title: esd7-1 mutant, 14 short days, biological rep1

status: Public on Oct 14 2010

type: RNA

city: Madrid

first: Jose Antonio

last: Jarillo

state: Madrid

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo Pozuelo de Alarcón

department: PLANT DEVELOPMENTAL BIOLOGY

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas (UPM-INIA)

description: Gene expression data from esd7-1 mutant

hyb_protocol: Three biological replicates for each condition were independently hybridized.If the quality control was correct, then 10 µg of fragmented cRNA were hybridized to the Arabidopsis ATH1 Genome array (Affymetrix, Santa Clara, CA), containing 22500 transcript variants from 24000 well -characterized Arabidopsis thaliana genes. Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: GeneChips were scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix) Data analyses were performed using GeneChip Operating Software (GCOS).

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, Bioinformatics (2006), 22, 897-899). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al (2003) Biostatistics, 4, 249-264). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg's method (False Discovery Rate) (Benjamini, Y and Hochberg, Y (1995) J.Roy.Stat.Soc, 57, 289-300, Reiner et al (2003) Bioinformatics, 19, 368-375). The data were visualized by FIESTA (http://bioinfogp.cnb.csic.es/tools/fiesta_server)

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA. The cRNA preparation (15 µg) were fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: Plants were grown in plastic pots containing a mixture of substrate and vermiculite (3:1). Controlled environmental conditions were provided in growth chambers at 22ºC and 65% RH.

extract_protocol: Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s protocol. Each RNA preparation was tested for degradation using the Agilent 2100 Bioanalyzer (Agilent technologies, Palo Alto, CA).

treatment_protocol: Ler and esd7-1 14-d-old seedlings grown under SD photoperiods

tag: tissue

value: seedlings

tag: genotype

value: esd7-1 mutant

tag: age


title: esd7-1 mutant, 14 short days, biological rep3

description: Gene expression data from esd7-1 mutant

source_name: esd7-1 14-d-old seedlings grown under SD photoperiods


title: Ler wt, 14 short days, biological rep3

description: Gene expression data from Ler wt

source_name: Ler 14-d-old seedlings grown under SD photoperiods

value: Ler wt


title: TNT-RepeatD4-24mg/kg-Rep6

status: Public on Oct 08 2010

city: Vicksburg

first: Natalie

last: Barker

state: MS

address: 3909 Halls Ferry Rd.

country: USA

institute: Engineer Research and Development Center

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt

hyb_protocol: 600 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 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array 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), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 seconds with Acetonitrile, and dried with Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned immediately after washing on GenePix 4200AL scanner at PMT gain level 350 using default setting (Scan resolution 5um, One channel-Green, Laser power 100%).

data_processing: The scanned images were analyzed with GenePix Pro 6.1  (Molecular Devices, Sunnyvale, CA) using default parameters and Agilient-provided GEML grid file 021219_G2_D_F_20080811.xml to obtain signal intensities.  Non-uniform spots and spots with a signal intensity outside the linear range were flagged.  Signal intensity was converted into relative RNA concentration based on the linear standard curve of spike-in RNAs.  The relative RNA concentration was normalized to the median value on each array.

organism: Eisenia fetida

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: Earthworms were kept in moistened sphagnum peat (pH 6.5–7.5, moisture content 50%) and fed ad libitum on a diet of with Magic Worm Food (Carolina Biological Supply).

extract_protocol: RNA was prepared using the RNeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Adults bearing clitelum, juveniles and cocoons were pulled out of the culture immediately before being used for RNA extraction.

value: whole organism


title: TNT-RepeatD4-6mg/kg-Rep7

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: Ler wt, 14 short days, biological rep2

description: Gene expression data from Ler wt

value: 14-d-old seedlings grown under SD photoperiods


title: esd7-1 mutant, 14 short days, biological rep2

description: Gene expression data from esd7-1 mutant


title: TNT-RepeatD4-6mg/kg-Rep6

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-RepeatD4-6mg/kg-Rep3

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-RepeatD4-6mg/kg-Rep10

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-RepeatD4-6mg/kg-Rep2

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-RepeatD4-6mg/kg-Rep8

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-RepeatD4-6mg/kg-Rep1

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: Ler wt, 14 short days, biological rep1

description: Gene expression data from Ler wt


title: TNT-RepeatD4-24mg/kg-Rep8

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-RepeatD4-24mg/kg-Rep7

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-RepeatD4-6mg/kg-Rep9

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-RepeatD4-24mg/kg-Rep5

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-RepeatD4-24mg/kg-Rep4

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-RepeatD4-24mg/kg-Rep10

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-RepeatD4-24mg/kg-Rep3

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-RepeatD4-24mg/kg-Rep2

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-RepeatD4-12mg/kg-Rep8

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-RepeatD4-12mg/kg-Rep5

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-RepeatD4-12mg/kg-Rep6

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-RepeatD4-12mg/kg-Rep3

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-RepeatD4-12mg/kg-Rep7

description: 252121910045_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-RepeatD4-12mg/kg-Rep4

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-RepeatD4-12mg/kg-Rep2

description: 252121910033_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-OrigD4-96mg/kg-Rep6

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-OrigD4-96mg/kg-Rep9

description: 252121910012_EW_focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-96mg/kg-Rep7

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-OrigD4-96mg/kg-Rep5

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-96mg/kg-Rep4

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-RepeatD4-12mg/kg-Rep10

description: 252121910047_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-OrigD4-6mg/kg-Rep8

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-OrigD4-6mg/kg-Rep9

description: 252121910011_EW_focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-OrigD4-6mg/kg-Rep7

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-OrigD4-96mg/kg-Rep3

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-OrigD4-96mg/kg-Rep8

description: 252121910012_EW_focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-OrigD4-6mg/kg-Rep4

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-OrigD4-96mg/kg-Rep1

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-OrigD4-6mg/kg-Rep6

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-6mg/kg-Rep5

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-OrigD4-6mg/kg-Rep10

description: 252121910011_EW_focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-6mg/kg-Rep1

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-OrigD4-48mg/kg-Rep7

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-OrigD4-48mg/kg-Rep9

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-OrigD4-48mg/kg-Rep6

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-OrigD4-48mg/kg-Rep2

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-OrigD4-48mg/kg-Rep10

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-OrigD4-48mg/kg-Rep5

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-OrigD4-48mg/kg-Rep3

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-OrigD4-24mg/kg-Rep8

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-OrigD4-48mg/kg-Rep1

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-OrigD4-24mg/kg-Rep7

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-24mg/kg-Rep5

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-OrigD4-24mg/kg-Rep4

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-OrigD4-24mg/kg-Rep6

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-OrigD4-24mg/kg-Rep3

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-24mg/kg-Rep2

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-OrigD4-24mg/kg-Rep10

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-12mg/kg-Rep9

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-OrigD4-12mg/kg-Rep6

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-6mg/kg-Rep8

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-OrigD4-12mg/kg-Rep5

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-OrigD4-12mg/kg-Rep8

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-OrigD4-12mg/kg-Rep10

description: 252121910030_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-D14-6mg/kg-Rep6

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-D14-6mg/kg-Rep9

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-OrigD4-12mg/kg-Rep3

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-D14-6mg/kg-Rep5

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-OrigD4-12mg/kg-Rep1

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-6mg/kg-Rep7

description: 252121910016_EW_focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-6mg/kg-Rep1

description: 252121910013_EW_focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-D14-6mg/kg-Rep2

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-D14-48mg/kg-Rep3

description: 252121910016_EW_focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-D14-48mg/kg-Rep8

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-D14-48mg/kg-Rep4

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-D14-48mg/kg-Rep7

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-D14-6mg/kg-Rep3

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-D14-48mg/kg-Rep10

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-D14-48mg/kg-Rep1

description: 252121910013_EW_focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-D14-48mg/kg-Rep2

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-D14-24mg/kg-Rep9

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-D14-24mg/kg-Rep5

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-24mg/kg-Rep2

description: 252121910013_EW_focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-D14-24mg/kg-Rep8

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: TNT-D14-24mg/kg-Rep6

description: 252121910016_EW_focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-D14-24mg/kg-Rep3

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: TNT-D14-48mg/kg-Rep6

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: TNT-D14-12mg/kg-Rep7

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-D14-12mg/kg-Rep9

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-D14-12mg/kg-Rep5

description: 252121910016_EW_focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-D14-12mg/kg-Rep4

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: TNT-D14-12mg/kg-Rep6

description: 252121910016_EW_focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: TNT-D14-12mg/kg-Rep2

description: 252121910013_EW_focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-24mg/kg-Rep1

description: 252121910013_EW_focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: TNT-D14-12mg/kg-Rep1

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-12mg/kg-Rep3

description: 252121910032_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RepeatDay4 Control-6

