title: Daudi HY-2 + anti-IFNAR1 MAb -24 hr -AV Phenotype -repeat 1 - mAdbID:95146

description: mAdb experiment ID: 95146

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 20 LaserPower: 3.14;; 2.72 Temperature: 22.75 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN hybrid 2; anti-IFNAR1 MAb 64.10
Treatment dose: 36 ng/ml; 1 ug/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an HY-2 concentration of 36 ng of HY-2/ml. Samples were manipulated to display the antiviral (AV) phenotype through subsequent neutralization with anti-IFNAR1 MAb 64.10 (1 ug/ml).


title: Daudi IFN-alpha2c -0.36 ng/ml -6 hr -AP Phenotype -repeat 1 - mAdbID:95490

status: Public on Oct 12 2011

type: RNA

city: Bethesda

first: Hana

last: Schmeisser

state: MD

address: 50 Center Drive

department: CBS

country: USA

institute: NIAID

description: mAdb experiment ID: 95490

hyb_protocol: Hybridization Protocol Other: The hybridization protocol was previously published by Han et al. (Han, J., H. Lee, N. Y. Nguyen, S. L. Beaucage, and R. K. Puri. 2005. Novel multiple 5 -amino-modified primer for DNA microarrays. Genomics 86:252– 258.) After washing, arrays were dried using a Labnet Spectrafuge Mini (Labnet, Edison, NJ).

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 20 LaserPower: 3.08;; 2.65 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

data_processing: Calculation Method: Array data were normalized by 50th percentile normalization, and the spot intensity was calculated by subtracting the local median background from the mean foreground intensity. Array replicates were averaged across treatments, and gene expression fold values were obtained from the normalized Cy5/Cy3 ratios.

molecule: total RNA

organism: Homo sapiens

source_name: Untreated Control Sample

label_protocol:
Cy3 Sample Labeling Protocol
Other: A 5-ug portion of total RNA was labeled by using a modified Cy3 aminoallyl labeling method.

extract_protocol:
RNAeasy Kit
Other: RNA was isolated by using an RNeasy minikit (Qiagen, Stanford, CA). Cells were homogenized by using QIA shredder columns, and samples were eluted in 50 ul of RNase-free water. To ensure that there was no residual DNA contamination, samples were treated with RNase-free DNase (Qiagen) as described in the RNeasy protocol.

tag: treatment

tag: tissue

value: blood

tag: cell line

value: Daudi cell line

tag: cell type

value: B cells

tag: disease state

value: Burkitt's lymphoma

label_protocol:
Cy5 Sample Labeling Protocol
Other: A 5-ug portion of total RNA was labeled by using a modified Cy5 aminoallyl labeling method.

treatment_protocol:
Treatment type: compound
Agent: IFN-alpha2c
Treatment dose: 0.36 ng/ml
Treatment time: 6 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 6 hours at an IFN concentration of 0.36 ng of IFN-alpha2c/ml (displays antiproliferative (AP) phenotype).


title: Canephora vs Arabica cv. 'Java' at 30-26°C – rep6

city: MONTPELLIER

first: Benoit

last: Bertrand

address: 911 Avenue Agropolis - BP 64501 F

department: RPB

country: France

institute: IRD - CIRAD

hyb_protocol: Prior to hybridization, excess oligonucleotide was removed from the arrays by shaking them twice1min in 0.2% SDS. Arrays were then washed 2 times in distilled water. The two labelled aRNA were added to microarray hybridization buffer version 2 (GE Healthcare) in a final concentration of 50% formamide, denaturated at 95°C for 3 min and applied to the microarrays in individual chambers of an automated slide processor (GE Healthcare). Hybridization was carried out at 37°C for 12 h. Hybridized slides were washed at 37°C successively with 1X SSC, 0.2% SDS for 10 min, twice with 0.1X SSC, 0.2% SDS for 10 min, with 0.1X SSC for 1 min and with isopropanol before air drying.

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation.

data_processing: ArrayVision software was used for feature extraction. Spots with high local background or contamination fluorescence were flagged manually. A local background was calculated for each spot as the median values of the fluorescence intensities of 4 squares surrounding the spot. This background was subtracting from the foreground fluorescence intensity.

organism: Coffea arabica

source_name: Canephora at 30-26°C

label_protocol: For the preparation of the labelled Cy3- and Cy5- aRNA target, one microgram of total RNA samples were amplified and labelled using Amino Allyl Message Amp II aRNA amplification kit (Ambion, Austin, TX, USA), according the manufacturer's instructions.

growth_protocol: C. arabica and C. canephora fresh mature seeds were obtained from La Cumplida, Matagalpa, Nicaragua. C. eugenioides mature seeds were provided by Coffee Research Foundation, Kenya. The species C. arabica was represented by two accessions, namely cv. ‘Java’ derived from the wild Arabica Ethiopian pool and cv. ‘T18141’, an Arabica homozygous line derived from an interspecific hybrid between C. arabica and C. canephora, and consequently introgressed by C. canephora genes. The C. canephora species was represented by a cv. ‘Nemaya’ derived from the cross between two wild Congolese genotypes. Finally, the C. eugenioides accession seeds were collected from trees originating from the Mount Elgon forest in Kenya (1°8’ N 34°33’ E).The coffee seedlings were grown in a greenhouse with natural daylight and a constant temperature of 24°C, and watered as necessary. After 120 days, the plants were transferred to a phytotron chamber (CRYONEXT, France, model RTH 1200L).

extract_protocol: Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Hilden Germany) according to the recommendations of the manufacturer but with some slight modifications. A DNase treatment (RNase free DNase set, Qiagen) was carried out on the RNA during the extraction protocol and the total RNA was eluted in a smaller volume of 65 µl. Each RNA sample was quantified on a Nanodrop (ThermoFisher Scientific Inc., Waltham MA USA). RNA quality was confirmed on a Bioanalyser (Agilent technologies, CA, USA).

treatment_protocol: The study consisted in comparing the transcriptome of different species under two sets of growing conditions, which differed through the diurnal and nocturnal temperatures. In the two phytotron chambers, the photoperiod, humidity and luminosity were set at 12-hour days, 80-90% and 600 μE m-2s-1, respectively. The plants were subjected to a diurnal temperature of 26°C and a nocturnal temperature of 22°C in one phytotron (namely the ‘coldest’ temperature) and 30°C and 26°C respectively in a second phytotron (namely the ‘hottest’ temperature). In each phytotron chamber, from each accession, three plants were grown in a randomized complete block design. After 45 days for the ‘hottest’ temperature and 60 days for the ‘coldest’, plant size and number of newly formed leaves were similar. Then, two fully mature leaves were collected from each plant at midday (6-8 h after lights on), and then flash-frozen in nitrogen and stored at -80°C until extraction.

value: leaf

tag: cultivar

value: Canephora

tag: diurnal temperature

tag: nocturnal temperature

source_name: Arabica cv. 'Java' at 30-26°C

value: Java


title: Eugenioides vs Arabica cv. 'Java' at 30-26°C – rep1

source_name: Eugenioides at 30-26°C

value: Eugenioides


title: Eugenioides vs Arabica cv. 'Java' at 30-26°C – rep3


title: Eugenioides vs Arabica cv. 'Java' at 30-26°C – rep2


title: Daudi IFN-alpha2c + anti-IFNAR1 MAb -24 hr -AV Phenotype -repeat 1 - mAdbID:95144

description: mAdb experiment ID: 95144

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.1;; 2.71 Temperature: 22.5 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN-alpha2c; anti-IFNAR1 MAb 64.10
Treatment dose: 0.36 ng/ml; 1 ug/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an IFN concentration of 0.36 ng of IFN-alpha2c/ml. Samples were manipulated to display the antiviral (AV) phenotype through subsequent neutralization with anti-IFNAR1 MAb 64.10 (1 ug/ml).


title: Daudi IFN-alpha2c -0.36 ng/ml -6 hr -AP Phenotype -repeat 3 - mAdbID:95494

description: mAdb experiment ID: 95494

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 20 LaserPower: 3.2;; 2.71 Temperature: 23.75 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi IFN-alpha2c + anti-IFNAR1 MAb -24 hr -AV Phenotype -repeat 3 - mAdbID:95035

description: mAdb experiment ID: 95035

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.21;; 2.68 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi IFN-alpha2c -0.36 ng/ml -24 hr -AP Phenotype -repeat 1 - mAdbID:95143

description: mAdb experiment ID: 95143

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 20 LaserPower: 3.05;; 2.69 Temperature: 22 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN-alpha2c
Treatment dose: 0.36 ng/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an IFN concentration of 0.36 ng of IFN-alpha2c/ml (displays antiproliferative (AP) phenotype).


title: Daudi HY-2 + anti-IFNAR1 MAb -24 hr -AV Phenotype -repeat 3 - mAdbID:95037

description: mAdb experiment ID: 95037

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.27;; 2.7 Temperature: 23 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -36 ng/ml -24 hr -AP Phenotype -repeat 1 - mAdbID:95145

description: mAdb experiment ID: 95145

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 10 LaserPower: 3.12;; 2.7 Temperature: 22.5 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

source_name: HY-2 -36 ng/ml -24 hr -AP Phenotype

treatment_protocol:
Treatment type: compound
Agent: IFN hybrid 2
Treatment dose: 36 ng/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an HY-2 concentration of 36 ng of HY-2/ml (displays antiproliferative (AP) phenotype).

value: HY-2 -36 ng/ml -24 hr -AP Phenotype


title: Canephora vs Arabica cv. 'Java' at 30-26°C – rep3


title: Daudi HY-2 + anti-IFNAR1 MAb -24 hr -AV Phenotype -repeat 2 - mAdbID:94480

description: mAdb experiment ID: 94480

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 15 LaserPower: 3.29;; 2.75 Temperature: 22.44 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -36 ng/ml -24 hr -AP Phenotype -repeat 3 - mAdbID:95036

description: mAdb experiment ID: 95036

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.25;; 2.7 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Canephora vs Arabica cv. 'Java' at 30-26°C – rep5


title: Daudi IFN-alpha2c -0.36 ng/ml -24 hr -AP Phenotype -repeat 3 - mAdbID:95034

description: mAdb experiment ID: 95034

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 20 LaserPower: 3.17;; 2.66 Temperature: 22.25 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Canephora vs Arabica cv. 'Java' at 30-26°C – rep4


title: Daudi HY-2 -36 ng/ml -24 hr -AP Phenotype -repeat 2 - mAdbID:94479

description: mAdb experiment ID: 94479

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 15 LaserPower: 3.28;; 2.75 Temperature: 22.25 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Canephora vs Arabica cv. 'Java' at 30-26°C – rep2


title: Canephora vs Arabica cv. 'Java' at 30-26°C – rep1


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 26-22°C – rep6

source_name: Arabica cv. 'Java' at 26-22°C

source_name: Arabica cv. 'T18141' at 26-22°C


title: Daudi HY-2 -0.0036 ng/ml -24 hr -no AV activity -repeat 1 - mAdbID:91756

description: mAdb experiment ID: 91756

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 40;; 25 LaserPower: 3.41;; 2.81 Temperature: 22.88 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN hybrid 2
Treatment dose: 0.0036 ng/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an HY-2 concentration of 0.0036 ng of HY-2/ml (no antiviral (AV) activity observed).


