK48 LAZ1

value: F1 hybrid between accession CS28492 and UK48 LAZ1

value: 5th or 6th true leaf


title: HA-DPY-30_EMB

source_name: dpy30mut with HA-DPY-30 rescuing array TY2095 XX embryo

value: dpy-30 mutant carrying a rescuing HA-DPY-30 array. TY2095

value: embryo

value: input

value: ChIP fraction


title: 14426 PTCL-U


title: 14386 AITL

value: AITL


title: DPY-30_WT_EMB_rep1

value: SDIX


title: 13981 AITL


title: DPY-30_WT_EMB_rep2


title: DPY-30_sdc3mut_TY2205_EMB_rep1

source_name: sdc-3 mutant TY2205 XO hermaphrodite embryo

value: sdc-3 mutant TY2205

value: XO


title: DPY-30_sdc3mut_TY2205_EMB_rep2


title: CS28758:CS28165

value: F1 hybrid between accession CS28758 and CS28165


title: codYcovRS mutant at stationary phase, biological rep5

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

institute: University of Oklahoma Health Sciences Center

description: Gene transcription data from planktonic culture at early stationary phase

hyb_protocol: Following fragmentation, 3 μ of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. pyogenes Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix)

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

organism: Streptococcus pyogenes NZ131

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol.

growth_protocol:
Cells were grown to the mid-exponential phase (OD600 = 0.3-0.4) or early-stationary phase ( 1 hour after reaching the maximum optical density) and harvested by centrifugation.
Cells were grown aerobically in C-medium (0.5% proteose peptone #3, 1.5% yeast extract, 10 mM K2SO4, 0.4 mM MgSO4, 17 mM NaCl).

extract_protocol: Cells were lysed using beat-beater. Extraction of total RNA was performed using TRIzol reagent (Invitrogen) according to the manufacturers protocol.

value: planktonic cells

value: codYcovRS mutant

tag: growth phase

value: stationary phase


title: DPY-30_sdc2mut_TY2222_EMB_rep2

value: sdc-2 mutant TY2222


title: 14221_NK-T

value: lymphoma

value: NKTL (nasal)


title: DPY-30_sdc2mut_TY2222_EMB_rep1


title: codYcovRS mutant at stationary phase, biological rep4

tag: cell type


title: DPY-27_ypT28_EMB_rep2

source_name: ypT28 X:V fusion XX embryo

value: ypT28 X:V fusion

value: XX

value: Meyer Lab polyclonal rb699


title: CS28527:CS28420

value: leaf

value: F1 hybrid between accession CS28527 and CS28420

value: 5th or 6th true leaf

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: DPY-27_WT_fedL1_rep2

source_name: wild type N2 XX fed L1

growth_protocol: NG agar with E. coli HB101. Synchronous L1s fed in liquid culture for 3 hours with HB101

treatment_protocol: Briefly, gravid hermaphrodites were bleached and embryos were synchronized in M9 for 24 hours at 20 degrees celcius.  Synchronous L1s were fed for 3 hours with HB101 in liquid culture.  They were then crosslinked in 2% formaldehyde in M9 for 30 minutes at 20 degrees celcius and quenched with 100mM Tris-HCl.  They were washed in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF, PI inhibitor cocktail (EMD Biosciences)) and frozen.  Samples were then ground by mortar and pestle under liquid nitrogen and were resuspended in Homogenization buffer and snap frozen.  Samples were then sheared using a sonicator.

value: wild type N2

value: larval stage L1

value: input

value: ChIP fraction


title: CS22689:2BLA-1

value: F1 hybrid between accession CS22689 and 2BLA-1


title: 13786 PTCL-U

value: PTCL-U


title: 2BRO 1-6:FR391TOU

value: F1 hybrid between accession 2BRO 1-6 and FR391TOU


title: 13861 AITL

value: AITL


title: CS28725:2BLH-1_2

value: F1 hybrid between accession CS28725 and 2BLH-1_2


title: codYcovRS mutant at stationary phase, biological rep2

value: planktonic cells

value: codYcovRS mutant

value: stationary phase


title: CS28750:ShaA

value: F1 hybrid between accession CS28750 and ShaA


title: 12656_NK-T

value: lymphoma

value: NKTL (extranasal)