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt

source_name: RepeatDay4 Control


title: RepeatDay4 Control-5

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RepeatDay4 Control-8

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RepeatDay4 Control-7

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RepeatDay4 Control-4

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-RepeatD4-8mg/kg-Rep8

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RepeatDay4 Control-3

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RepeatDay4 Control-1

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RepeatDay4 Control-2

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-RepeatD4-8mg/kg-Rep4

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: TNT-OrigD4-12mg/kg-Rep4

description: 252121910009_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-RepeatD4-64mg/kg-Rep6

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-RepeatD4-8mg/kg-Rep3

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-8mg/kg-Rep7

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-8mg/kg-Rep6

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-RepeatD4-8mg/kg-Rep1

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-RepeatD4-8mg/kg-Rep2

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-RepeatD4-8mg/kg-Rep5

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-RepeatD4-64mg/kg-Rep8

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-RepeatD4-64mg/kg-Rep2

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-RepeatD4-64mg/kg-Rep5

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-RepeatD4-32mg/kg-Rep1

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-64mg/kg-Rep4

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-RepeatD4-16mg/kg-Rep8

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-RepeatD4-32mg/kg-Rep2

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-RepeatD4-64mg/kg-Rep7

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-RepeatD4-64mg/kg-Rep3

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: TNT-D14-24mg/kg-Rep7

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-RepeatD4-64mg/kg-Rep1

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-RepeatD4-16mg/kg-Rep5

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-RepeatD4-32mg/kg-Rep8

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-RepeatD4-32mg/kg-Rep7

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-RepeatD4-32mg/kg-Rep4

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-RepeatD4-32mg/kg-Rep6

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-32mg/kg-Rep3

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-RepeatD4-128mg/kg-Rep9

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-16mg/kg-Rep3

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-RepeatD4-32mg/kg-Rep10

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-RepeatD4-16mg/kg-Rep9

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-8mg/kg-Rep8

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-RepeatD4-128mg/kg-Rep2

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-RepeatD4-128mg/kg-Rep10

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-RepeatD4-16mg/kg-Rep7

description: 252121910027_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-8mg/kg-Rep3

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-RepeatD4-16mg/kg-Rep4

description: 252121910024_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-RepeatD4-128mg/kg-Rep7

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-OrigD4-8mg/kg-Rep4

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-OrigD4-8mg/kg-Rep2

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-RepeatD4-128mg/kg-Rep8

description: 252121910028_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-OrigD4-8mg/kg-Rep5

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-16mg/kg-Rep10

description: 252121910029_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-RepeatD4-128mg/kg-Rep3

description: 252121910025_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-RepeatD4-128mg/kg-Rep6

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-RepeatD4-128mg/kg-Rep5

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-OrigD4-64mg/kg-Rep5

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-8mg/kg-Rep1

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-OrigD4-8mg/kg-Rep6

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-OrigD4-8mg/kg-Rep7

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-32mg/kg-Rep6

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-OrigD4-32mg/kg-Rep5

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-OrigD4-64mg/kg-Rep3

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-OrigD4-64mg/kg-Rep9

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-OrigD4-64mg/kg-Rep4

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-64mg/kg-Rep7

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-OrigD4-64mg/kg-Rep6

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-OrigD4-64mg/kg-Rep8

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-OrigD4-32mg/kg-Rep7

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-OrigD4-16mg/kg-Rep8

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-OrigD4-32mg/kg-Rep8

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-OrigD4-32mg/kg-Rep4

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-32mg/kg-Rep1

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-RepeatD4-16mg/kg-Rep6

description: 252121910026_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-OrigD4-16mg/kg-Rep6

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-128mg/kg-Rep6

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-128mg/kg-Rep8

description: 252121910005_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-OrigD4-32mg/kg-Rep3

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-OrigD4-128mg/kg-Rep5

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-OrigD4-32mg/kg-Rep10

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-D14-8mg/kg-Rep6

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-D14-8mg/kg-Rep4

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-D14-8mg/kg-Rep5

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-OrigD4-16mg/kg-Rep5

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-OrigD4-64mg/kg-Rep2

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-16mg/kg-Rep4

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-OrigD4-16mg/kg-Rep9

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-D14-64mg/kg-Rep6

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-D14-8mg/kg-Rep10

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-D14-64mg/kg-Rep8

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-16mg/kg-Rep3

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-D14-64mg/kg-Rep9

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-D14-64mg/kg-Rep2

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-16mg/kg-Rep1

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-128mg/kg-Rep7

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-32mg/kg-Rep8

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-OrigD4-128mg/kg-Rep9

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-D14-8mg/kg-Rep9

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-D14-8mg/kg-Rep3

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-OrigD4-128mg/kg-Rep10

description: 252121910006_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-D14-64mg/kg-Rep4

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-D14-16mg/kg-Rep9

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: RDX-D14-32mg/kg-Rep1

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-64mg/kg-Rep1

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-D14-16mg/kg-Rep5

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-D14-32mg/kg-Rep3

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-OrigD4-128mg/kg-Rep4

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-OrigD4-128mg/kg-Rep2

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-32mg/kg-Rep6

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-D14-8mg/kg-Rep1

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-D14-64mg/kg-Rep5

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-OrigD4-16mg/kg-Rep7

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-16mg/kg-Rep10

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-64mg/kg-Rep3

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-D14-128mg/kg-Rep8

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-D14-32mg/kg-Rep9

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-D14-128mg/kg-Rep6

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-D14-128mg/kg-Rep9

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-D14-32mg/kg-Rep5

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-D14-128mg/kg-Rep7

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: RDX-D14-32mg/kg-Rep10

description: 252121910023_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-D14-16mg/kg-Rep1

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: RDX-D14-32mg/kg-Rep2

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-D14-128mg/kg-Rep5

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-16mg/kg-Rep4

description: 252121910020_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: OriginalDay4 Control-5

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt

source_name: OriginalDay4 Control


title: Day14 Control-8

description: 252121910022_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt

source_name: Day14 Control


title: RDX-D14-128mg/kg-Rep1

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: OriginalDay4 Control-4

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: RDX-D14-8mg/kg-Rep8

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: OriginalDay4 Control-3

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: RDX-D14-16mg/kg-Rep8

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: RDX-D14-128mg/kg-Rep3

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: OriginalDay4 Control-8

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: RDX-D14-16mg/kg-Rep3

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: Day14 Control-6

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_4.txt


title: OriginalDay4 Control-2

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: Day14 Control-7

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: RDX-D14-128mg/kg-Rep2

description: 252121910019_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: OriginalDay4 Control-7

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: Day14 Control-3

description: 252121910016_EW_focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: OriginalDay4 Control-9

description: 252121910011_EW_focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: Day0 Control-3

description: 252121910003_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt

source_name: Day0 Control


title: Day0 Control-2

description: 252121910002_EW_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: OriginalDay4 Control-6

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_1_2.txt


title: Day14 Control-2

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: Day14 Control-4

description: 252121910017_EW_focus_PMT350_GE1-v5_95_Feb07_1_4.txt


title: Day0 Control-7

description: 252121910008_EW_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: Day0 Control-10

description: 252121910011_EW_focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: Day0 Control-9

description: 252121910010_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: Day0 Control-6

description: 252121910007_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt


title: Day14 Control-1

description: 252121910031_Ew_Focus_PMT350_GE1-v5_95_Feb07_1_3.txt


title: normal human small airway epithelial cell line treated with 5-AZA rep 2

status: Public on Oct 07 2010

city: Baltimore

first: Chad

last: Glazer

state: MD

address: 1550 Orleans St. CRB II-574

institute: Johns Hopkins Medical Institutions

description: no additional information

hyb_protocol: Hybridization cocktail is made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA is loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.

scan_protocol: All arrays are scanned in the Affymetrix GeneChip Scanner 3000

data_processing: Raw analysis performed with Affymetrix GeneChip Operating System (GCOS) 1.4

label: Biotin

organism: Homo sapiens

source_name: SAEC AZA rep 2

label_protocol: T7 oligo(dT) primer (Sigma-Proligo) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf , Hamburg, Germany) an in vitro transcription reaction is performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions are cleaned up using RNeasy Mini Kit (Qiagen) and concentration determined via Nanodrop Spectrophotometer.  15ug cRNA is fragmented using 5X fragmentation buffer (made in-house).

extract_protocol: Total cellular RNA was isolated using Trizol (Life Technologies, Gaithersburg, MD) and the RNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: NHBE and SAEC cells were split to low density (1×106 cells/T-75 flask) 24 hours before treatment. Stock solutions of 5Aza-dC (Sigma, St. Louis, MO) and TSA (Sigma) were dissolved in 50% Acetic Acid or 100% ethanol, respectively. Cells were treated with 5 µM 5-Aza-deoxycytidine for 3 days and 300 nM TSA for last 24 hours. Baseline expression was established by mock-treated cells with the same volume of 50% Acetic Acid or ethanol.