title: Daudi IFN-alpha2c -0.36 ng/ml -24 hr -AP Phenotype -repeat 2 - mAdbID:94419

description: mAdb experiment ID: 94419

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.19;; 2.73 Temperature: 22.19 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi IFN-alpha2c -0.0036 ng/ml -24 hr -AV activity -repeat 5 - mAdbID:93934

description: mAdb experiment ID: 93934

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 35;; 25 LaserPower: 3.37;; 2.77 Temperature: 22.06 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN-alpha2c
Treatment dose: 0.0036 ng/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an IFN concentration of 0.0036 ng of IFN-alpha2c/ml (allowing antiviral (AV) activity only).


title: Daudi IFN-alpha2c -0.00036 ng/ml -24 hr -no AV activity -repeat 4 - mAdbID:93935

description: mAdb experiment ID: 93935

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 35 LaserPower: 3.38;; 2.76 Temperature: 22.19 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

treatment_protocol:
Treatment type: compound
Agent: IFN-alpha2c
Treatment dose: 0.00036 ng/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an IFN concentration of 0.00036 ng of IFN-alpha2c/ml (no antiviral (AV) activity observed).


title: Daudi IFN-alpha2c -0.00036 ng/ml -24 hr -no AV activity -repeat 5 - mAdbID:93936

description: mAdb experiment ID: 93936

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 30 LaserPower: 3.38;; 2.77 Temperature: 22.25 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi IFN-alpha2c + anti-IFNAR1 MAb -24 hr -AV Phenotype -repeat 2 - mAdbID:94456

description: mAdb experiment ID: 94456

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 20;; 15 LaserPower: 3.25;; 2.76 Temperature: 22.44 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 26-22°C – rep5

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation.


title: Daudi IFN-alpha2c -0.0036 ng/ml -24 hr -AV activity -repeat 4 - mAdbID:93933

description: mAdb experiment ID: 93933

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 35;; 30 LaserPower: 3.33;; 2.73 Temperature: 22 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -0.036 ng/ml -24 hr -AV activity -repeat 1 - mAdbID:91755

description: mAdb experiment ID: 91755

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 40;; 20 LaserPower: 3.41;; 2.81 Temperature: 22.75 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).

source_name: HY-2 -0.036 ng/ml -24 hr -AV activity

treatment_protocol:
Treatment type: compound
Agent: IFN hybrid 2
Treatment dose: 0.036 ng/ml
Treatment time: 24 hours
In-vitro treatment: Daudi cells (3 x 10(6) in 10 ml of RPMI) were treated for 24 hours at an HY-2 concentration of 0.036 ng of HY-2/ml (allowing antiviral (AV) activity).

value: HY-2 -0.036 ng/ml -24 hr -AV activity


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 26-22°C – rep4


title: Daudi IFN-alpha2c -0.0036 ng/ml -24 hr -AV activity -repeat 3 - mAdbID:91631

description: mAdb experiment ID: 91631

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 15 LaserPower: 3.32;; 2.71 Temperature: 21.81 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -0.036 ng/ml -24 hr -AV activity -repeat 3 - mAdbID:91633

description: mAdb experiment ID: 91633

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 15 LaserPower: 3.39;; 2.77 Temperature: 22.19 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi IFN-alpha2c -0.0036 ng/ml -24 hr -AV activity -repeat 1 - mAdbID:91753

description: mAdb experiment ID: 91753

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 40;; 25 LaserPower: 3.37;; 2.79 Temperature: 22.06 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 26-22°C – rep2


title: Eugenioides vs Arabica cv. 'T18141' at 26-22°C – rep5

source_name: Eugenioides at 26-22°C


title: Daudi IFN-alpha2c -0.00036 ng/ml -24 hr -no AV activity -repeat 1 - mAdbID:91754

description: mAdb experiment ID: 91754

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 40;; 30 LaserPower: 3.4;; 2.79 Temperature: 22.63 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -0.036 ng/ml -24 hr -AV activity -repeat 2 - mAdbID:91507

description: mAdb experiment ID: 91507

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 35;; 25 LaserPower: 3.43;; 2.8 Temperature: 22.31 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 26-22°C – rep3


title: Daudi IFN-alpha2c -0.00036 ng/ml -24 hr -no AV activity -repeat 2 - mAdbID:91506

description: mAdb experiment ID: 91506

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 35;; 20 LaserPower: 3.41;; 2.78 Temperature: 22 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -0.0036 ng/ml -24 hr -no AV activity -repeat 3 - mAdbID:91634

description: mAdb experiment ID: 91634

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 10 LaserPower: 3.39;; 2.78 Temperature: 22 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Daudi HY-2 -0.0036 ng/ml -24 hr -no AV activity -repeat 2 - mAdbID:91508

description: mAdb experiment ID: 91508

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 15 LaserPower: 3.43;; 2.79 Temperature: 22.38 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Arabica cv. 'Java' vs  Arabica cv. 'T18141' at 26-22°C – rep1


title: Daudi IFN-alpha2c -0.00036 ng/ml -24 hr -no AV activity -repeat 3 - mAdbID:91632

description: mAdb experiment ID: 91632

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 15;; 15 LaserPower: 3.38;; 2.74 Temperature: 22 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Eugenioides vs Arabica cv. 'T18141' at 26-22°C – rep6


title: Eugenioides vs Arabica cv. 'T18141' at 26-22°C – rep4


title: Eugenioides vs Arabica cv. 'T18141' at 26-22°C – rep2


title: Daudi IFN-alpha2c -0.0036 ng/ml -24 hr -AV activity -repeat 2 - mAdbID:91504

description: mAdb experiment ID: 91504

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4200A 01 [99052] ScanPower: 25;; 15 LaserPower: 3.38;; 2.74 Temperature: 21.75 Scanning Protocol Other: Arrays were scanned using an Axon GenePix 4200A microarray scanner with GenePix Pro 5.1 software (Molecular Devices, Sunnyvale, CA).


title: Eugenioides vs Arabica cv. 'T18141' at 26-22°C – rep1


title: Eugenioides vs Arabica cv. 'T18141' at 26-22°C – rep3


title: Control transfection, biological replicate 1

city: Seattle

first: Manu

last: Setty

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

hyb_protocol: According to Affymetrix protocol.

scan_protocol: According to Affymetrix protocol.

data_processing: Quantile normalization using affy package of Bioconductor

label: Biotin

source_name: PDGFRA amplified neurospheres, Control transfection

label_protocol: According to Affymetrix protocol.

growth_protocol: The human glioma neurosphere line was seeded at 200,000 cells/ml in 5 ml of Neural Stem Cell (NSC) media plus 10% NSC proliferation supplement (Stem Cell Technologies) additionally supplemented with 10 ng/ml EGF, 20 ng/ml basic FGF, 1 mg/ml heparin

extract_protocol: The RNA was extracted from neurospheres using Trizol.

treatment_protocol: 24-hours after seeding, miRNA mimetics (Thermo Scientific) were mixed with 25 ul HiPerFect Transfection Reagent (Qiagen 301704) in 500 ul Opti-MEM reduced serum media (Invitrogen 31985), incubated for 10 minutes at room temperature, and added dropwise to the cells (final miR concentration = 100 nM).

value: PDGFRA amplified neurospheres

tag: transfection

value: Control transfection


title: miR448 transfection, biological replicate 2

source_name: PDGFRA amplified neurospheres, miR448 transfection

value: miR448 transfection


title: miR448 transfection, biological replicate 3


title: hIL-17C_24h_Replicate 5

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description:
Biological replicate 5 of 5. HEKn cells, treated with human IL-17, harvested after 24 hours.
SAM627594

hyb_protocol: Hybridization and washing were performed using a fully automated hybridization apparatus, the Tecan HS4800 Pro Hybridization Station (TECAN U.S., Research Triangle Park, NC).

scan_protocol: Arrays were scanned in the Agilent G2505C model Scanner using Agilent Scan Control Software (version A.8.4.1).

data_processing: Expression signals were calculated using the Agilent Feature Extraction software (version 10.7.3.1 Agilent Technologies, Santa Clara, CA).

source_name: HEKn hIL-17C 24h

label_protocol: 1 ug of total RNA was converted into double-stranded cDNA using a T7 Promoter Primer and MMLV-RT (Agilent, Low RNA Input Fluorescent Linear Amplification Kit, Product #  5184-3523).  After cDNA synthesis, cRNA was synthesized using T7 RNA polymerase, which simultaneously incorporated cyanine 3- or cyanine 5- labeled CTP.  The labeled cRNA was purified on an affinity resin column (RNeasy Mini Kits, Qiagen).  The amount of labeled cRNA was determined by measuring absorbance at 260 nm and using the convention that 1 OD at 260 nm corresponds to 40 ug/ml of RNA.  Incorporation of dye was determined by measuring the sample using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) which measured the absorbance of cyanine 3- and cyanine 5- labeled CTP.  Eight hundred twenty-five nanograms of cyanine 3-labeled Universal Human Reference cRNA (Stratagene, La Jolla, CA, Product # 740000) and 825 ng of cyanine 5-labeled cRNA was fragmented by incubating at 60°C for 30 minutes in fragmentation buffer (Agilent In situ Hybridizatyion kit-plus, Product # 5184-3568).  Fragmentation was terminated by adding hybridization buffer containing LiCl and lithium lauryl sulfate.

growth_protocol: HEKn keratinocytes (Invitrogen) were cultured in EpiLife medium (Invitrogen) supplemented with Human Keratinocyte Growth Supplement (HKGS, Invitrogen). For experiments, HEKn were grown to confluence in 12 well plates treated with  Coating Matrix (Invitrogen).

extract_protocol: Whole RNA was isolated via RNeasy kit (Qiagen).

treatment_protocol: HEKn cells were incubated in the absence (n = 3) and presence (n = 5) of 500 ng/ml recombinant human IL-17C (in-house) for 3 and 24 hours.