title: 2LISSE:FR165MIB

value: leaf

value: F1 hybrid between accession 2LISSE and FR165MIB

value: 5th or 6th true leaf


title: codYcovRS mutant at stationary phase, biological rep1


title: 10845 PTCL-U


title: codYcovRS mutant at stationary phase, biological rep3


title: covRS mutant at stationary phase, biological rep5

value: covRS mutant


title: DPY-27_ypT28_EMB_rep1

value: ypT28 X:V fusion

value: XX

value: embryo

value: input

value: Meyer Lab polyclonal rb699


title: DPY-27_WT_EMB_rep1

value: wild type N2

value: ChIP fraction


title: Dnmt3L heterozygous spermatids 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: no additional information

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Un-normalized summary probe profiles were output from BeadStudio for two Illumina Mouse Whole-Genome Version 1.1 BeadChips. The raw intensities were transformed by variance stabilising transformation (vst) and quantile normalised using the lumi package of the Bioconductor open-source software project (http://www.bioconductor.org).

source_name: Mouse round spermatids

label_protocol: Standard Illumina protocol

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

value: 8-12 weeks

value: Testis

tag: genome/variation

value: Dnmt3L heterozygous

value: spermatids


title: CS28407:2CS6034

value: F1 hybrid between accession CS28407 and 2CS6034

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: DPY-27_WT_EMB_rep2

tag: developmental stage


title: DPY-27_WT_fedL1_rep1

value: larval stage L1

tag: sample type


title: Dnmt3L heterozygous spermatids 2

description: no additional information


title: CS28743:FR165MIB

value: leaf

value: F1 hybrid between accession CS28743 and FR165MIB


title: covRS mutant at stationary phase, biological rep4

value: planktonic cells

value: covRS mutant

value: stationary phase


title: Oy-0:CS28201

value: F1 hybrid between accession Oy-0 and CS28201

value: 5th or 6th true leaf


title: covRS mutant at stationary phase, biological rep3


title: Dnmt3L heterozygous spermatids 1

description: no additional information


title: covRS mutant at stationary phase, biological rep2


title: MNFCHE2:FR27VOU-2

value: F1 hybrid between accession MNFCHE2 and FR27VOU-2


title: Dnmt3L wildtype spermatids 3

description: no additional information

value: wildtype


title: DPY-27_sdc3mut_TY2205_EMB_rep2

value: sdc-3 mutant TY2205

value: XO

value: embryo

value: input

value: ChIP fraction

tag: chip antibody

value: Meyer Lab polyclonal rb699


title: Dnmt3L wildtype spermatids 2

description: no additional information

value: 8-12 weeks

value: Testis

value: spermatids


title: covRS mutant at stationary phase, biological rep1


title: DPY-27_sdc2mut_TY2222_EMB_rep2

value: sdc-2 mutant TY2222

tag: chip antibody provider


title: WT MEFs IFNb 8hr

city: La Jolla

first: Alexander

last: Hoffmann

address: UCSD m/c 0375, NSB 3318 9500, Gilman Dr

department: Chemistry and Biochemistry

institute: UCSD

description: MEF expression in response to LPS or IFNb

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized using Illumina Inc. BeadStudio

source_name: Primary mouse embryonic fibroblasts (MEFs)

label_protocol: Biotinylated cRNA was prepared with the Ambion Message Amp kit for Illumina arrays

growth_protocol: MEF cells were maintained in DMEM supplemented with 10% bovine calf serum (BCS) to passages 5 to 6

extract_protocol: Total RNA was extracted from MEFs with Rneasy columns (Qiagen)

treatment_protocol: MEFs were stimulated with LPS or IFNb

value: MEF

value: wild type

tag: agent

value: IFNb

tag: time


title: TDR3:FR391TOU

value: leaf

value: F1 hybrid between accession TDR3 and FR391TOU

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: DPY-27_sdc2mut_TY2222_EMB_rep1