value: Lung

tag: cell line

value: SAEC

tag: agent

value: 5-aza-dC and TSA


title: normal human small airway epithelial cell line control rep 1

description: no additional information

source_name: SAEC control rep 1

value: mock-treated


title: normal human small airway epithelial cell line control rep 2

description: no additional information

source_name: SAEC control rep 2


title: normal human small airway epithelial cell line treated with 5-AZA rep 1

description: no additional information

source_name: SAEC AZA rep 1


title: normal human bronchial epithelial cell line treated with 5-AZA rep 2

description: no additional information

source_name: NHBE AZA rep 2

value: NHBE


title: normal human small airway epithelial cell line control rep 3

description: no additional information

source_name: SAEC control rep 3


title: Day14 Control-5

description: 252121910018_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_1.txt


title: normal human small airway epithelial cell line treated with 5-AZA rep 3

description: no additional information

source_name: SAEC AZA rep 3


title: normal human bronchial epithelial cell line control rep 2

description: no additional information

source_name: NHBE control rep 2


title: normal human bronchial epithelial cell line control rep 1

description: no additional information

source_name: NHBE control rep 1


title: normal human bronchial epithelial cell line treated with 5-AZA rep 1

description: no additional information

source_name: NHBE AZA rep 1


title: normal liver 2

status: Public on Oct 06 2010

city: Taipei

first: Chan-Yen

last: Tsai

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: Yang-Ming University

description: total RNA isolated from normal liver of stage D colorectal carcinoma patient 2

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: RMA through R based affy module

source_name: normal liver from stage D colorectal carcinoma patient 2

label_protocol: Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Total RNA extracted using standard Trizol protocol, followed by Qiagen RNeasy column clean-up

value: liver

tag: tumor stage of patient

value: stage D


title: Mutant sdg2-1 young flowers Replicate 1

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

description: Biological replicate 1 of mutant young flowers

hyb_protocol: Standard Agilent protocol

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction. Signal intensity were normalized using Quantile method. Signal : raw Cy3 signal intensity ; Log2NormSignal : Log2 transformed Normalized Signal

source_name: Mut1 flower buds

label_protocol: 2 µg of total RNA were labeled according Aligent's instructions.

growth_protocol: Plants were grown in the greenhouse under 16h light and 8h dark at 22°C.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up according to manufacturer's instructions.

tag: ecotype

value: Columbia

value: whole flower buds

value: sdg2-1 mutant


title: Day0 Control-4

description: 252121910004_EW_Focus_PMT350_GE1-v5_95_Feb07_2_3.txt


title: normal human bronchial epithelial cell line treated with 5-AZA rep 3

description: no additional information

source_name: NHBE AZA rep 3


title: RDX-D14-16mg/kg-Rep7

description: 252121910021_Ew_Focus_PMT350_GE1-v5_95_Feb07_2_2.txt


title: Mutant sdg2-1 young flowers Replicate 2

description: Biological replicate 2 of mutant young flowers

source_name: Mut2 flower buds


title: normal liver 1

description: total RNA isolated from normal liver of stage D colorectal carcinoma patient 1

source_name: normal liver from stage D colorectal carcinoma patient 1


title: liver metastasis 2

description: total RNA isolated from liver metastasis of stage D colorectal carcinoma patient 2

source_name: liver metastasis from stage D colorectal carcinoma 2

tag: primary site

value: colon


title: Day0 Control-1

description: 252121910001_EW_Focus_PMT350_GE1-v5_95_Feb07_1_1.txt

source_name: Day0 Control


title: Wild-type young flowers Replicate 2

description: Biological replicate 2 of Wild-type young flowers

source_name: WT2 flower buds

value: wild-type


title: liver metastasis 1

description: total RNA isolated from liver metastasis of stage D colorectal carcinoma patient 1

source_name: liver metastasis from stage D colorectal carcinoma patient 1


title: Transcription profile of Aplysia californica premtamorphosis (stage 6) (DAA)

status: Public on Oct 05 2010

city: Guelph

first: Andreas

last: Heyland

state: ON

address: 50 Stone Rd East

department: Integrative Biology

country: Canada

institute: University of Guelph

description: Pre-metamorphic (stage6) stage were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

hyb_protocol: The recommended amount of 750 ng of labeled cRNA was fragmented and hybridized to the arrays using recommended procedures described in the In situ Hybridization Kit PlusTM (Agilent Technologies). Controls provided in the In situ Hybridization Kit were spiked in at the time of hybridization. The arrays were washed according to the manufactures recommended protocol.

scan_protocol: The arrays were scanned on an Agilent Technologies G2565AA Microarray ScannerTM. Data were extracted after scanning using Agilent’s Feature Extraction 5.1.1TM software

data_processing: The balancing between the Cy3 and Cy5 signals within each array was performed by the RANK order method using LOWESS smoothing procedure as implemented in the Agilent feature extraction software version 7.0 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=30997). The background on all arrays analyzed for the Cy3 and Cy5 channels was observed to be nearly identical (41.8  1.1) over all 44,000 features. No local background subtraction was performed; instead the data was filtered by P-values obtained from fitting the signal and background values and spatial detrending algorithm. Only data that had P-values of less than or equal to 0.01 (meaning feature signal is significantly and positively higher than background signal) on both Cy3 and Cy5 channels from each array was used for further analysis (“floor”). A suite of algorithms are also included in the processing of the final TIFF image involving an error-model proprietary to Agilent that has been pre-determined to give the best corrected data for downstream analysis.

organism: Aplysia californica

source_name: Premetamorphosic stage (Stage 6)

label_protocol: Label protocol cRNA production was preformed using Agilent’s Low RNA Input Linear Amplification kitTM (Agilent Technologies). All amplification reactions involved only one round of amplification. Concentration of the cRNA was determined by GeneSpec IIITM and the 2100 Bioanalyzer both described above. The cRNA was labeled either using the direct method in Agilent’s Low RNA Input Linear Amplification kit or with an indirect technique using the MicroMax ASAP RNA labeling kitTM (PerkinElmer).

growth_protocol: Cultured at the Whitney Laboratory in filtered, sterile seawater until processing

extract_protocol: RNAqueous-MicroTM (Ambion, Austin, TX) kits. Before further processing of the RNA, quality was checked using a 2100 BioanalyzerTM (Agilent Technologies). Small aliquots of extracted RNA were loaded on a 6000 Nano Lab chip that produces an electropherogram image along with a gel-like image of the sample representing peak ratios of the 28s/18s RNA contained in the sample.

tag: developmental stage

value: Premetamorphoic stage(Stage 6)

source_name: Reference sample

value: reference sample containing equal amounts of RNA from each sample used int his experiment:cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.


title: Wild-type young flowers Replicate 1

description: Biological replicate 1 of Wild-type young flowers

source_name: WT1 flower buds


title: Transcription profile of Aplysia californica gastrulation (DAA)

description: Gastrula stages were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Gastrula stages

value: Gastrula stages


title: Transcription profile of Aplysia californica post-metamorphosis 60 hours (pm60) (DAA)

description: Post-metamorphic 60 hours (pm60) stage were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Post-metamorphosic stage (60 hours)

value: Post-metamorphosic stage (60 hours)


title: Transcription profile of Aplysia californica trochophore stage (DAA)

description: Trochophore stages were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Trochophore stage

value: Trochophore stage


title: Transcription profile of Aplysia californica post-metamorphic juveniles (60 hours) (AAA)

description: Post-metamorphic larvae (60 hours) were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.


title: primary colorectal carcinoma 2

description: total RNA isolated from primary colorectal carcinoma of stage D colorectal carcinoma patient 2

source_name: primary colorectal carcinoma from stage D colorectal carcinoma 2


title: Transcription profile of Aplysia californica metamorphically competent larvae (stage6) (AAA)

description: Metamorphicaly competent  veliger larvae were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Metamorphically competent larvae (stage 6)


title: Transcription profile of Aplysia californica first veliger stage (AAA)

description: First veliger stages were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: First veliger stage

value: First veliger stage


title: primary colorectal carcinoma 1

description: total RNA isolated from primary colorectal carcinoma of stage D colorectal carcinoma patient 1

source_name: primary colorectal carcinoma from stage D colorectal carcinoma patient 1


title: Transcription profile of Aplysia californica post-metamorphosis (stage7) (DAA)

description: Post-metamorphic (stage7) stage were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: post-metamorphosis (Stage7)

value: post-metamorphosis (Stage7)


title: Transcription profile of Aplysia californica post-metamorphic stage (stage7) (AAA)

description: Post-metamorphic larvae (stage7) were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Post-metamorphosic stage (stage7)

value: Post-metamorphosic stage (stage7)


title: Transcription profile of Aplysia californica trochophore stage (AAA)


title: Transcription profile of Aplysia californica cleavage stages (AAA)

description: Cleavage stages were hybridized against a reference sample containing equal amounts of RNA from each sample used int his experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Mixed cleavage stages within 48 hours of fertilization

value: reference sample containing equal amounts of RNA from each sample used in this experiment:cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.