value: Human keratinocytes (HEKn)

tag: treatment agent

value: recombinant human IL-17C (hIL-17C)

tag: timepoint

value: 24 hours

source_name: Stratagene Universal Human Reference RNA

tag: sample type

value: reference


title: hIL-17C_24h_Replicate 4

description:
Biological replicate 4 of 5. HEKn cells, treated with human IL-17, harvested after 24 hours.
SAM627593


title: Control transfection, biological replicate 2


title: miR433 transfection, biological replicate 3

source_name: PDGFRA amplified neurospheres, miR433 transfection

value: miR433 transfection


title: Control_24h_Replicate 3

description:
Biological replicate 3 of 3. HEKn cells, untreated, harvested after 24 hours.
SAM627592

source_name: HEKn Control 24h

value: control (untreated)


title: Control_24h_Replicate 2

description:
Biological replicate 2 of 3. HEKn cells, untreated, harvested after 24 hours.
SAM627591


title: hIL-17C_3h_Replicate 5

description:
Biological replicate 5 of 5. HEKn cells, treated with human IL-17, harvested after 3 hours.
SAM627590

source_name: HEKn hIL-17C 3h

value: 3 hours


title: miR433 transfection, biological replicate 2


title: Control transfection, biological replicate 3


title: miR433 transfection, biological replicate 1


title: Control_3h_Replicate 3

description:
Biological replicate 3 of 3. HEKn cells, untreated, harvested after 3 hours.
SAM627589

source_name: HEKn Control 3h


title: miR380 transfection, biological replicate 2

source_name: PDGFRA amplified neurospheres, miR380 transfection

value: miR380 transfection


title: miR448 transfection, biological replicate 1


title: Canephora vs Arabica cv. 'T18141' at 26-22°C – rep6

source_name: Canephora at 26-22°C

value: leaf


title: Canephora vs Arabica cv. 'T18141' at 26-22°C – rep5

value: Canephora


title: miR380 transfection, biological replicate 1


title: miR380 transfection, biological replicate 3


title: miR132 transfection, biological replicate 3

source_name: PDGFRA amplified neurospheres, miR132 transfection

value: miR132 transfection


title: hIL-17C_3h_Replicate 3

description:
Biological replicate 3 of 5. HEKn cells, treated with human IL-17, harvested after 3 hours.
SAM627350


title: Control_3h_Replicate 2

description:
Biological replicate 2 of 3. HEKn cells, untreated, harvested after 3 hours.
SAM627588


title: hIL-17C_3h_Replicate 4

description:
Biological replicate 4 of 5. HEKn cells, treated with human IL-17, harvested after 3 hours.
SAM627351


title: Canephora vs Arabica cv. 'T18141' at 26-22°C – rep4


title: miR132 transfection, biological replicate 2


title: Canephora vs Arabica cv. 'T18141' at 26-22°C – rep3


title: Control_3h_Replicate 1

description:
Biological replicate 1 of 3. HEKn cells, untreated, harvested after 3 hours.
SAM620265


title: hIL-17C_24h_Replicate 3

description:
Biological replicate 3 of 5. HEKn cells, treated with human IL-17, harvested after 24 hours.
SAM627091


title: Canephora vs Arabica cv. 'T18141' at 26-22°C – rep2


title: miR124 transfection, biological replicate 1

source_name: PDGFRA amplified neurospheres, miR124 transfection

value: miR124 transfection


title: hIL-17C_24h_Replicate 2

description:
Biological replicate 2 of 5. HEKn cells, treated with human IL-17, harvested after 24 hours.
SAM618825


title: miR124 transfection, biological replicate 3


title: miR132 transfection, biological replicate 1


title: hIL-17C_3h_Replicate 2

description:
Biological replicate 2 of 5. HEKn cells, treated with human IL-17, harvested after 3 hours.
SAM626753


title: Eugenioides vs Canephora at 26-22°C – rep6

value: Eugenioides


title: Canephora vs Arabica cv. 'T18141' at 26-22°C – rep1


title: BMMC_Young1

city: New Haven

first: Dietmar

last: Herndler-Brandstetter

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

hyb_protocol: Hybridization, washing and staining was performed with the GeneChip Hybridization, Wash and Stain Kit (#900720-900722; Affymetrix) according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G. The software used was AGCC Console v. 3.1.1.1229.

data_processing: The data were analyzed with CARMAweb (GC-RMA) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: bone marrow mononuclear cells collected from bone biopsies by density centrifugation after treatment with chromatographically purified collagenase for 1 hour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ex vivo isolation of human bone marrow mononuclear cells by density centrifugation following treatment of bone biopsies by chromatographically purified collagenase for 1 hour

extract_protocol: RNA was isolated from purified human bone marrow mononuclear cells using the Rneasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Bone biopsies were treated for 1 hour at 37°C with chromatographically purified collagenase (CLSPA; Worthington) in MEM with Glutamax supplemented with 20% FCS, 100 U/ml penicillin and 100 µg/ml streptomycin

tag: age

tag: gender

value: female


title: Eugenioides vs Canephora at 26-22°C – rep5


title: BMMC_Elderly1


title: BMMC_Elderly2

value: male


title: delta-vvd 28h vs WT 28h

city: Vienna

first: Doris

last: Tisch

state: Vienna

address: Gumpendorferstraße 1a

department: Chemical Engineering

country: Austria

institute: Technical University of Vienna

description: Strains were grown on Avicel for 28h or 40h, respectively.

hyb_protocol: Hybridization protocol The Pronto! Hybridization Kit (Corning, catalog no. 40076) was used for microarray hybridization according to the manufacturer’s specifications.

scan_protocol: Scan protocol Scanned on a GenePix 4000B scanner (Axon Instruments).

data_processing: Data processing GenePix Pro6 software was used to quantify hybridization signals and collect the raw data. Normalized expression values were analyzed by using BAGEL (Bayesian Analysis of Gene Expression Levels; PMID 12537560).

organism: Neurospora crassa

source_name: delta-vvd (FGSC 11556)

label_protocol: 10 µg of total RNA were used. The ChipShot Indirect Labeling/Clean-Up System (Promega, catalog no. Z4000) and CyDye Post-Labeling Reactive Dye Pack (GE, catalog no. RPN5661) were used to synthesize and label cDNA according to the manufacturer’s instructions.

growth_protocol: Strains were inoculated onto slants containing Vogel’s minimal medium at 25 °C for 7 days in constant light conditions (approx. 300 lux) to suppress synchronous gene expression associated with circadian rhythms. Conidia were harvested with water and inoculated into 50 ml of Bird’s medium with 2 % (w/v) Avicel cellulose (Sigma) as sole carbon source in 250 ml Erlenmayer flasks at a final concentration of 10^6 conidia/ml. Cells were grown under constant light at 25 °C for 28 or 40 hours at 200 rpm.

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

treatment_protocol: Mycelium was harvested, frozen in liquid nitrogen and kept at -80°C until RNA extraction was performed.

value: delta-vvd, 28h, Avicel

tag: genotype

value: delta-vvd

tag: time

source_name: wild type (FGSC 2489)

value: wild type FGSC 2489, 28h, Avicel

value: wild type FGSC 2489


title: WT 28h vs delta-vvd 28h


title: delta-vvd 40h vs delta-vvd 28h

value: delta-vvd, 40h, Avicel


title: delta-vvd 28h vs delta-vvd 40h


title: miR124 transfection, biological replicate 2

value: PDGFRA amplified neurospheres


title: BMMC_Young2


title: WT 40h vs delta-vvd 40h

value: wild type FGSC 2489, 40h, Avicel


title: WT 40h vs WT 28h


title: Eugenioides vs Canephora at 26-22°C – rep4

scan_protocol: Microarrays were immediately scanned at 10 µm resolution in both Cy3 and Cy5 channels with GenePix 4200AL scanner (Molecular Devices) with a variable PMT voltage to obtain maximal signal intensities with <0.1% probe saturation.


title: delta-vvd 40h vs WT 40h


title: hIL-17C_24h_Replicate 1

description:
Biological replicate 1 of 5. HEKn cells, treated with human IL-17, harvested after 24 hours.
SAM618824

value: Human keratinocytes (HEKn)

value: recombinant human IL-17C (hIL-17C)

value: 24 hours

value: reference


title: Eugenioides vs Canephora at 26-22°C – rep3

value: leaf

value: Canephora


title: HT1080 rLCC111 24h

city: Majadahonda

first: Patricia

last: Santos Valle

state: Madrid

address: Joaquín Rodrigo 2

department: Molecular Immunology Unit

country: Spain

institute: Hospital Universitario Puerta de Hierro Majadahonda

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials in a GeneChip® Hybridization Oven 640

scan_protocol: Affymetrix GeneChip® 3000 scanner

data_processing: The CEL files generated from the scanning were converted to gene expression signals using RMA Algorithm in Affymetrix® Expression Console

label: SAPE

source_name: fibrosarcoma cell line

label_protocol: cDNA was labeled with Affymetrix WT terminal Labeling kit

growth_protocol: HT1080 cells were cultured in DMEM supplemented with heat-inactivated 10% fetal calf serum (FCS), 2 mM L-glutamine, and penicillin/streptomycin (all from Invitrogen Life Technologies, Carlsbad, CA, USA).