source_name: sdc-2 mutant TY2222 XO hermaphrodite embryo

tag: genotype/variation


title: 2WIL-1:UKLD06059

value: F1 hybrid between accession 2WIL-1 and UKLD06059

value: 5th or 6th true leaf


title: Dnmt3L wildtype spermatids 1

description: no additional information

value: wildtype


title: codY mutant at stationary phase, biological rep4

value: planktonic cells

value: codY mutant

value: stationary phase


title: DPY-27_dpy30mut_TY1119_rep2

source_name: dpy-30 mutant TY1119 XX embryo

value: dpy-30 mutant TY1119

value: XX

value: embryo

value: input

value: ChIP fraction

value: Meyer Lab polyclonal rb699


title: Dnmt3L heterozygous spermatocytes 2

description: no additional information

source_name: Mouse pachytene spermatocytes

value: 8-12 weeks

value: Testis

value: Dnmt3L heterozygous

value: spermatocytes


title: p50KO MEFs LPS 8hr

value: MEF

value: LPS


title: DPY-27_dpy30mut_TY1119_rep1


title: FR390TOU:CS28326

value: leaf

value: F1 hybrid between accession FR390TOU and CS28326

value: 5th or 6th true leaf

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: DPY-27_sdc3mut_TY2205_EMB_rep1

value: sdc-3 mutant TY2205

value: XO


title: codY mutant at stationary phase, biological rep5

value: planktonic cells

value: codY mutant

value: stationary phase


title: codY mutant at stationary phase, biological rep3


title: codY mutant at stationary phase, biological rep2


title: Dnmt3L heterozygous spermatocytes 1

description: no additional information


title: WT MEFs IFNb 0hr

value: wild type

value: IFNb


title: p50KO MEFs LPS 1hr


title: codY mutant at stationary phase, biological rep1


title: Dnmt3L wildtype spermatocytes 3

description: no additional information

value: 8-12 weeks

value: wildtype


title: Dnmt3L wildtype spermatocytes 2

description: no additional information

value: Testis


title: CS28732:CS28810

value: F1 hybrid between accession CS28732 and CS28810


title: WT at stationary phase, biological rep5

source_name: WT at stationary phase, biological rep5

value: WT


title: p50KO MEFs LPS 0hr

value: MEF

value: LPS


title: DPY-26_WT_EMB_rep1

value: wild type N2

value: XX

value: embryo

value: input

value: ChIP fraction

value: Meyer Lab polyclonal rb1450


title: WT MEFs LPS 8hr


title: VTA, 2 bottle choice, rep19

city: Richmond

first: Jonathan

last: Warner

state: Virginia

address: 1220 E. Broad St.

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

hyb_protocol: Labeled cRNA from individual animals (n=19) was hybridized to a single microarray for each brain region (n=58 total microarrays).  Array hybridization and scanning were performed exactly according to manufacturer’s protocols.  Arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: Microarray data were processed using the GeneChip Operating Software v4.1 (GCOS, Affymetrix) and normalized to a mean total hybridization intensity of 190.  Array quality was assessed by accepting arrays with scaling factor < 3, 3’-5’-actin ratio <2, and by examining linearity and inter-chip correlations of intensity values.  Arrays determined to be acceptable (57/58) were further analyzed using the Robust Multichip Average (RMA) low-level analysis algorithm to summarize probeset expression data (Irizarry et al. 2003).  Probesets with RMA expression values < 4.5 consistently across all microarrays were filtered to reduce variance from low expressing genes. To identify genes with expression values correlated with ethanol drinking behavior across individual mice, RMA values for each brain region were correlated (Pavlidis and Noble 2001) to a drinking scale calculated from each mouse’s ethanol intake averaged over the last 8 drinking days using the template matching tool in T-Mev (TIGR Multiple expression viewer (Saeed AI 2003)).  P-values from the template matching analysis were then used in estimating the false discovery rate (FDR) using the q value method (Storey and Tibshirani 2003) in the R programming environment (Team 2009). Probesets were considered significant using a FDR of 1%. Significant probesets were then used in subsequent bioinformatics analyses to identify genes with the most robust changes. All analyses were performed in each brain region separately.

