title: normoxic 3h

status: Public on Jul 31 2011

type: RNA

city: Tsukuba

first: Yasunobu

last: Terabayashi

country: Japan

institute: Tsukuba University

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

scan_protocol: Genechips were scanned using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with GCOS program (version 1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Aspergillus oryzae RIB40

source_name: A. oryzae AERO 1H

label_protocol: Biotinylated cRNA were prepared from 250 ng total RNA using GeneChip 3' IVT Express Kit.

growth_protocol: Conidia of Aspergillus oryzae RIB40 obtained from NBRC ( http://www.nbrc.nite.go.jp ) ( 2 x 10^9 ) were shaken at 120 rpm at 30oC in 500-mL Erlenmeyer flasks containing 100 mL of MM medium comprising 2% glucose, 20 mM NaNO3, 15 mM KH2PO4, 7 mM KCl, 2 mM MgSO4 and 0.2% Hutner\222 ( v/v ) ( Hutner et al. 1950 ) and plugged with cotton wool ( normoxic conditions ) . After incubation for 16 h the head space in the flasks was replaced with nitrogen gas by purging the air for 15 min. The flasks were sealed with butyl rubber stoppers and shaken at 30oC at 120 rpm ( hypoxic conditions ) . The stoppers were removed 6 h later and the culture broth was re-oxidized by vigorously shaking the flasks, which were incubated once again under the normoxic conditions described above.

extract_protocol: Mycelia were immediately frozen in liquid nitrogen and powdered to prepare total RNA using the RNeasy plant mini kit (Qiagen, Venlo, Netherlands)

treatment_protocol: Mycelia were harvested by filtration and washed by ddH2O.

tag: treatment

value: normoxic condition for 3h after reoxygenation


title: hypoxic 3h

source_name: A. oryzae ANAERO 3H

value: hypoxic condition for 3h after exposure to hypoxia


title: nornoxic 1h

value: normoxic condition for 1h after reoxygenation


title: normoxic

source_name: A. oryzae 0H

value: normoxic condition for 16 h before exposure to hypoxia


title: 253274110069_MC58_CY5_MK1202_03_CY3.mev.refIsIB.out

type: genomic

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

country: USA

institute: J Craig Venter Institute

hyb_protocol: Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol.  Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization.  The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius.   Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.

scan_protocol: Scanned on Axon GenePix 4000 scanner.  PMT values were optimized during scanning to balance channel intensities.

data_processing:
Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Query/Reference) from the normalized .mev file:
    3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
    3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
    3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.

molecule: genomic DNA

organism: Neisseria meningitidis

source_name: Genomic DNA purified from wild type bacteria

label_protocol: 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen).  Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).

growth_protocol: cells were grown in blood agar plates  overnight at 37 degrees celcius.

extract_protocol: Genomic DNA was isolated by lysozyme and proteinase K treatment.