title: Transcription profile of Aplysia californica first veliger stage (DAA)

description: First veliger stage were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.


title: Transcription profile of Aplysia californica gastrulation (AAA)

source_name: Gastrulation stages


title: Transcription profile of Aplysia californica cleavage stages (DAA)

description: cleavage stages were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Cleavage stages

value: Cleavage stages


title: Transcription profile of Aplysia californica hatching (DAA)

description: Hatchjing veliger stages were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: hatching stage

value: Hatching veliger


title: Transcription profile of Aplysia californica hatching veliger (AAA)

description: Hatching veliger stages were hybridized against a reference sample containing equal amounts of RNA from each sample used in this experiment: cleavage stages, gastrula, trochophore, first veliger, hatching, pre-metamorphosis (Stage6), post-metamorphosis (stage7), post-metamorphosis (pm60; 60 hours post stage 7.

source_name: Hatching veliger


title: MSC_day28_donor3

status: Public on Oct 02 2010

city: Philadelphia

first: Alice

middle: H

last: Huang

state: PA

address: 424 Stemmler Hall, 3450 Hamilton Walk

department: Bioengineering

institute: University of Pennsylvania

description: mesenchymal stem cells derived from bone marrow of juvenile calves (3-6 months), matched to chondrocytes.

hyb_protocol: cDNA yields ranged from 5-10 μg, and 5 μg were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to 9 Bovine GeneChips (Affymetrix Inc., Santa Clara, CA).

scan_protocol: Microarrays were washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. Fluorescence signals were collected after excitation at 570 nm by the Affymetrix Gene Chip Scanner 3000 (Affymetrix Inc.)

data_processing: data normalization was performed with the RMA algorithm.

organism: Bos taurus

source_name: mesenchymal stem cells from bone marrow, chondrogenic, 28 days culture

label_protocol: the resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated.

extract_protocol: total RNA was extracted by two sequential isolations of trizol-chloroform. total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated a synthetic RNA sequence.  Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript

treatment_protocol: MSC-seeded agarose was cultured in chemically defined media containing 10 ng/mL TGF-beta3 for 28 days.

value: bone marrow

tag: cell type

value: chondrogenic mesenchymal stem cells

value: 3-6 months

tag: days in culture

tag: donor


title: IRBP-GFP + human photoreceptors

city: Seattle

first: Thomas

last: Reh

state: WA

address: 815 Mercer St

department: Biological Structure

institute: University of Washington

description: IRBP-GFP + human photorecepotrs

hyb_protocol: Following fragmentation, cRNA were hybridized on Human Gene 1.0 ST array, washed and stained as per manufacturer guidelines.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software.

source_name: FACS IRBP-GFP cells from 90 day human retina

label_protocol: Cy3 cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Retinas were either directly used or maintained in culture with IRBP-GFP lentivirus for 4 days till GFP was observed

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

treatment_protocol: Cultured retina from human fetal day 90 was treated with IRBP-GFP lentivirus

value: photoreceptor cells


title: MSC_day0_donor1

source_name: mesenchymal stem cells from bone marrow, undifferentiated, 0 days culture

extract_protocol: total RNA was extracted using two sequential isolations of trizol-chloroform.total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated a synthetic RNA sequence.  Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript

treatment_protocol: undifferentiated MSC-seeded agarose was harvested immediately after encapsulation.

value: undifferentiated mesenchymal stem cells


title: MSC_day0_donor2


title: MSC_day0_donor3


title: MSC_day28_donor1

description: mesenchymal stem cells from bone marrow dissected from juvenile joints, matched to chondrocytes.


title: MSC_day28_donor2


title: chondrocytes_day28_donor3

description: chondrocytes isolated from cartilage dissected from juvenile (3-6 months) calves.

data_processing: data normalization was performed with the RMA algorithm

source_name: chondrocytes from articular cartilage, 28 days culture

treatment_protocol: chondrocyte-seeded agarose was cultured in chemically defined media containing 10 ng/mL TGF-beta3 for 28 days.

value: articular cartilage

value: chondrocytes


title: chondrocytes_day28_donor2

description: cartilage was dissected from juvenile (3-6 months) calves and encapsulated in agarose immediately after isolation.


title: wild type vs GPCR mutant

status: Public on Oct 01 2010

city: New Delhi

first: Nandula

last: Raghuram

email: raghuram98@hotmail.com, ravipathak@aol.in, pathakster@gmail.com, navjyoti.chakraborty@gmail.com

state: Delhi

address: Dwarka, Sector -16C

department: School of Biotechnology

country: India

institute: Guru Gobind Singh Indraprastha University

description:
The Arabidopsis oligo arrays were procured from the Galbraith laboratory
ATv3_02_0271.gpr

hyb_protocol: Brief flow chart 1. cDNA Synthesis from mRNA 2. Hydrolysis of RNA 3. Purification of Amino allyl labeled cDNA 4. Dye binding with Amino allyl labeled cDNA 5. Purification of dye labeled cDNA For additional description kindly follow the link (http://arrayit.com/Products/Labeling_Kits/AAL/aal.html)

scan_protocol: Scanning performed using the AXON Instruments Scanner 4200 Autoloader. Feature intensity values are extracted from the resulting image using Gene PixPro

data_processing: The median intensity after background intensity subtraction provided by Genepix Pro  software with the scan results was used for further calculations.  Average of background corrected intensity of all spots was calculated.  Average normalization was performed as described below: The normalization factor was calculated by dividing the average of spot intensities in the mutant sample by the average of spot intensities in the wildtype sample.  The background corrected intensity of each spot in the mutant was divided by the normalization factor.  To correct for low values all values below 100 were replaced with a nominal value of 100.  Fold change for each spot was calculated by dividing processed values for the mutant sample by those for the wildtype sample.  If log2fold change was above 1 in both replicate experiments the gene was considered upregulated and if it was below -1 the gene was considered downregulated.

molecule: polyA RNA

source_name: wild type leaves

label_protocol: ARRAYIT protocol (based on manufacturer's instructions) for hybridization and subsequent labeling using Amersham dyes.

extract_protocol: Total RNA isolation using "Hot-Phenol" method and subsequent polyA RNA isolation using AMBION MICROPLOY(A) Purist kit Catalogue:1919

tag: Columbia variety Wild Type

source_name: GPCR mutant leaves

tag: GPCR Mutant


title: wild type vs GPCR mutant (flip-dye)

description:
The Arabidopsis oligo arrays were procured from the Galbraith laboratory
ATV3.02.272.gpr

data_processing: The median intensity after background intensity subtraction provided by Genepix Pro software with the scan results was used for further calculations. Average of background corrected intensity of all spots was calculated. Average normalization was performed as described below: The normalization factor was calculated by dividing the average of spot intensities in the mutant sample by the average of spot intensities in the wildtype sample. The background corrected intensity of each spot in the mutant was divided by the normalization factor. To correct for low values all values below 100 were replaced with a nominal value of 100. Fold change for each spot was calculated by dividing processed values for the mutant sample by those for the wildtype sample. If log2fold change was above 1 in both replicate experiments the gene was considered upregulated and if it was below -1 the gene was considered downregulated.

label_protocol: Protocol as described in the Microarray cDNA Synthesis Kit from ROCHE APPLIED SCIENCE. Labeling performed using Amersham dyes

extract_protocol: Total RNA isolation using "Hot-Phenol" method

extract_protocol: Total RNA isolation using "Hot-Phenol"


title: wild type vs G-alpha mutant (flip-dye)

description:
The Arabidopsis oligo arrays were procured from the Galbraith laboratory
ATv3.02.278.gpr

hyb_protocol: Protocol as described in the Microarray cDNA Synthesis Kit from ROCHE APPLIED SCIENCE.

extract_protocol: Total RNA isolation using "Hot-Phenol" method.

source_name: G-alpha mutant leaves

tag: G-alpha Mutant


title: wild type vs G-alpha mutant

description:
The Arabidopsis oligo arrays were procured from the Galbraith laboratory
ATv3.02.277.gpr

label_protocol: Protocol as described in the Microarray cDNA Synthesis Kit from ROCHE APPLIED SCIENCE. Labeling performed using Amersham dyes.