source_name: Ventral tegmental area, 6 days following final ethanol drinking session

label_protocol: Biotin-labeled cRNA was synthesized from cDNA, purified and fragmented according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from PFC, NAc and VTA from individual mice in STAT 60 reagent (Tel-Test, Friendswood, TX) according to the manufacturer’s protocol.  RNA concentration and quality was assessed by Experion-automated electrophoresis (BioRad, Hercules, CA).  Total RNA (2 ug) was reversed transcribed into double-stranded cDNA using the One-cycle Targeting and Control Reagent kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Voluntary two-bottle choice drinking was performed as described previously (Khisti et al. 2006).  Briefly, two bottles containing 10%(w/v) ethanol (Aaper Alcohol and Chemical Co. Shelbyville, KY) or tap water were placed into the home cage at the beginning of the dark cycle.  Tube position was varied every two days (L, L, R, R).  Drinking sessions lasted 18 hours/day followed by 6 hours access to water only.  Mice had four consecutive drinking sessions followed by four days of abstinence repeated four times to give 16 total drinking sessions.  Three brain regions were harvested 6 days after the last drinking session: prefrontal cortex (PFC), nucleus accumbens (NAc) and ventral tegmental area (VTA) as previously described (Kerns et al. 2005).  Labeled cRNA from individual animals (n=19) was hybridized to a single microarray for each brain region (n=58 total microarrays).

value: male

tag: region

value: Ventral tegmental area


title: Dnmt3L wildtype spermatocytes 1

description: no additional information

value: spermatocytes


title: WT MEFs LPS 3hr

value: wild type


title: WT at stationary phase, biological rep4

source_name: WT at stationary phase, biological rep4

value: planktonic cells

value: stationary phase


title: ASH-2_WT_EMB_rep2

tag: gender

value: Meyer Lab polyclonal rb590


title: DRAIV6-16:Nfa-10

source_name: total RNA

value: leaf

value: F1 hybrid between accession DRAIV6-16 and Nfa-10

value: 5th or 6th true leaf

tag: growth condition

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: p50KO MEFs LPS 3hr

value: MEF

value: LPS


title: Uod-7:Edi-0

value: F1 hybrid between accession Uod-7 and Edi-0

tag: age


title: WT at stationary phase, biological rep3

source_name: WT at stationary phase, biological rep3

value: WT


title: WT at stationary phase, biological rep2

source_name: WT at stationary phase, biological rep2


title: CS28613:2GD-1

tag: tissue

value: F1 hybrid between accession CS28613 and 2GD-1


title: VTA, 2 bottle choice, rep16

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR) and scanned using the GeneChip Scanner 3000 (Affymetrix).


title: WT MEFs LPS 1hr


title: 2GR-1:CS28049

tag: genotype

value: F1 hybrid between accession 2GR-1 and CS28049


title: ASH-2_WT_EMB_rep1

value: wild type N2

value: XX

value: embryo

value: input

value: ChIP fraction


title: FR36PAR-4:CS28610

value: F1 hybrid between accession FR36PAR-4 and CS28610


title: DPY-26_WT_EMB_rep2

value: Meyer Lab polyclonal rb1450


title: VTA, 2 bottle choice, rep18

value: male

tag: strain

value: Ventral tegmental area


title: VTA, 2 bottle choice, rep15


title: ASH-2_sdc2mut_TY2222_EMB_rep2_BP-72

value: sdc-2 mutant TY2222

value: XO

value: Meyer Lab polyclonal rb590


title: WT MEFs LPS 0hr

value: MEF

value: wild type

value: LPS


title: CS28685:CS28628

value: leaf

value: F1 hybrid between accession CS28685 and CS28628

value: 5th or 6th true leaf

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: VTA, 2 bottle choice, rep17


title: MNFPOT48:CS28459

value: F1 hybrid between accession MNFPOT48 and CS28459


title: After treatment (week 4)_RAB47

city: Debrecen

first: Bertalan

last: Mesko

address: Egyetem tér 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: Patient 12

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix).

data_processing: Gene Spring GX 10 was used for data analysis. CHP files were generated using Affymetrix Expression Control. Affymetrix data files were imported using RMA algorithm and median normalization was performed.

source_name: PBMC

label_protocol: Ambion WT Expression Kit (Applied Biosystems) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 250 ng of RNA samples.

extract_protocol: Peripheral blood momonuclear cells were separated by Ficoll gradient centrifugation.