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Micro kit according to manufacturer´s instructions.

treatment_protocol: HT1080 cells were incubated 24h in wells coated with BSA or rLCC111 (24w-plates).

tag: ecm


title: Eugenioides vs Canephora at 26-22°C – rep2

source_name: Eugenioides at 26-22°C


title: delta-wc-2 28h vs delta-wc-2 40h

source_name: delta-wc-2 (FGSC 11124)

value: delta-wc-2, 28h, Avicel

value: delta-wc-2, 40h, Avicel


title: Eugenioides vs Arabica cv. 'Java' at 26-22°C – rep4

value: Eugenioides

source_name: Arabica cv. 'Java' at 26-22°C

value: Java


title: Eugenioides vs Arabica cv. 'Java' at 26-22°C – rep3


title: hIL-17C_3h_Replicate 1

description:
Biological replicate 1 of 5. HEKn cells, treated with human IL-17, harvested after 3 hours.
SAM618822

value: 3 hours


title: Control_24h_Replicate 1

description:
Biological replicate 1 of 3. HEKn cells, untreated, harvested after 24 hours.
SAM618823

value: control (untreated)


title: delta-wc-2 40h vs delta-wc-2 28h


title: WT 40h vs delta-wc-1 40h

source_name: delta-wc-1 (FGSC 11712)

value: delta-wc-1, 40h, Avicel


title: Eugenioides vs Arabica cv. 'Java' at 26-22°C – rep5


title: normal testis i

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

hyb_protocol: standard Affymetrix protocol

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing: CEL files were processed using MAS 5.0 analysis algorithm with Affymetrix Expression Console software 1.1

organism: Rattus norvegicus

source_name: testis sample untreated

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA were extract with Rneasy Mini RNA extraction kit (Qiagen), then 250 ng of total RNA were amplified using GeneChip 3' IVT Express Kit from Affymetrix.

value: testis

tag: treatment

value: untreated

value: 5 d

tag: strain

value: Sprague-Dawley


title: Eugenioides vs Arabica cv. 'Java' at 26-22°C – rep6

tag: tissue


title: Eugenioides vs Canephora at 26-22°C – rep1


title: normal testis L


title: normal testis K


title: HT1080 BSA 24h

tag: cell line


title: WT 28h vs delta-wc-2 28h

value: wild type FGSC 2489, 28h, Avicel

value: wild type FGSC 2489


title: delta-wc-1 40h vs WT 40h

value: wild type FGSC 2489, 40h, Avicel


title: WT 28h vs WT 40h


title: treated testis D

source_name: testis sample after TCDD treatment

value: TCDD


title: treated testis B


title: delta-wc-2 28h vs WT 28h


title: delta-wc-1 28h vs delta-wc-1 40h

value: delta-wc-1, 28h, Avicel


title: delta-wc-1 28h vs WT 28h


title: Arabica cv. 'Java' vs Canephora at 26-22°C – rep5

value: leaf

value: Canephora


title: Eugenioides vs Arabica cv. 'Java' at 26-22°C – rep2


title: treated testis A


title: normal ovary L

source_name: ovary sample untreated

value: ovary


title: normal ovary i


title: Arabica cv. 'Java' vs Canephora at 26-22°C – rep2


title: Arabica cv. 'Java' vs Canephora at 26-22°C – rep3


title: Arabica cv. 'Java' vs Canephora at 26-22°C – rep6


title: Arabica cv. 'Java' vs Canephora at 26-22°C – rep1


title: WT 40h vs delta-wc-2 40h

value: delta-wc-2, 40h, Avicel


title: delta-wc-1 40h vs delta-wc-1 28h


title: treated ovary D

source_name: ovary sample after TCDD treatment


title: treated ovary A


title: delta-wc-2 40h vs WT 40h


title: Choe_HMVEC - Shiga toxin rep5

status: Public on Oct 11 2011

city: Toronto

first: Philip

last: Marsden

state: ON

address: Li Ka Shing Knowledge Institute, St. Michael's Hospital 209 Vicotria St, rm 526

department: Faculty of Medicine

country: Canada

institute: University of Toronto

description: Gene expression data from human microvascular endothelial cells treated with Shiga toxin

hyb_protocol: According to the standard protocol of Affymetrix

data_processing: Raw signal intensities were pre-processed using 13 different computational methods.  The base affy package was used to compute MAS5.0, RMA, dChip.PM, and dChip.PM-MM summary expression measures.  GCRMA, PLIER, VSN, mgMOS, mmgMOS, q.FARMS, l.FARMS, and the method of Choe et al, were computed using Bioconductor packages or packages made freely available by the package developers.  PDNN summary expression measures were determined using PerfectMatch v2.3.  All pre-processing methods were used in their default implementations.  Probe sets were then filtered to remove those called 'absent' by the affy package, and then submitted to Cyber-T for statistical analysis.

source_name: primary dermal neonatal microvascular endothelial cells, 10 fM Shiga toxin, 24 h

growth_protocol: Primary human dermal neonatal microvascular endothelial cells (HMVEC) isolated from a single donor were maintained in EGM-2MV medium (Lonza) and grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total cellular RNA was purified by cesium chloride ultracentrifugation, as described previously (Chirgwin et al, 1979, Biochemistry)

treatment_protocol: Post-confluent cells were treated with 10 fM Shiga toxin-2 (Stx2) for 24 and compared to untreated cells

value: male


title: WT 28h vs delta-wc-1 28h


title: Eugenioides vs Arabica cv. 'Java' at 26-22°C – rep1

value: Eugenioides

value: Java


title: normal ovary K


title: Arabica cv. 'Java' vs Canephora at 26-22°C – rep4


title: Choe_HMVEC - Shiga toxin rep6

scan_protocol: According to the standard protocol of Affymetrix


title: Choe_HMVEC - Shiga toxin rep3

label_protocol: According to the standard protocol of Affymetrix


title: Choe_HMVEC control rep6

description: Gene expression data from untreated human microvascular endothelial cells

source_name: primary dermal neonatal microvascular endothelial cells, untreated


title: Choe_HMVEC - Shiga toxin rep1


title: treated ovary B


title: Choe_HMVEC - Shiga toxin rep4


title: Choe_HMVEC control rep5


title: Choe_HMVEC - Shiga toxin rep2


title: Choe_HMVEC control rep1


title: mmgMOS_HMVEC control rep6


title: mmgMOS_HMVEC - Shiga toxin rep4


title: mmgMOS_HMVEC - Shiga toxin rep6


title: mmgMOS_HMVEC control rep2


title: mmgMOS_HMVEC - Shiga toxin rep2


title: Choe_HMVEC control rep3


title: mmgMOS_HMVEC control rep3


title: Choe_HMVEC control rep4


title: Choe_HMVEC control rep2


title: mmgMOS_HMVEC control rep1


title: mmgMOS_HMVEC - Shiga toxin rep5


title: mmgMOS_HMVEC - Shiga toxin rep3


title: mmgMOS_HMVEC - Shiga toxin rep1


title: mmgMOS_HMVEC control rep5


title: mgMOS_HMVEC - Shiga toxin rep6


title: mgMOS_HMVEC - Shiga toxin rep4


title: mmgMOS_HMVEC control rep4


title: mgMOS_HMVEC - Shiga toxin rep5


title: mgMOS_HMVEC - Shiga toxin rep3


title: mgMOS_HMVEC control rep5


title: mgMOS_HMVEC - Shiga toxin rep2


title: mgMOS_HMVEC - Shiga toxin rep1


title: mgMOS_HMVEC control rep6


title: mgMOS_HMVEC control rep3


title: mgMOS_HMVEC control rep1


title: PDNN_HMVEC - Shiga toxin rep6


title: mgMOS_HMVEC control rep2


title: PDNN_HMVEC - Shiga toxin rep3


title: PDNN_HMVEC control rep5


title: PDNN_HMVEC - Shiga toxin rep5


title: PDNN_HMVEC - Shiga toxin rep2


title: PDNN_HMVEC - Shiga toxin rep4


title: PDNN_HMVEC control rep6


title: PDNN_HMVEC control rep3


title: PDNN_HMVEC control rep4


title: l.FARMS_HMVEC - Shiga toxin rep5


title: mgMOS_HMVEC control rep4


title: l.FARMS_HMVEC - Shiga toxin rep4


title: PDNN_HMVEC control rep1


title: l.FARMS_HMVEC - Shiga toxin rep3


title: PDNN_HMVEC - Shiga toxin rep1


title: l.FARMS_HMVEC - Shiga toxin rep1


title: l.FARMS_HMVEC - Shiga toxin rep2


title: l.FARMS_HMVEC control rep6


title: l.FARMS_HMVEC control rep5


title: PDNN_HMVEC control rep2


title: q.FARMS_HMVEC - Shiga toxin rep6


title: l.FARMS_HMVEC control rep3


title: l.FARMS_HMVEC - Shiga toxin rep6


title: q.FARMS_HMVEC - Shiga toxin rep5


title: l.FARMS_HMVEC control rep1


title: l.FARMS_HMVEC control rep4


title: q.FARMS_HMVEC - Shiga toxin rep4


title: q.FARMS_HMVEC control rep6


title: q.FARMS_HMVEC - Shiga toxin rep3


title: q.FARMS_HMVEC - Shiga toxin rep1


title: q.FARMS_HMVEC control rep4


title: q.FARMS_HMVEC control rep2


title: q.FARMS_HMVEC - Shiga toxin rep2


title: q.FARMS_HMVEC control rep5


title: q.FARMS_HMVEC control rep3


title: q.FARMS_HMVEC control rep1


title: dChipPM-MM_HMVEC - Shiga toxin rep6


title: dChipPM-MM_HMVEC control rep5


title: dChipPM-MM_HMVEC - Shiga toxin rep3


title: dChipPM-MM_HMVEC - Shiga toxin rep4


title: dChipPM-MM_HMVEC - Shiga toxin rep5


title: dChipPM_HMVEC - Shiga toxin rep6


title: dChipPM-MM_HMVEC - Shiga toxin rep1


title: dChipPM-MM_HMVEC control rep6


title: dChipPM-MM_HMVEC control rep4


title: l.FARMS_HMVEC control rep2


title: dChipPM-MM_HMVEC control rep2


title: dChipPM-MM_HMVEC control rep3


title: dChipPM-MM_HMVEC control rep1


title: dChipPM_HMVEC - Shiga toxin rep4


title: dChipPM_HMVEC control rep1


title: dChipPM_HMVEC control rep6


title: dChipPM_HMVEC - Shiga toxin rep1


title: VSN_HMVEC - Shiga toxin rep5


title: dChipPM_HMVEC control rep2


title: dChipPM_HMVEC control rep3


title: VSN_HMVEC - Shiga toxin rep6


title: dChipPM_HMVEC control rep5


title: dChipPM_HMVEC - Shiga toxin rep2


title: dChipPM_HMVEC - Shiga toxin rep3


title: VSN_HMVEC - Shiga toxin rep1


title: VSN_HMVEC - Shiga toxin rep3


title: VSN_HMVEC control rep6


title: dChipPM-MM_HMVEC - Shiga toxin rep2


title: VSN_HMVEC control rep4


title: PLIER_HMVEC - Shiga toxin rep5


title: VSN_HMVEC control rep3


title: dChipPM_HMVEC control rep4


title: PLIER_HMVEC - Shiga toxin rep6


title: VSN_HMVEC control rep5


title: VSN_HMVEC control rep2


title: VSN_HMVEC control rep1


title: PLIER_HMVEC - Shiga toxin rep4


title: VSN_HMVEC - Shiga toxin rep2


title: PLIER_HMVEC - Shiga toxin rep1


title: GCRMA_HMVEC - Shiga toxin rep2


title: dChipPM_HMVEC - Shiga toxin rep5


title: PLIER_HMVEC - Shiga toxin rep3


title: GCRMA_HMVEC control rep3


title: VSN_HMVEC - Shiga toxin rep4


title: PLIER_HMVEC control rep1


title: GCRMA_HMVEC - Shiga toxin rep6


title: PLIER_HMVEC control rep5


title: GCRMA_HMVEC control rep6


title: PLIER_HMVEC control rep2


title: PLIER_HMVEC control rep6


title: GCRMA_HMVEC - Shiga toxin rep1


title: PLIER_HMVEC control rep4


title: GCRMA_HMVEC - Shiga toxin rep3


title: PLIER_HMVEC - Shiga toxin rep2


title: PLIER_HMVEC control rep3


title: GCRMA_HMVEC control rep2


title: GCRMA_HMVEC - Shiga toxin rep5


title: GCRMA_HMVEC control rep1


title: GCRMA_HMVEC - Shiga toxin rep4


title: GCRMA_HMVEC control rep4


title: GCRMA_HMVEC control rep5


title: RMA_HMVEC - Shiga toxin rep6


title: RMA_HMVEC - Shiga toxin rep1


title: RMA_HMVEC - Shiga toxin rep5


title: RMA_HMVEC - Shiga toxin rep4


title: RMA_HMVEC control rep6


title: BC5547

city: Köln

first: Karsten

middle: Ernst

last: Weber

address: Nattermannallee 1

country: Germany

institute: Sividon Diagnostics GmbH

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: primary breast cancer sample, fresh-frozen