tag: G-alpha mutant


title: chondrocytes_day28_donor1

extract_protocol: two sequential extractions of trizol-chloroform was used to extra total RNA.  total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated a synthetic RNA sequence.  Second-strand cDNA synthesis was followed by ribo-SPIA (Single Primer Isothermal Amplification, NuGEN Technologies Inc. San Carlo, CA) for linear amplification of each transcript


title: MEFs_wild_type_replicate_I2

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

institute: INSTITUTO DE SALUD CARLOS III - IIER

description: CodeLinkTM Mouse Whole Genome microarrays (Applied Microarrays Inc., Tempe, AZ) were used to analyze gene expression profiles. Total RNA was isolated with TriReagent (Sigma) and its integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Labeling and hybridization were performed using the CodeLinkTM iExpress assay reagent kit according to manufacturers instructions. After hybridization and washing, slides were scanned in an Axon GenePix Scanner (Arlington, TX) and analyzed using CodeLinkTM Expression Analysis Software. Data were median normalized, log2-transformed and exported to the MeV software (TIGR, Rockville, MD) for additional statistical analysis and graphical visualization. We analyzed three independent preparations of early passage, MEF for each genotype, each derived from an individual embryo. Genes with ratios between Ing1-deficient and wild type higher than 2 or lower than 0.5, with statistical significance (P < 0.05, Students T Test) were selected for further analysis.

hyb_protocol: Hybridization was performed according manufacturer's instructions described in the CodeLink Expression Bioarray System protocol.

scan_protocol: Slides were scanned in an Axon GenePix Scanner.

data_processing: Images were analyzed using CodeLink Expression Analysis Software 4.1. Raw data were median-normalized and exported to MeV Software for graphical visualization and statistical analyses.

organism: Mus musculus

source_name: Mouse embryonic fibroblasts isolated from wild type mice

label_protocol: Labeling was performed using the CodeLink iExpress Expression Assay Reagent kit according manufacturer's instructions.

extract_protocol: Total RNA was isolated with TRI-REAGENT (Sigma) and integrity assayed with an Agilent 2100 Bioanalyzer.

value: Mouse embryonic fibroblasts

value: embryos

tag: genome/variation

value: wild type


title: MEFs_wild_type_replicate_H3


title: MEFs_Ing1_deficient_replicate_B1

source_name: Mouse embryonic fibroblasts isolated from Ing1 deficient mice

value: Ing1 locus inactivated by the insertion of a gene trap cassette


title: MEFs_wild_type_replicate_H2


title: CTL3

city: Ikoma

first: Woong

last: Kim

state: Nara

department: Biosciences

country: Japan

institute: NAIST

description: Transcriptome profiles were acquired using Applied Biosystems AB1700 technology. Human Genome Survey Microarrays V2.0 feature numerous control probes and 32878 target gene specific 60 mer probes detecting more than 27000 different genes.

hyb_protocol: 10 ug of digoxigenin-labeled cRNA samples were fragmented for 30 min at 60℃ and hybridized for 16h to Human Genome Survey Microarrays V2.0 (Applied Biosystems) at a temperature of 55℃. After several washing steps of increasing stringency, an anti-digoxigenin-antibody conjugated to alkaline phosphatase (Roche Diagnostics) was added.

scan_protocol: Chemiluminescence and fluorescence signals were detected on an AB1700 microarray reader. Reagents from the Chemiluminescence Detection Kit (Applied Biosystems) were used in this procedure. Human Genome Survey Microarrays V2.0 feature numerous control probes and 32878 target gene specific 60 mer probes detecting more than 27000 different genes

data_processing: Detectable probes were determined by a signal to noise ratio (S/N) > 3 and quality flag < 5,000 determined by the AB1700 microarray software tool.

label: Digoxigenin

source_name: Embryo of littermate wildtype mouse

label_protocol: 1-2 ug total RNA were introduced into an RT-IVT reaction: the RNA was reverse-transcribed into ds-cDNA and then converted into labelled cRNA by in vitro transcription (Nano-Amp RT-IVT Labeling Kit, Applied Biosystems) using digoxigenin-conjugated UTP nucleotides (Roche).

extract_protocol: Total RNA was isolated from PSM cells using SV total RNA Isolation Kit (Promega) according to the manufacturer’s instructions. The purity and quantity of the RNA were assessed by the Gene Quant pro (Amersham Biosciences)

treatment_protocol: PSM cells were dissected from E10.5 embryo and immediately preserved in liquid nitrogen for 1-2 weeks.

tag: tissue

value: Presomitic mesoderm (PSM) cells

tag: stage


title: CTL1


title: Nrarp3

source_name: Embryo of Nrarp knockout mouse


title: CTL2


title: Nrarp1


title: MEFs_Ing1_deficient_replicate_C3


title: HCT116_siATF3_24hr

city: Chiyodaku

first: Yujiro

last: Tanaka

state: Tokyo

address: 2-3-10 Kandasurugadai

department: School of Biomedical Science

institute: Tokyo Medical and Dental University

description: Gene expression in HCT116 cells transfected with siRNA against ATF3 and stimulated with methyl methanesulfonate (MMS) for 24 hr.

hyb_protocol: Probes were hybridized to Whole Human Genome Microarray Kit, 4 x 44K according to One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) Ver. 5.7 (Agilent, Japan).

scan_protocol: Arrays were scanned by Agilent DNA Microarray Scanner using Feature Extraction 9.5.3 (Agilent, Japan).

data_processing: Normalization between arrays was done by using average signals of seven house keeping genes (RPS13, RPL27, RPS20, RPL30, RPL13A, RPL9, and SRP14) according to de Jonge HJ et al. Evidence based selection of housekeeping genes. PLoS One. 2007 Sep 19;2(9):e898.

source_name: HCT116 cells, siATF3, 24hr, replicate 1

label_protocol: RNA was labelled with Cy3 according to One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling) Ver. 5.7 (Agilent, Japan).

growth_protocol: HCT116 cells were cultured in 0.25% FCS for 24 hours, transfected with either control siRNA or siRNA for ATF3 knockdown, and after further 24 hours stimulated with MMS.

extract_protocol: Total RNA was extracted from MMS-treated HCT116 cells by using Sepasol RNA I Super (nacalai tesque, Japan).

treatment_protocol: HCT116 cells pre-transfected with siRNA were stimulated by methyl methanesulfonate (MMS) at 50 ng/ml for 0, 6, 12, and 24 hours.

value: colorectal cancer

tag: protocol

value: ATF3 knockdown

tag: time


title: HCT116_siAtf3_0hr

description: Gene expression in HCT116 cells transfected with siRNA against ATF3 and stimulated with methyl methanesulfonate (MMS) for 0 hr.

source_name: HCT116 cells, siATF3, 0hr, replicate 1

tag: cell line


title: HCT116_siCont_24hr

description: Gene expression in HCT116 cells transfected with control siRNA and stimulated with methyl methanesulfonate (MMS) for 24 hr.

source_name: HCT116 cells, siCont, 24hr, replicate 1

value: control


title: HCT116_siATF3_12hr

description: Gene expression in HCT116 cells transfected with siRNA against ATF3 and stimulated with methyl methanesulfonate (MMS) for 12 hr.

source_name: HCT116 cells, siATF3, 12hr, replicate 1


title: Nrarp2


title: HCT116_siCont_12hr

description: Gene expression in HCT116 cells transfected with control siRNA and stimulated with methyl methanesulfonate (MMS) for 12 hr.

source_name: HCT116 cells, siCont, 12hr, replicate 1


title: HCT116_siCont_0hr

description: Gene expression in HCT116 cells transfected with control siRNA and stimulated with methyl methanesulfonate (MMS) for 0 hr.

source_name: HCT116 cells, siCont, 0hr, replicate 1


title: HCT116_siATF3_6hr

description: Gene expression in HCT116 cells transfected with siRNA against ATF3 and stimulated with methyl methanesulfonate (MMS) for 6 hr.

source_name: HCT116 cells, siATF3, 6hr, replicate 1


title: HCT116_siCont_6hr

description: Gene expression in HCT116 cells transfected with control siRNA and stimulated with methyl methanesulfonate (MMS) for 6 hr.

source_name: HCT116 cells, siCont, 6hr, replicate 1


title: MEFs_Ing1_deficient_replicate_C4


title: LNCaP HG18 (ChIP-chip)

type: genomic

description: ChIP-chip for ATF3 in LNCaP cells.

hyb_protocol: According to NimbleGen's protocol (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Peak calling was carried out using MA2C software using 500 bp window, scoring by trimmed mean, lower-bound of false discovery rate at 0.2%, and default setting for else (Song J.S., et al., Model-based analysis of two-color arrays (MA2C), Genome Biology 2007, 8:R178, doi:10.1186/gb-2007-8-8-r178).