treatment_protocol: Treatment was tocilizumab infusion at week 0 and at week 4.

tag: time point

value: After treatment (week 4)

value: tocilizumab


title: After treatment (week 4)_RAB54

description: Patient 13


title: WT at stationary phase, biological rep1

source_name: WT at stationary phase, biological rep1

tag: cell type

value: planktonic cells

value: WT

tag: growth phase

value: stationary phase


title: S294BEL4:BroA

value: F1 hybrid between accession S294BEL4 and BroA


title: codYcovRS mutant at mid-exponential phase, biological rep5

description: Gene transcription data from planktonic culture at mid exponential phase

value: codYcovRS mutant

value: mid-exponential phase


title: codYcovRS mutant at mid-exponential phase, biological rep4


title: ASH-2_sdc2mut_TY2222_EMB_rep1

description: Briefly, gravid hermaphrodites were bleached and crosslinked with 2% formaldehyde in M9 at room temperature for 30 minutes.  Crosslinking was quenched with 100mM Tris-HCl (pH 7.5).  Embryos were resuspended and frozen in Homogenization buffer (50mM HEPES-KOH (pH 7.6), 0.5% NP-40, 140mM KCl, 1mM EDTA, 5mM DTT, 1mM PMSF).  Samples were sheared with a sonicator.

value: sdc-2 mutant TY2222

value: XO

tag: developmental stage

value: embryo

value: input

value: ChIP fraction

value: Meyer Lab polyclonal rb590


title: After treatment (week 4)_RAB44

description: Patient 11


title: After treatment (week 4)_RAB39

description: Patient 10


title: codYcovRS mutant at mid-exponential phase, biological rep2


title: codYcovRS mutant at mid-exponential phase, biological rep3


title: After treatment (week 4)_RAB36

description: Patient 9


title: Lz-0:CS28099

value: leaf

value: F1 hybrid between accession Lz-0 and CS28099

value: 5th or 6th true leaf


title: Bay0B:STE-3

value: F1 hybrid between accession Bay0B and STE-3

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: PAW3:2KOLN

value: F1 hybrid between accession PAW3 and 2KOLN


title: After treatment (week 4)_RAB32

description: Patient 8

value: After treatment (week 4)

value: tocilizumab


title: VTA, 2 bottle choice, rep11

value: male

value: Ventral tegmental area


title: CS28013:Sq-8

value: F1 hybrid between accession CS28013 and Sq-8


title: codYcovRS mutant at mid-exponential phase, biological rep1

value: planktonic cells

value: codYcovRS mutant

value: mid-exponential phase


title: covRS mutant at mid-exponential phase, biological rep5

value: covRS mutant


title: CS28350:CS28833

value: F1 hybrid between accession CS28350 and CS28833


title: covRS mutant at mid-exponential phase, biological rep4


title: CS28053:CS28217

value: F1 hybrid between accession CS28053 and CS28217


title: VTA, 2 bottle choice, rep14


title: After treatment (week 4)_RAB25

description: Patient 6


title: VTA, 2 bottle choice, rep12


title: covRS mutant at mid-exponential phase, biological rep3


title: After treatment (week 4)_RAB33

description: Patient 7


title: VTA, 2 bottle choice, rep10


title: VTA, 2 bottle choice, rep8


title: After treatment (week 4)_RAB20

description: Patient 5


title: After treatment (week 4)_RAB13

description: Patient 4


title: VTA, 2 bottle choice, rep9


title: covRS mutant at mid-exponential phase, biological rep1


title: VTA, 2 bottle choice, rep6


title: codY mutant at mid-exponential phase, biological rep5

value: codY mutant


title: VTA, 2 bottle choice, rep5


title: VTA, 2 bottle choice, rep13


title: After treatment (week 4)_RAB09

description: Patient 3


title: CS28622:2SAP-0

value: leaf

value: F1 hybrid between accession CS28622 and 2SAP-0


title: After treatment (week 4)_RAB10

description: Patient 2


title: VTA, 2 bottle choice, rep7


title: VTA, 2 bottle choice, rep4


title: After treatment (week 4)_RAB11

description: Patient 1


title: VTA, 2 bottle choice, rep3


title: codY mutant at mid-exponential phase, biological rep4


title: UKCW06202:CS28800

value: F1 hybrid between accession UKCW06202 and CS28800

value: 5th or 6th true leaf


title: codY mutant at mid-exponential phase, biological rep3


title: covRS mutant at mid-exponential phase, biological rep2


title: Bur0B:2IN-0

value: F1 hybrid between accession Bur0B and 2IN-0

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: codY mutant at mid-exponential phase, biological rep2