label_protocol: from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit (Roche Applied Science, Mannheim, Germany), according to the manufacturer’s instructions

growth_protocol: primary tumor tissue, fresh-frozen after surgery

extract_protocol: RNeasy kit, Qiagen. according to the manufacturer's instructions

tag: center/subcohort

value: Frankfurt

tag: metastasis (1

value: yes, 0:no/censored):0

tag: metastasis free interval (months)

tag: tumor size

tag: positive lymph nodes

value: unknown

tag: adjuvant patient treatment

value: Tamoxifen


title: RMA_HMVEC control rep5


title: BC5550


title: BC5549


title: BC5541


title: RMA_HMVEC - Shiga toxin rep2


title: RMA_HMVEC - Shiga toxin rep3


title: RMA_HMVEC control rep2


title: BC6238

value: Mainz


title: RMA_HMVEC control rep3


title: RMA_HMVEC control rep1


title: BC5543


title: BC5548


title: BC5551

value: yes, 0:no/censored):1


title: BC5545


title: RMA_HMVEC control rep4


title: BC5540


title: BC5546


title: BC5544


title: BC6153


title: BC5542


title: BC5534


title: BC5535


title: BC5536


title: BC5537


title: MAS5_HMVEC control rep2


title: BC5539


title: BC5531


title: BC5532


title: BC5526


title: BC5530


title: BC5527


title: BC5523


title: BC5529


title: BC5528


title: BC5518


title: BC5525


title: BC5520


title: BC5514


title: BC5504


title: BC5522


title: BC5503


title: BC5516


title: BC5521


title: BC5508


title: BC5512


title: BC5501


title: BC5510


title: BC5506


title: BC5122

value: Hamburg


title: BC5123


title: BC5124


title: BC5120


title: BC5465


title: BC5435


title: BC5332


title: BC5134


title: BC5137


title: BC5341


title: BC5131


title: BC5117


title: BC5101


title: BC5111


title: BC5115


title: BC5110


title: BC5121


title: BC5091


title: BC5112


title: BC5105


title: BC5109


title: BC5084


title: BC5077


title: BC5079


title: BC5082


title: BC5083


title: BC5089


title: BC5113


title: BC5076


title: BC5074


title: BC5071


title: BC5068


title: BC5065


title: BC5072


title: BC5073


title: BC5062


title: BC5075


title: BC5050


title: BC5057


title: BC5064


title: BC5055


title: BC5049


title: BC5059


title: BC5053


title: BC5058


title: BC5063


title: BC5052


title: BC5048


title: BC5054


title: BC5042


title: BC5044


title: BC5036


title: BC5040


title: BC5037


title: BC5039


title: BC5038


title: BC5043


title: BC5028


title: BC5035


title: BC5022


title: BC5034


title: BC5020


title: BC5026


title: BC5029


title: BC5019


title: BC5024


title: BC5021


title: BC5015


title: BC5533


title: BC5014


title: BC5009


title: BC5013


title: BC5027


title: BC5016


title: BC5017


title: BC5018


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_68

type: genomic

city: Salamanca

first: Cristina

last: Robledo

address: Campus Miguel de Unamuno

institute: CIC

hyb_protocol: Labelled test and reference DNA samples were mixed equitably, co-precipitated in the presence of Cot-1 human DNA (Roche, Indianapolis, IN) with ethanol, washed, and resuspended in hybridization solution (50% formamide, 10% Dextran sulphate, 2X standard saline citrate, 10mM Tris pH 7.6, 2.7% sodium dodecyl sulphate and 10μg/μl of yeast tRNA). DNA mixtures were cohybridized to the arrays in a GENETAC (Genomic Solutions, Ann Arbor, Michigan, USA) for 48 hours at 42ºC in accordance with the manufacturer’s recommended protocol.

scan_protocol: Images and signal intensities were acquired using a GenePix 4000B (Axon Instruments, Burlingame, CA) dual laser scanner in combination with GenePix Pro4.0 (Axon Instruments, Burlingame, CA) imaging software.

data_processing: Fluorescence ratios were normalized using the median of the fluorescence ratios of every spot, computed as log2 values. The log2 ratio of each clone was normalized to the median log2 ratio of the 20 control hybridizations, after which the median of the three spots was calculated.

molecule: genomic DNA

source_name: DNA SMZL

label_protocol: 2 μg of unamplified genomic DNA (tumour DNA) was digested with DpnII restriction enzyme (New England Biolabs, Beverly, MA) and labelled using random primers (BioPrime Labeling System, Invitrogen, Carlsbad, Calif) and Cy5-dCTP (CyDyeTM 5-dCTP, Amersham Biosciences, Piscataway, NJ) fluorescent dye for paired hybridization samples. The incorporation of labelled nucleotide was quantified using a NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies).

extract_protocol: The DNA was extracted using the standard phenol-chloroform method. All DNA was quantified using the Nanodrop spectrophotometer (ND-1000, NanoDrop Technologies, Wilmington, DE USA). DNA quality was assessed by the 260:280 ratio and its integrity by agarose gel ethidium bromide visualization.

value: spleen

tag: disease state

value: Splenic marginal zone lymphomas

source_name: Control DNA

label_protocol: 2 μg of unamplified genomic DNA reference material (placental DNA) was digested with DpnII restriction enzyme (New England Biolabs, Beverly, MA) and labelled using random primers (BioPrime Labeling System, Invitrogen, Carlsbad, Calif) and Cy3-dCTP (CyDyeTM 3-dCTP Amersham Biosciences, Piscataway, NJ) fluorescent dye for paired hybridization samples. The incorporation of labelled nucleotide was quantified using a NanoDrop spectrophotometer (ND-1000, NanoDrop Technologies).

value: healthy

value: human placenta of healthy donors

value: placenta


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_63

value: peripheral blood

tag: sample type


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_65


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_67


title: BC5007


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_66


title: BC5006


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_62


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_64


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_61


title: BC5008


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_60


title: BC5011


title: BC5004


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_59


title: BC5001


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_57


title: BC5005


title: F9_BMS641_6h

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

institute: IGBMC

hyb_protocol: biotin-labeled-cDNAs were hybridized on Affymetrix GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The arrays were further washed and stained with streptavidine-phycoerythrin in an Affymetrix GeneChip® Fluidics station 450 using the script protocol F450-0007.

scan_protocol: The arrays were scanned with an Affymetrix Gene Chip Scanner 3000 7G.

data_processing: Expression values were generated with Affymetrix software Expression Console version 1.1, using sketch quantile normalization and median polish summarization as in Robust Multiarray Analysis (RMA).

organism: Mus musculus

source_name: F9 cells treated with BMS641 (6h)

label_protocol: biotin-labeled-cDNAs: “GeneChip® whole transcript sense target labeling assay manual” (P/N 701880 Rev.4).

growth_protocol: Embryonal carcinoma cells were cultured in Dubelcco’s modified Eagle’s medium supplemented with 10% foetal calf serum and 40ug/ml Gentamicin. Cells were seeded in gelatine-coated tissue culture plates (0.1%) and all-trans retinoic acid (ATRA), or the different RAR-specific agonists, were added to the plates in a final concentration of 1x10-6 M at different time points (for BMS961, the final concentration has been set to 1x10-7M).

extract_protocol: Total RNA was extracted from cells using the GENEEluteTM RNA extraction kit (Sigma)

value: F9 embryonal carcinoma cells

tag: agent


title: F9_BMS641_2h

source_name: F9 cells treated with BMS641 (2h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_58


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_55


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_54


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_51


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_53


title: F9_BMS641_48h

source_name: F9 cells treated with BMS641 (48h)


title: F9_BMS641_24h

source_name: F9 cells treated with BMS641 (24h)


title: F9_BMS753_6h

source_name: F9 cells treated with BMS753 (6h)


title: F9_BMS753_48h

source_name: F9 cells treated with BMS753 (48h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_50


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_56


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_49


title: F9_BMS753_24h

source_name: F9 cells treated with BMS753 (24h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_48


title: F9_BMS753_2h

source_name: F9 cells treated with BMS753 (2h)


title: F9_BMS961_6h

source_name: F9 cells treated with BMS961 (6h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_47


title: F9_BMS961_48h

source_name: F9 cells treated with BMS961 (48h)


title: F9_ATRA_48h

source_name: F9 cells treated with ATRA (48h)

value: ATRA


title: F9_BMS961_24h

source_name: F9 cells treated with BMS961 (24h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_45


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_43


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_41


title: F9_ATRA_2h

source_name: F9 cells treated with ATRA (2h)


title: F9_BMS961_2h

source_name: F9 cells treated with BMS961 (2h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_40


title: F9_EtOH_48h_rep2

source_name: F9 cells treated with EtOH (48h)

value: EtOH


title: F9_EtOH_48h_rep1


title: Caco-2 untransfected, rep3

city: Essen

first: Elke

last: Cario

state: NRW

address: Virchowstr. 171

department: Division of Gastroenterology and Hepatology

institute: University of Duisburg-Essen, University Hospital of Essen

description: Gene expression data from Caco-2 cells - untransfected

hyb_protocol: Following fragmentation, 15µg of cDNA were hybridized for 16h at 45°C on GeneChip HuGene 1.0 ST v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with fluidics protocol FS450_0001.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner using GCOS version 1.4 software with default settings.

data_processing: Raw CEL-files were imported into Expression Console 1.0 (Affymetrix). RMA was used for array normalization and signal calculation.

source_name: Caco-2 untransfected (naive)

label_protocol: Samples were enzymatically amplified, fragmented and biotinylated using GeneChip® Whole Transcript (WT) Sense Target Labeling Kit (Affymetrix).