1. MA2C $fCHIP IDg.bed, MA2C $fCHIP IDg.gff, MA2C $fCHIP IDg.xls, MA2C $fCHIP IDg.pdf, and MA2C $fCHIP IDg FDRtable.txt for peak locations and quality control. In MA2C $fCHIP IDg.xls, the column \Peak Pos" contains the location of peak with respect to the peak starting position. In some cases, two enriched regions may overlap and cause problems with some genome browsers, we resolve this issue by merging the overlapping peak regions, if necessary.
2. MA2C $fCHIP IDg.ratio.bar contains normalized probe ratios.
3. MA2C $fCHIP IDg.MA2Cscore.bar contains MA2C scores.

molecule: genomic DNA

source_name: ATF3 ChIP DNA from LNCaP cells

growth_protocol: LNCaP cells in standard culture.

extract_protocol: LNCaP cells were fixed with 0.01% formaldehyde for 10 min at RT and the reaction was stopped by glycine. After a wash PBS, cells were lysed and DNA was fragmented by 12 cycles of sonication at high power for 30 seconds using BioRuptor.

treatment_protocol: No treatment.

tag: disease state

value: prostate cancer

value: LNCaP

tag: antibody

value: anti-ATF3 antibody

source_name: Whole cell extract DNA from LNCaP cells (control)


title: normal human bronchial epithelial cell line control rep 3

description: no additional information

source_name: NHBE control rep 3

value: Lung

value: NHBE

tag: agent

value: mock-treated


title: Neurosphere cells rep 2

city: Lund

first: Ulrike

middle: A.

last: Nuber

address: Klinikgatan 26

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was background-corrected and summarized using BeadStudio software (Illumina) and further processed with the Bioconductor/Lumi package;  data were normalized applying quantile normalization and variance stabilization (function vst).

source_name: Spinal cord derived, cultured neurosphere cells

label_protocol: RNA amplification and biotin-labeling were achieved with the TargetAmp 2-Round Biotin-aRNA Amplification Kit (Epicentre)

extract_protocol: RNA was extracted and purified with QIAgen's RNeasy Micro Kit including DNase I treatment

tag: strain

tag: developmental stage

value: adult

tag: cell source

value: cells from neurosphere culture

tag: facs phenotype

value: not sorted


title: Neurosphere cells rep 3


title: HCT116+MMS HG18 (ChIP-chip)

description: ChIP-chip for ATF3 in HCT116 cells treated with 50 ng/ml MMS for 6 hours.

source_name: ATF3 ChIP DNA from HCT116 cells treated with MMS

label_protocol: According to NimbleGen's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: HCT116 cells were cultured in medium containing 0.25% FCS for 24 hours and then stimulated with 50 ng/ml methyl methanesulfonate (MMS).

extract_protocol: HCT116 cells were fixed with 0.01% formaldehyde for 10 min at RT and the reaction was stopped by glycine. After a wash PBS, cells were lysed and DNA was fragmented by 12 cycles of sonication at high power for 30 seconds using BioRuptor.

treatment_protocol: Treated with MMS at 50 ng/ml for 6 hours.

value: MMS

source_name: Whole cell extract DNA from HCT116 cells treated with MMS (control)


title: E14.5 radial glia cells rep 3

source_name: embryonic forebrain, radial glia cells, FACS isolated, CD133+/CD24neg/CD45neg/CD34neg

value: embryonic day 14.5

value: FACS sorted from tissue


title: E14.5 radial glia cells rep 1


title: Neurosphere cells rep 1


title: Spinal cord ependymal cells rep 2

source_name: Spinal cord ependymal cells, FACS isolated, CD133+/CD24+/CD45neg/CD34neg


title: E14.5 radial glia cells rep 2


title: Spinal cord ependymal cells rep 3


title: Lateral ventricle wall ependymal cells rep 3

source_name: Lateral ventricle wall ependymal cells, FACS isolated, CD133+/CD24+/CD45neg/CD34neg


title: Lateral ventricle wall ependymal cells rep 1


title: Lateral ventricle wall ependymal cells rep 2


title: Spinal cord ependymal cells rep 1


title: TH_1

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

institute: Taiwan National Health Research Institute

description: Hepatoblastoma (mixed type)

hyb_protocol: Array hybridizations were carried out with 490μl of hybridization mixtures for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37℃ in Oligo aCGH Wash Buffer 2 (Agilent).

scan_protocol: The hybridized arrays were scanned using an Agilent G2565BA DNA microarray scanner (Agilent Technologies). The ScanControl Software (Agilent Technologies) was used for image acquisition. In brief, the arrays were imaged at a resolution of 5 μm. Excitation of Cy3 and Cy5 was performed at a wavelength of 532 and 635 nm, respectively. A laser power of 100% was used. Each array was subjected to a series of scans. The signals were digitized into 16 bit/pixel, yielding a maximum detection range from 1 to 65536; i.e., almost five orders of magnitude.

data_processing: After image acquisition, data extraction, normalization and transformation were carried out by using Agilent Feature Extraction Software, version 8.1.1 (Agilent Technologies), procedures listed as follow:  (1) Place Grid, find and measure spots  -define what is the array format of the image to be processed.  (2) Flag outliers  a. Compute population outliers- flag features and local backgrounds as population outliers if the minimum number of replicates is met and the mean signals varies significantly from the distribution.  b. Compute NonUniform outliers- flag features and local backgrounds as NonUniform if the pixel distribution is outside the boundary defined by the three-parameter noise model.  (3)   Compute Background, bias and error              Background subtraction→ signal correction → choose error model   (4) Dye normalization –   a. Use rank consistent probes.  b. Normalization correction methods: Linear method  (5) Compute ratios- the log ratio values are capped to 4 with appropriate signs in positive and negative directions.  Subsequent data analysis was performed with the other custom analytical software, CGH Analytics (version 3.5.14, Agilent Technologies). The Linear smoothing algorithm is used in the Moving Average approach to smooth the data sets with window size of 5 Mb.

source_name: Hepatoblastoma patient 11

label_protocol: Genomic DNA was completely fragmented with AluI and RsaI (Promega, Madison, WI, USA ), followed by purification with QIAprep Spin Miniprep Kit (Qiagen). All of the digested DNAs were subjected to labeling reactions using Agilent’s Genomic DNA Labeling Kit PLUS per manufacturer’s instructions. For each array-CGH experiment, we used DNA isolated from NPC cell line as experimental genome (cyanine 5 UTP-labeled) and the commercial healthy Caucasian male genome (Promega) as reference (cyanine 3 UTP-labeled).

extract_protocol: Genomic DNA were isolated by using DNeasy Tissue Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The TW01 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). The HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. Both cell lines were without any treatment before extraction of genomic DNA.

tag: gender

value: male

tag: age

value: 2 months

value: Peripheral blood lymphocytes

tag: health state

value: Hepatoblastoma

source_name: Commercialized normal Caucasian genome pool

value: Healthy


title: HB_10

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 10

value: female

value: 18 months


title: TC_2

description: Identical twin of TH2, healthy

source_name: Healthy control 2

value: 12 months


title: HB_8

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 8

value: 48 months


title: RB+p53DD MAFs recurred, biological rep1

first: Erik

middle: S

last: Knudsen

address: 233 S 10th St

department: Cancer Biology

institute: Kimmel Cancer Center

description: Gene expression data from fibroblasts expressing wild-type Rb and p53DD, and recurred from cisplatin treatment

hyb_protocol: Each Affymetrix GeneChip for Mouse Genome 430 2.0 was hybridized for 16 h with biotin-labeled fragmented cRNA (10 µg) in 200 µL of hybridization cocktail according to Affymetrix protocol. Arrays were washed and stained using GeneChip Fluidic Station 450.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner 3000 using GeneChip Operating Software verson 3.0.

data_processing: The Robust Multichip Average (RMA) signal was computed on Affymetrix .CEL files using RMAexpress version 1.0 software

source_name: RB+p53DD mouse adult fibroblasts, recurred from cisplatin treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: Mouse adult fibroblasts were cultured in DMEM containing 10% fetal bovine serum supplemented with 100 U/mL penicillin/streptomycin and 2 mM L-glutamine at 37oC in 5% CO2.

treatment_protocol: Mouse adult fibroblasts were first infected with retrovirus expressing p53DD and/or adenovirus to selectively delete Rb. Cells were then treated with cisplatin for 24 hours and then allowed to recover from treatment.