title: VTA, 2 bottle choice, rep2


title: Before treatment (week 0)_RAB34

description: Patient 13

value: Before treatment (week 0)


title: Before treatment (week 0)_RAB22

description: Patient 11


title: CS28573_2:CS28580

value: F1 hybrid between accession CS28573_2 and CS28580


title: VTA, 2 bottle choice, rep1

value: male

value: Ventral tegmental area


title: WT at mid-exponential phase, biological rep5

value: planktonic cells

value: WT


title: WT at mid-exponential phase, biological rep4

value: mid-exponential phase


title: Before treatment (week 0)_RAB16

description: Patient 9


title: PFC, 2 bottle choice, rep20


title: KBSMAC8:HR-5

value: F1 hybrid between accession KBSMAC8 and HR-5


title: Before treatment (week 0)_RAB15

description: Patient 8


title: Before treatment (week 0)_RAB29

description: Patient 12


title: WT at mid-exponential phase, biological rep3


title: PFC, 2 bottle choice, rep18

source_name: Prefrontal cortex, 6 days following final ethanol drinking session

value: Prefrontal cortex


title: Before treatment (week 0)_RAB19

description: Patient 10


title: PFC, 2 bottle choice, rep19


title: Bor-1:Kno-18

value: F1 hybrid between accession Bor-1 and Kno-18


title: WT at mid-exponential phase, biological rep2


title: 2TOTTARP:CS28419

value: F1 hybrid between accession 2TOTTARP and CS28419


title: PFC, 2 bottle choice, rep17


title: Got7A:CS28814

value: leaf

value: F1 hybrid between accession Got7A and CS28814


title: codY mutant at mid-exponential phase, biological rep1

value: codY mutant


title: Before treatment (week 0)_RAB14

description: Patient 7


title: PFC, 2 bottle choice, rep16


title: ScrRed_A25Green

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite

description:
The ROSE 199 cell line is a rat ovarian epithelial cell line first described by  Anne T. Adams and Nelly Auersperg, Expl Cell Biol 1985;53:181-188 (PMID 4029476).
The ROSEA 25 cell line is a KRAS V12-transformed derivate of ROSE 199 cells, described by Tchernitsa et al. Oncogene. 2004 Jun 3;23(26):4536-55 (PMID 15064704).

hyb_protocol: The second round of hybridization was performed in a reaction mix containing equal of 3DNA capture Reagent Cy3 and 3DNA Capture Reagent Cy5. The composition of the reaction mix, hybridization and washing conditions were as described in the Genisphere instruction manual. For each target RNA, we performed 2 independent hybridizations by inverting the Cy3 and Cy5 fluorescent dyes in the labeling reactions (dye swap).

scan_protocol: Microarray images were obtained on an Agilent G2565AA scanner at 10 μm resolution. Image analysis was performed using ImaGene software (BioDiscovery, USA).

data_processing: Global scaling normalization was performed using the median to set the average to 1 for all arrays. Imagene software (Biodiscovery, USA) was used for feature extraction.

organism: Rattus norvegicus

source_name: ROSE A25 cell line

label_protocol: We applied dendrimer technology for cDNA labeling and array hybridization using the 3DNA Array 900 MPX Kit for Microarray (Genisphere, USA). The two samples of cDNA were synthesized from each RNA probe (4 μg) by reverse transcription with random primers. The primers contained capture sequences that are complementary to Cy3- or Cy5-fluorescent dyes carrying capture reagents. The concentration of cDNA, hybridization and washing were carried out according to the kit manual.

extract_protocol: Total RNA from cells was prepared from cells 48 h after the last transfection with the TRIZOL reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s instructions.