growth_protocol: HA-tagged TLR4-wildtype plasmid (TLR4-WT) was obtained from InvivoGen. TLR4 mutants (D299G, T399I) were generated within the TLR4-WT expression construct and confirmed by sequencing (Trenzyme). Plasmids (EndoFree Maxi, Qiagen) were transfected into Caco-2 cells on a 12-well-plate (poly-D-lysine coated)  using 1µg/well of TLR4-WT, TLR4-D299G or TLR4-T399I (Lipofectamine LTX, Invitrogen). Stable IEC transfectant clones expressing TLR4-WT, TLR4-D299G or TLR4-T399I were selected with 1 µg/ml blasticidin (InvivoGen). Controls were untransfected cells without any exogenous DNA. Transfection efficiency was evaluated by semiquantative RT-PCR analysis, as well as western blotting and immunohistochemistry with anti-HA.

extract_protocol: Cell samples were frozen in trizole at -80°C until further processing. Total RNA was isolated (RiboPure, Ambion) and purified (Rneasy, Qiagen) according to the manufacturers' recommendations. All RNA samples (n=3 per condition) were analyzed independently and microarray processing was performed at The Microarray Facility (Tübingen), according to the manufacturer's instructions.

treatment_protocol: Prior to analysis, cells (1.5 x 105 / ml) of Caco-2 stable cell lines expressing TLR4-WT, TLR4-D299G, TLR4-T399I or untransfected were cultured for 8 days in all experiments.

tag: cell type

value: intestinal epithelial


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_52

source_name: DNA SMZL

source_name: Control DNA


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_44


title: Caco-2-TLR4-T399I, rep2

description: Gene expression data from Caco-2 cells stably transfected with TLR4-T399I


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_42


title: Caco-2 untransfected, rep2


title: F9_ATRA_6h

source_name: F9 cells treated with ATRA (6h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_37


title: Caco-2-TLR4-T399I, rep3

source_name: Caco-2 cells stably transfected with TLR4-T399I


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_39


title: Caco-2-TLR4-D299G, rep2

description: Gene expression data from Caco-2 cells stably transfected with TLR4-D299G


title: Caco-2-TLR4-T399I, rep1


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_35


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_33


title: Caco-2-TLR4-D299G, rep3

source_name: Caco-2 cells stably transfected with TLR4-D299G


title: Caco-2 untransfected, rep1


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_32


title: Caco-2-TLR4-D299G, rep1


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_36


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_31


title: F9_ATRA_24h

source_name: F9 cells treated with ATRA (24h)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_27


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_28


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_30


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_23


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_24


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_22


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_34


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_25


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_21


title: HS01 (pCAR1)

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: RNA mapping on pCAR1 carried by HS01

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 130 µl of the hybridization cocktail was hybridized at 45˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the FlexFS450-0002 protocol of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.　The intensities were linearly scaled so that the median was 100. The replications of CEL files were together converted into the BAR files using pCAR1_8b520435FF-3 for the forward strand and pCAR1_8b520435FR-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of plasmid pCAR1. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas putida

source_name: cDNA prepared from succinate culture of HS01

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: 100 ml of NMM-4 (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 1.0 mg ml-1 sodium succinate or carbazole was inoculated by overnight culture in Luria broth to obtain initial optical densities at 600 nm (OD600) of 0.05. Cultures were incubated at 30˚C in a rotating shaker at 120 rpm to exponential phase.

extract_protocol: Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

tag: plasmid


title: JCM 2778 (pCAR1)

description: RNA mapping on pCAR1 carried byJCM 2778

organism: Pseudomonas chlororaphis subsp. chlororaphis

source_name: cDNA prepared from succinate culture ofJCM 2778(pCAR1)


title: Caco-2-TLR4-WT, rep2

description: Gene expression data from Caco-2 cells stably transfected with TLR4-FL

source_name: Caco-2 cells stably transfected with TLR4-WT


title: Caco-2-TLR4-WT, rep3


title: Caco-2-TLR4-WT, rep1


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_26


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_20


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_29


title: Pf0-1 (pCAR1)

description: RNA mapping on pCAR1 carried by Pf0-1

organism: Pseudomonas fluorescens

source_name: cDNA prepared from succinate culture of Pf0-1(pCAR1)


title: CA10 (pCAR1)

description: RNA mapping on pCAR1 carried by CA10

organism: Metapseudomonas resinovorans

source_name: cDNA prepared from succinate culture of CA10


title: PAO1 (pCAR1)

description: RNA mapping on pCAR1 carried by PAO1

organism: Pseudomonas aeruginosa

source_name: cDNA prepared from succinate culture of PAO1(pCAR1)


title: KT2440 (pCAR1)

description: RNA mapping on pCAR1 carried by KT2440

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_19


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_38


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_11


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_17


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_15


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_14


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_16


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_10


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_18


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_13


title: Splenic marginal zone lymphoma SMZL_Agilent_16

hyb_protocol: standard Agilent protocol, see see manufacturer's web site at http://www.agilent.com/


title: Splenic marginal zone lymphoma SMZL_Agilent_68

scan_protocol: standard Agilent protocol, see see manufacturer's web site at http://www.agilent.com/


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_39

hyb_protocol: standard NimbleGen protocol, see manufacturer's web site at http://www.nimblegen.com


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_12


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_43

scan_protocol: standard NimbleGen protocol, see manufacturer's web site at http://www.nimblegen.com


title: Splenic marginal zone lymphoma SMZL_Agilent_11

data_processing: standard Agilent protocol, see see manufacturer's web site at http://www.agilent.com/


title: Splenic marginal zone lymphoma SMZL_Agilent_14

label_protocol: standard Agilent protocol, see see manufacturer's web site at http://www.agilent.com/


title: Splenic marginal zone lymphoma SMZL_Agilent_27


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_09


title: Splenic marginal zone lymphoma SMZL_Agilent_38


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_44

data_processing: standard NimbleGen protocol, see manufacturer's web site at http://www.nimblegen.com


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_62

label_protocol: standard NimbleGen protocol, see manufacturer's web site at http://www.nimblegen.com


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_27


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_52


title: Splenic marginal zone lymphoma SMZL_Agilent_05


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_08


title: Splenic marginal zone lymphoma SMZL_Agilent_12


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_06


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_04


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_05


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_18


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_07


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_03


title: Frogs treated with artemisinin

city: Mainz

first: Marianne

last: Mathäs

address: Obere Zahlbacherstraße 67

institute: Universitätsmedizin Mainz

description: Gene expression data from artemisinin-treated Xenopus laevis.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on a GeneChip Xenopus laevis 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The images were processed by GeneChip Operating Software 1.3, and the raw data were normalized by Robust Multiarray Analysis (RMA).

organism: Xenopus laevis

source_name: liver, artemisinin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Xenopus laevis were kept in 22°C water.

extract_protocol: Total RNA extraction was performed with peqGOLD TriFast (Peqlab) according to the manufacturer's instructions.

treatment_protocol: Arteminisin (200 mg/kg) or pregnenolone (50 mg/kg), each dissolved in DMSO, were injected intraperitoneally into three frogs on two consecutive days. The control group received in parallel two DMSO injections. All frogs were sacrificed 24 h after the second injection by decapitation, and livers were immediately frozen in liquid nitrogen.

value: liver

tag: gender

value: female

value: artemisinin


title: Splenic marginal zone lymphoma SMZL_NimbleGen CHR7_14


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_02

hyb_protocol: see manufacturer's web site at http://www.nimblegen.com/


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_01

source_name: SMZL DNA


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_14


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_06

scan_protocol: see manufacturer's web site at http://www.nimblegen.com/


title: Splenic marginal zone lymphoma SMZL_NimbleGen4x_08


title: Frogs treated with pregnenolone

description: Gene expression data from pregnenolone-treated Xenopus laevis.

source_name: liver, pregnenolone

value: pregnenolone


title: HeLa_24h_10Amol/L5AZA

city: guangzhou

first: yao

middle: ting

last: ting

address: 107 Riverside Road

country: China

institute: SUN YAT-SEN  MEMORIAL,HOSPITAL,SUN YAT-SEN UNIVERSITY

description: Gene expression after 24hr in 10 Amol/L 5-aza-2'-deoxycytidine

hyb_protocol: 12.5 ul of Hy3-labelled sample mixed with 2×Hybridization buffer and Nuclease-free Buffer in a reaction volume of 180 ul was Prepare the hybridization mix in a PCR tube.Load the 180ul target hybridization mix into the hybridization assembly through the sample loading opening .Place the hybridization assembly into a 56C oven and set it on a rotator at 2 rotations per minute (RPM) for overnight.After hybridization, disassembled the hybridization assembly, and wash the slides at 56C for 2min. using Wash buffer A.Wash for 2min. at room temperature in Wash buffer B and C.Wash briefly in water.Dry the slides by centrifugation for 5 min at 200g (1000rpm).

scan_protocol: Slides were scanned immediately after washing on  the Axon GenePix 4000B microarray scanner.

data_processing: GenePix pro V6.0 is used to read the raw intensity of the image.The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged. Median Normalization Method was used to obtain 'Normalized Data',  Normalized Data = (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

label_protocol: Hy3™ labeled cRNA was prepared from 1 ug RNA using the miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the trizol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.  The protocol includes differential lysis of C33A, CASKI, HeLa, and SIHA cells, and RNasey Mini Kit(Qiagen p/n 74104). RNA quantification and quality control used a NanoDrop-1000 spectrophotometer.

treatment_protocol: Four cervical cancer cells were choosed for this study,No.1 samples were treated with 5-azacytidine for 24hrs,the other samples were untreated ,  then cultured with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum for 48 hours at 37 ℃ in a humidified incubator with 5% CO2 .

value: HELA

value: cervical cancer cells


title: SIHA_24h_10Amol/L5AZA

value: SIHA


title: HeLa_24h_untreated

source_name: untreated


title: CASKI_24h_untreated

value: CASKI


title: Splenic marginal zone lymphoma SMZL_NimbleGen CHR7_43

source_name: DNA SMZL

value: Splenic marginal zone lymphomas


title: Frogs treated with DMSO

description: Gene expression data from DMSO-treated Xenopus laevis.

source_name: liver, control

value: DMSO


title: Splenic marginal zone lymphoma SMZL_NimbleGen CHR7_06

value: spleen

source_name: Control DNA

value: healthy

value: human placenta of healthy donors


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_02

value: placenta


title: CASKI_24h_10Amol/L5AZA


title: SIHA_24h_untreated


title: C33A_24h_untreated


title: HeLa_MosIR plasmid_rep2

city: Prague 4

first: Matyas

last: Flemr

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics

description:
08-HeLa-500ng-2
Gene expression data from cultured HeLa cells 24 hours after transfection with control plasmid

hyb_protocol: Biotinylated cRNA (20 µg) was fragmented by heating with magnesium (as per Affymetrix's instructions) and 15 µg of fragmented cRNA was hybridized to Human U133 plus 2.0 GeneChips™.