value: fibroblasts from peritoneal fascia


title: RB-p53DD MAFs recurred, biological rep2

description: Gene expression data from fibroblasts with Rb-deletion and p53DD, and recurred from cisplatin treatment

source_name: RB-p53DD mouse adult fibroblasts, recurred from cisplatin treatment


title: RB-p53DD MAFs untreated, biological rep1

description: Gene expression data from fibroblasts with Rb-deletion and p53DD

source_name: RB-p53DD mouse adult fibroblasts, untreated


title: RB+p53DD MAFs recurred, biological rep2


title: HB_3

description: Hepatoblastoma (mixed type)

source_name: Hepatoblastoma patient 3


title: HB_5

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 5

value: 16 months


title: RB+p53DD MAFs untreated, biological rep2

description: Gene expression data from fibroblasts expressing wild-type Rb and p53DD

source_name: RB+p53DD mouse adult fibroblasts, untreated


title: RB-p53DD MAFs untreated, biological rep2


title: TNF

description: The control DNA pools were constructed by pooling equal amounts of DNA extracted from ten healthy women

source_name: Ten healthy control


title: RB+p53DD MAFs untreated, biological rep1


title: RB-p53DD MAFs recurred, biological rep1


title: mock.3

city: Coepnhagen N

first: Lea

middle: Haarup

last: Gregersen

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

hyb_protocol: After fragmentation at 94 °C for 35 min in 40 mM Tris, 30 mM MgOAc, 10 mM KOAc, samples were hybridized for 16 h to Affymetrix HG-U133 2.0 human arrays (Affymetrix, Santa Clara, CA).

scan_protocol: The arrays were washed and stained with phycoerythrin-conjugated streptavidin (SAPE), and the arrays were scanned in the Affymetrix GeneArray  2500 scanner, exactly as described in the Affymetrix GeneChip  protocol.

data_processing: The expression data was processed using the “affy” package in BioConductor in R. Probe set intensities were summarized using the Robust Multichip Average method and then transformed to generalized log values with the variance stable VSN method.

source_name: DLD-1 mock

label_protocol: Total cDNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA (BioArrayTM High Yield RNA Transcript Labeling kit; Enzo Diagnostics, Farmingdale, NY).

growth_protocol: DLD-1 cells were cultured in DMEM GlutaMAX™-I high glucose medium  (31966, Gibco Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS, CH30160.03, Hyclone), 50 U/ml penicillin and 50 µg/ml streptomycin (P/S, 15140 Gibco Invitrogen) and incubated in 5% CO2 plus 20% oxygen.

extract_protocol: Total RNA was isolated with TRIZOL 24.

treatment_protocol: Transfected with Lipofectamine™ 2000 Transfection Reagent (11668-019, Invitrogen) according to the manufactures protocol.

tag: cell type

value: colon cancer cell line

value: mock transfectant


title: HB_7

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 7

value: 9 months


title: HB_6

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 6

value: 31 months


title: HB_4

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 4

value: 82 months


title: TNM

description: The control DNA pools were constructed by pooling equal amounts of DNA extracted from ten healthy men


title: mock.1

tag: genome/variation


title: mock.2


title: HB_9

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 9

value: 8 months

tag: tissue


title: TC_1

description: Identical twin of TH1, healthy

source_name: Healthy control 1

value: male


title: miR-145.4

source_name: DLD-1 miR-145

value: miR-145 transfectant


title: TH_2

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 12

value: Peripheral blood lymphocytes

source_name: Commercialized normal Caucasian genome pool


title: miR-145.3


title: miR-145.1


title: miR-145.2


title: PerR regulon, 10 min after H2O2 exposure, technical replicate 2 of 3, set 2

status: Public on Sep 07 2010

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

institute: University of Ottawa

description: technical replicate 2 of 3

hyb_protocol: For each microarray experiment, the cDNA probes from one condition (e.g. H2O2 addition) were individually co-hybridized with cDNA probes from the relevant control sample. The fluor-labeled cDNA mix was dried under vacuum with a SpeedVac and resuspended in 15.14 µl of water, to which was added 2.5 µl of salmon sperm DNA (10 mg/ml), 9 µl of 20x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate, pH 7), 0.36 µl of 10% sodium dodecyl sulfate (SDS), and 9 µl of formamide. Prior to hybridization, microarray slides were prehybridized at 42°C for 45 min in prehybridization buffer (25% formamide, 5x SSC buffer, 0.1% SDS, and 1% bovine serum albumin), rinsed with water, and dried by spinning. The probe was denatured by boiling for 2 min, followed by cooling to 42°C. The probe was then applied to the microarray slide under a coverslip, placed in a humidified chamber (ArrayIt), and incubated at 42°C overnight. Following hybridization, slides were washed in 2x SSC-0.1% SDS for 5 min at 42°C, 0.1x SSC-0.1% SDS for 10 min at room temperature, and four times in 0.1x SSC for 1 min at room temperature. Slides were then rinsed with distilled water and dried by centrifugation.

scan_protocol: Microarray slides were scanned at 532 nm (Cy3) and 635 nm (Cy5) wavelengths using a laser-activated confocal scanner (ScanArray Gx, Perkin Elmer) at a 10µm resolution.

data_processing: The signal intensities for each spot were collected using GenePix Pro4 software (Axon Instruments, Foster City, Calif.). Spots with signal intensities below 3 times the standard deviation of the local background in both channels were excluded from further analysis. The fluorescent intensity in each wavelength (channel 1 for indodicarbocyanine (Cy5) and channel 2 for indocarbocyanine (Cy3)) was normalized using the MIDAS software (available from TIGR, http://www.tigr.org/software/) and by applying a locally weighted linear regression (Lowess). Finally, the ratio of the channels 2 to 1 was converted to log2.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Total RNA of Campylobacter jejuni

label_protocol: Total RNA was converted to cDNAs in the presence of aminoallyl-dUTP with Superscript II (Invitrogen) at 42°C. The reverse transcription reaction was performed as follows: 16 µg of total RNA was combined with 10 µg of random hexamers in a 34.35-µl reaction mixture containing 8 µl of 5x Superscript II reverse transcriptase buffer and 2 µl of 0.1 M dithiothreitol. After a 5-min incubation at 65°C, the reaction mixture was brought to a final volume of 40 µl by adding (final concentrations): 0.5 mM each of dGTP, ATP, and CTP; 0.16 mM dTTP; 0.34 mM aminoallyl-dUTP; and 2 µl of Superscript II and incubated at 42°C for 120 min. At the end of the first-strand synthesis, the reaction was stopped and the RNA was hydrolyzed by adding 4 µl of 50 mM EDTA and 2 µl of 10 N NaOH and incubating at 65°C for 20 min. This reaction was neutralized by adding 4 µl of 5 M acetic acid. The aminoallyl-labeled cDNA was purified from free amines and unincorporated aminoallyl-dUTP by adding 450 µl of water and spinning through a Microcon YM-30 filter (Millipore) for 8 min at 8,000 x g. This washing step was repeated three times. After the last wash, the aminoallyl-labeled probes were concentrated to less than 8 µl under vacuum in a SpeedVac and adjusted to a final volume of 10 µl by adding 1 µl of 1 M sodium carbonate (pH 9.0) and water. The resulting aminoallyl-labeled cDNA was coupled to monoreactive fluors (Amersham) by adding 10 µl of dimethyl sulfoxide containing one-sixth of one reaction vial FluoroLink indocarbocyanine or indodicarbocyanine dye and incubating for 45 min at room temperature in the dark. This reaction was quenched by adding 4.5 µl of 4 M hydroxylamine and incubating for 15 min at room temperature in the dark.

growth_protocol: C. jejuni NCTC 11168 cells were incubated overnight with stirring at 37°C under microaerophilic conditions in a 500 ml flask containing 250 ml of MEMα medium. At mid-log phase, 50 ml of the culture were dispended into flasks of 100 ml capacity and kept under microaerophilic growth conditions.

extract_protocol: Immediately after collection of samples for RNA extraction, 0.1 volumes of cold RNA degradation stop solution (10% (v/v) buffer-saturated phenol in ethanol) were added to prevent RNA turnover (14). Cells were collected by centrifugation (8, 000 x g, 10 min, 4°C) and the cell pellet was resuspended in TE buffer (50 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.5 mg mL-1 (final concentration) lysozyme. Total RNA was extracted using a hot phenol-chloroform method, precipitated with ethanol, and resuspended in RNase-free H2O. The RNA preparation was treated with DNase I to remove any contaminating genomic DNA, further purified using a QIAGEN RNeasy mini Kit (QIAGEN, Valencia, CA), and quantitated using either the RiboGreen RNA quantitation kit (Molecular Probes, Eugene, OR) or A260 values. RNA integrity was assessed by agarose gel electrophoresis, and PCR amplification was used to confirm that the preparation was free of genomic DNA. RNA samples were stored at -80°C.