tag: cell line

value: ROSE A25

value: rat ovary surface epithelium cells

source_name: ROSE A25 cell line transfected with scrambled siRNA

tag: sirna

value: scrambled


title: WT at mid-exponential phase, biological rep1


title: CS28014:CS28583

value: F1 hybrid between accession CS28014 and CS28583

value: 5th or 6th true leaf

value: Seeds were cold stratified in water for 5 days, sown in 96 cell flats in Promix 1:1 Metro:C2 soil. Plants were grown at 21 degrees C with 18 hours of fluorescent light.


title: Before treatment (week 0)_RAB05

description: Patient 5

value: Before treatment (week 0)


title: Before treatment (week 0)_RAB04

description: Patient 4


title: ScrGreen_A25Red


title: ScrRed_siRelaN2Green

source_name: ROSE A25 cell line transfected with Rela siRNA N2

value: Rela

tag: sirna #


title: Before treatment (week 0)_RAB03

description: Patient 3

tag: agent


title: 2HOD:CS28568

value: F1 hybrid between accession 2HOD and CS28568


title: PFC, 2 bottle choice, rep14

value: male


title: PFC, 2 bottle choice, rep13


title: ScrGreen_siRelaN2Red


title: PFC, 2 bottle choice, rep12


title: Before treatment (week 0)_RAB06

description: Patient 6


title: PFC, 2 bottle choice, rep11


title: Before treatment (week 0)_RAB02

description: Patient 2


title: ScrRed_siRelaN1Green

source_name: ROSE A25 cell line transfected with Rela siRNA N1


title: PFC, 2 bottle choice, rep10


title: 2GE-0:Pu2-23

value: F1 hybrid between accession 2GE-0 and Pu2-23


title: 2 LIARUM:2DUK

value: F1 hybrid between accession 2 LIARUM and 2DUK


title: 328PNA054:CS28279

value: F1 hybrid between accession 328PNA054 and CS28279


title: 2LOM 1-1:CS28141

value: F1 hybrid between accession 2LOM 1-1 and CS28141


title: ScrGreen_siRelaN1Red


title: ScrRed_siOtx1N2Green

source_name: ROSE A25 cell line transfected with Otx1 siRNA N2


title: Before treatment (week 0)_RAB01

description: Patient 1


title: PFC, 2 bottle choice, rep9

value: Prefrontal cortex


title: PFC, 2 bottle choice, rep15


title: multiple sclerosis_7

city: Nashville

first: Fanglin

last: Zhang

state: TN

address: 2201 Childrens' way

institute: Vanderbilt University

hyb_protocol: The biotinylated cDNA (5 µg) was fragmented and hybridized to an Affymetrix GeneChip Human Gene 1.0 ST Array

scan_protocol: GeneChips were then scanned using GeneChip Scanner 3000 7G Plus 2 and Command Console Software (AGCC) version 1.0

data_processing: Raw gene expression data in the generated CEL files  were then normalized using the GC Robust MultiChip Averaging (GC-RMA) algorithm as implemented in Bioconductor. To identify groups of functionally related genes that were differentially expressed, we conducted gene set analysis using the mixed effects models approach.

source_name: multiple sclerosis_7

label_protocol: A total of 100ng of total RNA was reverse transcribed to cDNA which was then used as template in an in-vitro transcription reaction followed by fragmentation of the single stranded cDNA and labeling through a terminal deoxy-transferase reaction.  The biotinylated cDNA (5 µg) was fragmented

extract_protocol: Total RNA was extracted from PBMC by RNeasy mini kit and treated with RNase-free DNase set, following manufacturer’s recommendation.

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation with Ficoll-Hypaque from freshly heparinized blood. The cells were washed in PBS and re-suspended at 1´106 cells/ml in complete medium RPMI-1640 for 48h before harvested for RNA extraction.

value: peripheral blood mononuclear cells

tag: disease state

value: multiple sclerosis


title: multiple sclerosis_8

source_name: multiple sclerosis_8


title: PFC, 2 bottle choice, rep7


title: PFC, 2 bottle choice, rep8


title: ScrRed_siOtx1GreenN1

source_name: ROSE A25 cell line transfected with Otx1 siRNA N1

value: ROSE A25


title: multiple sclerosis_5

source_name: multiple sclerosis_5


title: multiple sclerosis_6

source_name: multiple sclerosis_6