scan_protocol: Standard Affymetrix procedures

data_processing: All arrays were normalized using the GCRMA algorithm with quantile normalization composed of 100 bins using Genedata's Refiner application. Per chip normalization was performed by scaling the median of the genes called present (detection P-value < 0.04) to a value of 500.

source_name: HeLa cells transfected with MosIR plasmid

label_protocol: Total RNA (5 µg) from each replicate was reverse transcribed with the Affymetrix cDNA synthesis kit and cRNA was produced by in vitro transcription (IVT) by T7 RNA polymerase using the Affymetrix IVT kit as per manufacturer's instructions.

growth_protocol: HEK293 and HeLa cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) supplemented with 10 % FCS (Invitrogen), penicillin (100 U/mL, Invitrogen), and streptomycin (100 µg/mL, Invitrogen) at 37 °C and 5 % CO2 atmosphere.

extract_protocol: Total RNA was extracted from HEK293 or HeLa cells in a confluent 6-well dish 24 hours post-transfection using Absolutely RNA Miniprep Kit (Stratagene).

treatment_protocol: HEK293 and HeLa cells grown in a 6-well plate were transfected with 500ng control parental MosIR plasmid expressing EGFP or with 500ng MosIR plasmid expressing EGFP with 3'UTR containing long inverted repeat derived from mouse c-Mos coding sequence.

value: HeLa cells

tag: transfection

value: MosIR plasmid


title: HeLa_MosIR plasmid_rep1

description:
07-HeLa-500ng-1
Gene expression data from cultured HeLa cells 24 hours after transfection with control plasmid


title: HeLa_control plasmid_rep2

description:
06-HeLa-0ng-2
Gene expression data from cultured HeLa cells 24 hours after transfection with control plasmid

source_name: HeLa cells transfected with control plasmid

value: control plasmid


title: C33A_24h_10Amol/L5AZA


title: HeLa_control plasmid_rep1

description:
05-HeLa-0ng-1
Gene expression data from cultured HeLa cells 24 hours after transfection with control plasmid


title: Linezolid treated Replicate 1

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

institute: Jilin university

description: Biological replicate 1 of 2. Control DMSO treated, harvested after several passages.

hyb_protocol: The samples were hybridized with Agilent whole genome oligo microarray,performed by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)in Agilent’s SureHyb Hybridization Chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis_Linezolid

label_protocol: The samples were labeled using the Agilent Quick Amp labeling kit.

growth_protocol: Mycobacterium tuberculosis H37Rv was incubated in a rotary shaker. Subsequently, Linezolid stock solution, prepared in dimethyl sulfoxide (DMSO), and DMSO was added to the culture,respectively. Then, the the cells were further incubated for a certain time.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Mycobacterium tuberculosis H37Rv

source_name: Mycobacterium tuberculosis_DMSO


title: Splenic marginal zone lymphoma BAC_ARRAY_SMZL_46

value: peripheral blood


title: Splenic marginal zone lymphoma SMZL_NimbleGen CHR7_18


title: HEK293_MosIR plasmid_rep2

description:
04-Hek-500ng-2
Gene expression data from cultured HEK293 cells 24 hours after transfection with MosIR plasmid

source_name: HEK293 cells transfected with MosIR plasmid

value: HEK293 cells


title: gill 9_day 7_elevated pCO2_rep6

status: Public on Oct 10 2011

city: Winnipeg

first: Sandra

last: Fehsenfeld

state: MB

address: 509 Buller Building, 45 Chancellors Circle

department: Biological Science

institute: University of Manitoba

description: Contig IDs (CMX) according to Towle DW, Henry RP, Terwilliger NB: Microarray-detected changes in gene expression in gills of green crabs (Carcinus maenas) upon dilution of environmental salinity. Comp.Biochem. Physiol.D 2010.

hyb_protocol: following provided protocols by MAUI hybridization system (MAUI Mixer SC Hybridization Chamber mixers, Biomicro Cat.no. 02A00830) + Protnto!Universal Hybridization Kit

scan_protocol: Axon GenePix 4000B dual wavelength scanner + GenePix 6.0 software

data_processing: lowess-normalization (by Acuity 4.0 software; Input parameter: Smoothing = 0.19, Iterations = 3, Delta = 0.01); further processing in Excel: filtering by excluding low-quality features (according to flags assigned by Acuity software 4.0); exluding of features with fluorescence intensity of one or both channels lower than 30 % of the background fluorescence intensity; excluding of features with a variance of more than 20 % in the 4 technical replicated included on one microarray slide for each transcript.

organism: Carcinus maenas

source_name: homogenized whole posterior gill 9, exposed to control (39 Pa) pCO2

label_protocol: following provided protocols of SuperScript™ Plus Direct cDNA Labeling System (Invitrogen #L1015-06)

growth_protocol: The experiment took place in April 2009 at the IFM-GEOMAR, Kiel, Germany. C. maenas were acclimated for 24h in a flow-through seawater manipulation systen at IFM-GEOMAR and then exposed to 39 or 400 Pa CO2 for 3 or 7 days using an automatic gas mixing facility (Linde gas, HTK Hamburg, Germany). Temperature was held constant at 13 °C, Salinity was app. 15.

extract_protocol: Gills were homogenized with an OMNI international TH/G7-196STW for 50 s in 4 ml buffer RLT (of kit as follows). Total RNA was then extracted using the RNeasy Midi-Kit (Qiagen #75144)

treatment_protocol: After dissection, gills were immediately stored in RNAlater until RNA was isolated.

value: whole posterior gill 9

tag: exposure

value: day 7 control pCO2

value: female

tag: origin

value: Baltic Sea / Kiel Fjord

source_name: homogenized whole posterior gill 9, exposed to elevated (400 Pa) pCO2

value: day 7 elevated pCO2


title: HEK293_MosIR plasmid_rep1

description:
03-Hek-500ng-1
Gene expression data from cultured HEK293 cells 24 hours after transfection with MosIR plasmid


title: gill 9_day 7_elevated pCO2_rep4

tag: tissue


title: gill 9_day 3_elevated pCO2_rep5

value: day 3 control pCO2

value: day 3 elevated pCO2


title: gill 9_day 3_elevated pCO2_rep6


title: HEK293_control plasmid_rep1

description:
01-Hek-0ng-1
Gene expression data from cultured HEK293 cells 24 hours after transfection with control plasmid

source_name: HEK293 cells transfected with control plasmid


title: gill 9_day 3_elevated pCO2_rep4


title: gill 9_day 7_elevated pCO2_rep1


title: gill 9_day 7_elevated pCO2_rep2


title: E1Cmyc3_P7

city: Singapore

first: TianSheng

last: CHEN

address: 8A Biomedical Grove, Immunos, 05-16

country: Singapore

institute: Institute of Medical Biology

description:
5388905036_G
group 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were extracted using Illumina BeadStudio v.3.2 and normalised using quantile normalisation with IlluminaGUI in R

source_name: Mesencymal stem cell

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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

value: Mesencymal stem cell

tag: strain

value: ES H9 derived MSCs

tag: cell passage number

tag: genotype/variation

value: overexpression of MYC clonal 3


title: gill 9_day 7_elevated pCO2_rep3


title: HEK293_control plasmid_rep2

description:
02-Hek-0ng-2
Gene expression data from cultured HEK293 cells 24 hours after transfection with control plasmid


title: gill 9_day 3_elevated pCO2_rep3


title: E1cmyc1_P5

description:
5388905036_E
group 2

value: overexpression of MYC clonal 1


title: E1Cmyc1_P3

description:
5388905036_C
group 2


title: E1Cmyc3_P8

description:
5388905036_H
group 3


title: MSCE1_P15

description:
5388905036_A
group 1

value: original


title: gill 9_day 7_elevated pCO2_rep5


title: E1Cmyc3_P4

description:
5388905036_F
group 3


title: gill 7_day 7_elevated pCO2_rep6

source_name: homogenized whole posterior gill 7, exposed to control (39 Pa) pCO2

value: whole posterior gill 7

source_name: homogenized whole posterior gill 7, exposed to elevated (400 Pa) pCO2


title: gill 9_day 3_elevated pCO2_rep1


title: gill 9_day 3_elevated pCO2_rep2


title: gill 7_day 7_elevated pCO2_rep5


title: MSCE1_P16

description:
5388905036_B
group 1


title: gill 7_day 7_elevated pCO2_rep3


title: Linezolid treated Replicate 2


title: gill 7_day 3_elevated pCO2_rep6


title: gill 7_day 7_elevated pCO2_rep2


title: gill 7_day 3_elevated pCO2_rep5


title: E1Cmyc1_P4

description:
5388905036_D
group 2


title: No_code Limbal-peripheral Cornea

city: Hong Kong

first: Gary

last: Yam

address: 147K Argyle St, Mongkok

institute: Chinese University of Hong Kong

description: Fresh human cornea specimen dissected limbal-peripheral cornea

hyb_protocol: The dried and labeled miRNA sample was resuspended in 18 ul nuclease-free water, 4.5 ul 10X GE Blocking Agent (Agilent) and 22.5 ul 2X Hi-RPM hybridization buffer (Agilent), followed by heating at 100°C for 5 minutes. Upon cooling in ice water bath for 5 mintues, the mixture was hybridized to Human miRNA Microarray (V1) based on Sanger miRbase (release 9.1).   (G4112A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: 016436_F_D_20091031) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Limbal-peripheral Cornea_No code

label_protocol: 100 ng RNA was dephosphorylated and labeled by miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions, followed by vacuum concentrate for 3 hours.

growth_protocol: Human corneal specimen.

extract_protocol: Total RNA was extracted by Trizol/chloroform (Invitrogen) and purified with RNeasy mini spin column (Qiagen, Valencia, CA). RNA quantity and integrity were assayed by RNA 6000 Pico Chip Kit (Agilent, Santa Clara, CA) on Agilent 2100 Bioanalyzer. RNA samples with 28S/18S ratios in the range of 1.4 to 1.8 were used.

treatment_protocol: Human corneal rims from adult donors were processed for cryosectioning. LPC and CC epithelia, separated by 1-mm in width, were dissected for small RNA extraction.