treatment_protocol: To investigate the transcriptional responses of C. jejuni to oxidant exposure, hydrogen peroxide (H2O2), cumene hydroperoxide (CHP), or menadione sodium bisulfite (MND) was added to the 50 ml broth at a final concentration of 1 mM. The stock solutions of H2O2 and MND were prepared in water at a concentration of 0.882 M and 1 M respectively, while the stock solution of CHP was prepared in DMSO at a concentration of 0.578 M. The same amount of water or DMSO was added to the bacterial culture that served as reference samples for the transcriptional profile study in response to H2O2, MND or CHP. Furthermore, to investigate the transcriptional response of C. jejuni to H2O2 exposure in the presence of excess iron, ferrous sulfate was added to the bacterial culture at a final concentration of 40 µM, 15 min prior to H2O2 exposure. To identify the PerR regulon, the wild-type strain C. jejuni NCTC 11168 and the perR mutant were grown in 500 ml flasks containing 250 ml of MEMα medium. At mid-log phase, 50 ml of the cultures were transferred to 100 ml flasks and ferrous sulfate and/or H2O2 were added as described above. Ten minutes following the addition of H2O2 the cells were collected and the total RNA extracted.

tag: phase

value: mid-log phase

tag: medium

value: MEM

tag: treatment

value: 10 min after addition of H2O2 exposure

source_name: Total RNA of Campylobacter jejuni perR mutant

value: perR mutant of Campylobacter jejuni NCTC 11168


title: PerR regulon, 10 min after H2O2 exposure, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3


title: PerR regulon, after iron addition and 10 min exposure to H2O2, technical replicate 2 of 3, set 2

description: technical replicate 2 of 3


title: NOV-R-S-0 PSU-BA-212

status: Public on Sep 10 2010

city: Beaverton

first: Maria

last: Smit

state: OR

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

description:
A sector of a 4X2K CustomArray with 2240 features representing 2234 unique probes was hybridized with an aliquot of Cy5-labeled cDNA.

Sample 212

hyb_protocol: Hybridization of CustomArray™ microarrays was performed as recommended by the manufacturer (http://www.combimatrix.com/docs/PTL005_00_4x2K_Hyb_Imaging.pdf), using the single-color experimental scheme. The microarrays were hybridized at 46˚C for 16 hours, using Cy5-labeled cDNA targets, 1.5-2 mg per sector for the 4X2K format.

scan_protocol: Hybridization images were obtained using a ScanArray 4000 fluorescent scanner (PerkinElmer, Waltham, MA) at 5 micron.

data_processing: Quantification was done with Microarray Imager software (CombiMatrix). Data normalization based on the quantile algorithm was done using the Probe Weaver software from CombiMatrix. Data QC was done with scatter plot analysis of replicate hybridizations, and calculation of pair-wise correlation coefficients among samples using NCI-supported software BRB-ArrayTools (http://linus.nci.nih.gov/pilot/index.html). Then the triplicate samples were used to calculate average normalized signal intensities for each probe in each sample.

organism: uncultured prokaryote

source_name: filtered environmental water sample, BA

label_protocol: Total RNA samples were converted into cDNA using the Superscript III Reverse Transcriptase Kit with random hexamer primers, and then RNA was removed with RNase H, as described by the kit manufacturer (Invitrogen, Carlsbad, CA). The cDNA samples were purified using QIAQuick Nucleotide Removal Kit (Qiagen), and fluorescently labeled using LabelIT uArray Cy5 Kit (Mirus Bio, Madison WI) as described by the manufacturer. The Cy5-labeled cDNA samples were purified using Illustra ProbeQuant G-50 Micro Columns (GE Healthcare, Piscataway, NJ), dried in a SpeedVac centrifuge and applied for microarray hybridization.

growth_protocol: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms.

extract_protocol: Total RNA was isolated using a protocol described in Griffiths et al. (Griffiths et al, 2000), and modified for working with Sterivex filters in the following manner:  Each filter was removed from the holder, cut longitudinally into 5 mm strips and placed into 2 ml screw-top eppendorf tubes containing CTAB extraction buffer (5% CTAB, 0.8 M NaCl in 0.1 M phosphate buffer, pH 8.0) and 0.5 mL zirconia/silica beads (1:1 mixture of 0.1 and 1 mm, BioSpec Products, Bartlesville, OK). Bead beating for microbial cell disruption was performed for 1 min using a FastPrep FP120 machine (Thermo Fisher Scientific, Waltham, MA), and the extract was collected after 3 min centrifugation at maximum speed. The filter strips were re-extracted 3 times to maximize RNA yield, after which the extracts were pooled together and supplemented with an equal volume of 1:1 mixture of phenol:chloroform,  and 0.1 volume each of 10%  SDS, and 10% Sodium Lauryl Sarcosine.  The sample extracts were further incubated for 20 min at room temperature with intense shaking, followed by standard phenol:chloroform purification and isopropanol precipitation. The extracted RNA was treated with DNase using the RNase-free DNase Set (Qiagen, Germantown, MD), and then purified using the RNeasy Kit (Qiagen) as recommended by the manufacturer. The RNA content was measured spectrophotometrically with a Nanodrop 3300 instrument (Thermo Fisher Scientific  ), and RNA quality was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: After filtration, samples were preserved in RNAlater and stored at -80oC.

tag: location

value: BA

tag: date

tag: salinity (psu)

tag: depth (m)

tag: temperature (c)

tag: oxygen (mg/l)

tag: silicic acid (um)

tag: nitrate (um)

tag: phosphate (um)

tag: ammonium (um)

tag: chlorophyll a content (ug/l)

tag: pheophytin content (ug/l)

tag: bacterial production (mg c/l*h)

tag: rna (ug/l)

tag: dissolved organic carbon (mg/l)


title: HB_1

description: Hepatoblastoma (epithelial type)

source_name: Hepatoblastoma patient 1

tag: gender

tag: age

tag: tissue

tag: health state

value: Hepatoblastoma

value: Healthy


title: PerR regulon, 10 min after H2O2 exposure, technical replicate 1 of 3, set 2

description: technical replicate 1 of 3

tag: phase

tag: medium

tag: treatment

tag: strain


title: PerR regulon, after iron addition and 10 min exposure to H2O2, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3


title: PerR regulon, after iron addition and 10 min exposure to H2O2, technical replicate 1 of 3, set 2

description: technical replicate 1 of 3


title: Triple fusioned hippocampus of APPV717I-CT100 mice

status: Public on Sep 28 2010

city: Seoul

first: Yoo-Hun

last: Suh

address: 28 Yongon-dong

country: South Korea

institute: Seoul National University

description: male

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 18 hr at 37C on GE Healthcare/Amersham Biosciences CodeLink UniSet

scan_protocol: Processed slides were scanned using an Axon GenePix 4000B Scanner with the laser set to 635 nm, the photomultiplier tube (PMT) voltage to 600 and the scan resolution to 10 µm. Images for each slide were analyzed using the CodeLinkTM Expression Analysis Software v4.1(GE Healthcare Life Science).

data_processing: The CodeLinkTM Expression Analysis Software v4.1(GE Healthcare Life Science) was used

source_name: Triple fusioned hippocampus of 11month-old APPV717I-CT100 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit         Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

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


title: PerR regulon, 10 min after iron addition, technical replicate 1 of 3, set 2

description: technical replicate 1 of 3

value: 10 min after iron addition


title: PerR regulon in MEM medium, technical replicate 1 of 3, set 2

description: technical replicate 1 of 3


title: PerR regulon in MEM medium, technical replicate 2 of 3, set 2

description: technical replicate 2 of 3


title: AAF-OX_3-week-old_rep2

status: Public on Sep 30 2010

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

hyb_protocol: Standard Affymetrix GeneChip hybridization protocol

scan_protocol: Standard Affymetrix GeneChip scanning protocol

label_protocol: Standard Affymetrix GeneChip labeling protocol

extract_protocol: Pine Tree Method, for preparation of total RNA from plant tissues. Plant Molecular Biology Reporter(1993) 11: 113-116

tag: transgenic arabidopsis

value: Over-expression of AAF

tag: background

tag: developmental stage

value: Rosette leaf

tag: growth condition

value: 16hr light/ 8hr dark


title: PerR regulon, 10 min after H2O2 exposure, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3


title: PerR regulon, 10 min after iron addition, technical replicate 2 of 3, set 2

description: technical replicate 2 of 3


title: PerR regulon in MEM medium, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3


title: PerR regulon, 10 min after iron addition, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3


title: PerR regulon, 10 min after H2O2 exposure, technical replicate 1 of 3, set 1

description: technical replicate 1 of 3


title: Col-0_3-week-old_rep2

tag: genotype


title: PerR regulon, after iron addition and 10 min exposure to H2O2, technical replicate 3 of 3, set 1

description: technical replicate 3 of 3


title: 10 min exposure to menadione, technical replicate 2 of 3, set 2

description: technical replicate 2 of 3

value: 10 min exposure to menadione


title: 10 min exposure to menadione, technical replicate 3 of 3, set 2

description: technical replicate 3 of 3


title: PerR regulon, 10 min after H2O2 exposure, technical replicate 2 of 3, set 1

description: technical replicate 2 of 3