value: Corneal epithelium


title: No_code Central Cornea

description: Fresh human cornea specimen dissected central cornea

source_name: Central Cornea_No code


title: gill 7_day 3_elevated pCO2_rep4


title: gill 7_day 3_elevated pCO2_rep3


title: 3911 Limbal-peripheral Cornea

source_name: Limbal-peripheral Cornea_3911


title: gill 7_day 3_elevated pCO2_rep1


title: gill 7_day 3_elevated pCO2_rep2


title: 3911 Central Cornea

source_name: Central Cornea_3911


title: 3902 Limbal-peripheral Cornea

source_name: Limbal-peripheral Cornea_3902


title: gill 7_day 7_elevated pCO2_rep4


title: 3902 Central Cornea

source_name: Central Cornea_3902


title: 3846 Limbal-peripheral Cornea

source_name: Limbal-peripheral Cornea_3846


title: 13903669

city: Sophia Antipolis cedex

first: frederique

last: hilliou

address: 400 route des chappes, BP167

department: SPE

institute: INRA

description:
M-Sf9R1_Mtp
Date:2009/10/20

hyb_protocol: Corning Pronto : 1542.0 ng at 42 degree_C during 15 hours

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

data_processing:
Unnormalized, log (base 2) transform of the (Ch1/Ch2) ratio of the medians shown in the data table below.
Normalized data [i.e., Log (base 2) transform of the (Ch1/Ch2) ratio of the medians;limma package: normalizeWithinArray(loess, background:subtract) normalizeBetweenArrays (quantile); lmFit ;eBayes] linked as supplementary files on the Series record.

molecule: polyA RNA

organism: Spodoptera frugiperda

label_protocol: Promega Chipshot labeling

extract_protocol: Trizol

tag: cell line


title: 13903668

description:
M-Sf9R1_Mtp
Date:2009/10/20

hyb_protocol: Corning Pronto : 1830.0 ng at 42 degree_C during 15 hours


title: 13903656

description:
M-Sf9R2_Mtfz
Date:2009/10/08

hyb_protocol: Corning Pronto : 2156.0 ng at 42 degree_C during 16 hours


title: 13903670

description:
M-Sf9R2_Mtp
Date:2009/10/20

hyb_protocol: Corning Pronto : 1623.0 ng at 42 degree_C during 15 hours


title: 13903673

description:
M-Sf9R3_Mtp
Date:2009/10/20

hyb_protocol: Corning Pronto : 1331.0 ng at 42 degree_C during 15 hours


title: Normal sample 3 (Mouse #140)

city: Saint Louis

first: Katherine

middle: Parker

last: Ponder

state: MO

address: 660 S. Euclid Avenue

institute: Washington University St Louis

description: Normal mice with aorta not dilated

hyb_protocol: Standard Illumina Hybridization protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: The data were normalised using quantile normalisation  using Illumina genome Studio Software. Data was loaded into Partek Software for analysis.

source_name: Normal aorta

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with a Qiagen column and DNase I treatment. Quality control was performed with Agilent Bioanalyser.

value: normal

tag: age

value: 7 months

value: ascending aorta


title: 13903661

description:
M-Sf9R3_Mtfz
Date:2009/10/08

hyb_protocol: Corning Pronto : 1918.0 ng at 42 degree_C during 16 hours


title: 13903655

description:
M-Sf9R1_Mtfz
Date:2009/10/01

hyb_protocol: Corning Pronto : 1483.0 ng at 42 degree_C during 16 hours


title: 13903671

description:
M-Sf9R2_Mtp
Date:2009/10/20

hyb_protocol: Corning Pronto : 1450.0 ng at 42 degree_C during 15 hours


title: MPS VII not dilated sample 2 (Mouse #6023)

description: MPS VII mice with  aorta not dilated

source_name: MPS VII not dilated aorta

value: male

value: MPS VII

value: 6.7 months


title: Normal sample 2 (Mouse #145)

description: Normal mice with aorta not dilated

value: 6.4 months


title: 3846 Central Cornea

source_name: Central Cornea_3846


title: 13903659

description:
M-Sf9R3_Mtfz
Date:2009/10/08

hyb_protocol: Corning Pronto : 2094.0 ng at 42 degree_C during 16 hours


title: 13903657

description:
M-Sf9R2_Mtfz
Date:2009/10/08

hyb_protocol: Corning Pronto : 2169.0 ng at 42 degree_C during 16 hours


title: MPS VII dilated sample 2 (Mouse #78)

description: MPS VII mice with dilated aorta

source_name: MPS VII dilated aorta

value: female

value: 9.1 months


title: HCE_Scramble_24h_0404

description: Gene expression after 24hr in scrambled sequence transfected human corneal epithelial cell line

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 2.2 ul 25x Agilent fragmentation buffer and 11.0 ul 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human Corneal Epithelial Cells, Srambled sequence tranfected, 24hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human corneal epithelial cells (HCE) cells were cultured in DMEM/F12 medium supplemented with 10 % heat-inactivated fetal bovine serum.It was maintained at 37 °C in a humidified incubator with 5% CO2

treatment_protocol: Human corneal epithelial cell line were transfected with mMIRH145PA-1 or pCDH-CMV-MCS-EF1-copGFP (System Biosciences, MountainView, CA, US) in DMEM/F12 medium supplemented with 10% heat-inactivated fetal bovine serum for 24 hours at 37 ºC in a humidified incubator with 5% CO2.


title: MPS VII not dilated sample 1 (Mouse #5608)

description: MPS VII mice with aorta not dilated

value: 5.8 months


title: 13903672

description:
M-Sf9R3_Mtp
Date:2009/10/20

hyb_protocol: Corning Pronto : 1507.0 ng at 42 degree_C during 15 hours


title: MPS VII dilated  sample 3 (Mouse #263)

description: MPS VII mice with dilated aorta

source_name: MPS VII dilated  aorta

value: 6.0 months


title: 13903654

description:
M-Sf9R1_Mtfz
Date:2009/10/01

hyb_protocol: Corning Pronto : 1544.0 ng at 42 degree_C during 16 hours


title: Normal sample 1 (Mouse #142)

description: Normal mice with aorta not dilated


title: HCE_Hsa-mir-145_24h_0404

description: Gene expression after 24hr in hsa-mir-145 transfected human corneal epithelial cell line

source_name: Human Corneal Epithelial Cells, Hsa-mir-145 tranfected, 24hr


title: MPS VII dilated  sample 1 (Mouse #190)

description: MPS VII mice with dilated aorta

value: 7.8 months


title: SARRC-2089-02-A

status: Public on Oct 09 2011

city: Philadelphia

first: mark

last: alter

state: PA

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

institute: University of Pennsylvania

hyb_protocol: Two hundred microliters (containing 10 micrograms of fragmented cRNA) of each cocktail was separately hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array for 16h at 45 degree Celsius in the Hybridization Oven 640.

scan_protocol: Arrays were washed on Affymetrix’s GeneChip Fluidics Station 450 using a primary streptavidin phycoerythrin (SAPE) stain, subsequent biotinylated antibody stain, and secondary SAPE stain. Arrays were scanned on Affymetrix’s GeneChip Scanner 3000 7G with AutoLoader. Scanned images obtained by the Affymetrix GeneChip Operating Software (GCOS) v1.2 were used to extract raw signal intensity values per probe set on the array.

data_processing: RMA

source_name: lymphocytes

label_protocol: Isolated total RNA was double round amplified, cleaned, and biotin-labeled using Affymetrix’s GeneChip Two-Cycle Target Labeling kit (Santa Clara, CA) with a T7 promoter and Ambion’s MEGAscript T7 High Yield Transcription kit (Austin, TX) as per manufacturer’s protocol. Amplified and labeled cRNA was quantified on a spectrophotometer and run on a 1% TAE gel to check for an evenly distributed range of transcript sizes. Twenty micrograms of cRNA was fragmented to approximately 35-200bp by alkaline treatment (200 mM Tris-acetate, pH 8.2, 500 mM KOAc, 150 mM MgOAc) and run on a 1% TAE gell to verify fragmentation. Separate hybridization cocktails were made using 15 micrograms of fragmented cRNA from each sample as per Affymetrix’s protocol.

extract_protocol: Qiagen Qiaquick kit (Germantown, MD).

tag: scan batch

value: Batch 1

tag: group

value: autism

tag: subject age

tag: paternal age

tag: maternal age


title: SARRC-1021-01-A


title: SARRC-1100-03-Aq


title: gill 7_day 7_elevated pCO2_rep1

hyb_protocol: following provided protocols by MAUI hybridization system (MAUI Mixer SC Hybridization Chamber mixers, Biomicro Cat.no. 02A00830) + Protnto!Universal Hybridization Kit

source_name: homogenized whole posterior gill 7, exposed to control (39 Pa) pCO2

value: day 7 control pCO2

value: Baltic Sea / Kiel Fjord

value: day 7 elevated pCO2


title: 2117-01-A


title: 2119-03-A

value: Batch 2


title: SARRC-0248-01-A


title: 1200-03-A


title: 2097-03-A


title: 2098-03-A


title: 2112-01-A


title: 2120-03-A


title: 1204-03-A-b


title: 1209-03-A


title: 2096-03-A


title: 2103-03-A


title: 1205-01-A


title: 1194-03-A


title: 1193-03-A-b


title: 1199-01-A


title: 1197-03-A


title: 1198-03-A


title: 1203-03-A


title: 1164-03-A


title: 1156-03-A


title: 1163-03-A


title: 1202-03-A


title: 2095-03-A


title: 1195-03-A


title: 1186-03-A-b


title: 2107-03-A


title: 1132-03-A


title: 1138-03-A-b


title: 1119-03-A


title: 1122-03-A


title: 1116-03-A


title: 1124-02-A


title: 1106-03-A


title: 1064-03-A


title: 1061-03-A-b


title: 1082-01-C


title: 1056-05-A


title: 1056-03-A


title: 1076-03-A


title: 1052-03-A


title: 1051-03-A-b


title: 1083-03-A


title: 1065-03-C


title: 1053-03-A


title: 1099-03-A


title: 1044-03-A


title: 1067-03-A


title: 1049-03-A


title: 1030-03-A-b


title: 1025-04-A


title: 1015-01-A


title: 1011-03-A-b


title: 1023-01-A-b


title: 1009-03-A


title: 0844-01-A


title: 0952-01-A


title: 1006-03-A


title: 0922-01-A


title: 0949-01-A


title: 0833-01-C


title: 0790-01-A


title: 0950-01-A


title: 0810-01-A


title: 0943-01-A


title: 0959-01-A


title: 0947-01-A-b


title: 1005-01-A


title: 0820-01-A


title: 0238-01-A


title: 0577-01-A


title: 0705-01-A


title: 0105-01-A


title: 0561-01-A


title: 166-01-C

value: control


title: 0151-01-C