tag: strain


title: hypoxic 1h

source_name: A. oryzae ANAERO 1H

value: hypoxic condition for 1h after exposure to hypoxia


title: normoxic 6h

source_name: A. oryzae AERO 6H

value: normoxic condition for 6h after reoxygenation


title: hypoxic 6h

source_name: A. oryzae ANAERO 6H

value: hypoxic condition for 6h after exposure to hypoxia


title: 253274110062_MC58_CY5_M13458_CY3.mev.refIsIB


title: 253274110069_MC58_CY5_05106C_CY3.mev.refIsIB.out


title: 253274110061_MC58_CY5_M16238_CY3.mev.refIsIB.out


title: 253274110061_MC58_CY5_M13220_CY3.mev.refIsIB.out


title: 253274110060_MC58_CY5_NG123_CY3.mev.refIsIB.out


title: 253274110027_MC58_CY5_M15782_CY3.mev.refIsIB.out


title: 253274110062_MC58_CY5_M15427_CY3.mev.refIsIB.out


title: 253274110025_MC58_CY5_M16224_CY3.mev.refIsIB.out


title: 253274110025_MC58_CY5_M17277_CY3.mev.refIsIB.out


title: 253274110060_MC58_CY5_M18935_CY3.mev.refIsIB.out


title: 253274110063_MC58_CY5_HF38_CY3.mev.refIsIB.out


title: 253274110024_MC58_CY5_SM1027_CY3.mev.refIsIB.out


title: 253274110025_MC58_CY5_M21262_CY3.mev.refIsIB.out


title: 253274110061_MC58_CY5_M14900_CY3.mev.refIsIB


title: 253274110025_MC58_CY5_M10699_CY3.mev.refIsIB.out


title: 253274110062_MC58_CY5_M14745_CY3.mev.refIsIB.out


title: 253274110061_MC58_CY5_S7759_CY3.mev.refIsIB


title: 253274110027_MC58_CY5_M17075_CY3.mev.refIsIB.out


title: 253274110027_MC58_CY5_M15447_CY3.mev.refIsIB.out


title: 253274110069_MC58_CY5_MK_353_03_CY3.mev.refIsIB.out


title: 253274110027_MC58_CY5_M17089_CY3.mev.refIsIB.out


title: 253274110023_MC58_CY5_M15527_CY3.mev.refIsIB.out


title: 253274110024_MC58_CY5_M15645_CY3.mev.refIsIB.out


title: 253274110022_MC58_CY5_M20918_CY3.mev.refIsIB.out


title: 253274110024_MC58_CY5_M20899_CY3.mev.refIsIB.out


title: 253274110023_MC58_CY5_M15563_CY3.mev.refIsIB.out


title: 253274110023_MC58_CY5_M15113_CY3.mev.refIsIB.out


title: 253274110024_MC58_CY5_M11791_CY3.mev.refIsIB.out


title: 253274110021_MC58_CY5_B3757_CY3.mev.refIsIB.out


title: 253274110022_MC58_CY5_M18575_CY3.mev.refIsIB.out


title: 253274110021_MC58_CY5_B3941_CY3.mev.refIsIB.out


title: 253274110022_MC58_CY5_M14106_CY3.mev.refIsIB.out


title: 253274110022_MC58_CY5_M15112_CY3.mev.refIsIB.out


title: 253274110020_MC58_CY5_Z2491_CY3.mev.refIsIB.out


title: 253274110020_MC58_CY5_SU960_CY3.mev.refIsIB.out


title: 253274110021_MC58_CY5_05104_CY3.mev.refIsIB.out


title: 253274110021_MC58_CY5_01114_CY3.mev.refIsIB.out


title: 253274110019_MC58_CY5_05101_CY3.mev.refIsIB.out


title: 253274110019_MC58_CY5_N05_06_CY3.mev.refIsIB.out


title: 253274110019_MC58_CY5_MK365_02_CY3.mev.refIsIB.out


title: 253274110020_MC58_CY5_01107_CY3.mev.refIsIB.out


title: 253274110018_MC58_CY5_NmgNor24_CY3.mev.refIsIB.out


title: 253274110019_MC58_CY5_06101BC_CY3.mev.refIsIB.out


title: 253274110020_MC58_CY5_BZ221_CY3.mev.refIsIB.out


title: 253274110067_MC58_CY5_N32_01_CY3.mev.refIsIB.out

treatment_protocol: None.


title: 253274110023_MC58_CY5_M15141_CY3.mev.refIsIB.out


title: 253274110068_MC58_CY5_HF94_CY3.mev.refIsIB.out


title: 253274110071_MC58_CY5_M16207_CY3.mev.refIsIB.out


title: 253274110018_MC58_CY5_NG44_76_CY3.mev.refIsIB.out


title: 253274110071_MC58_CY5_M16219_CY3.mev.refIsIB.out


title: 253274110068_MC58_CY5_81139_CY3.mev.refIsIB.out


title: 253274110067_MC58_CY5_BF10_96_CY3.mev.refIsIB.out


title: 253274110067_MC58_CY5_134_PA_V1_CY3.mev.refIsIB.out


title: 253274110066_MC58_CY5_NK183_CY3.mev.refIsIB.out


title: 253274110057_MC58_CY5_M07092_CY3.mev.refIsIB.out


title: 253274110057_MC58_CY5_M16105_CY3.mev.refIsIB.out


title: 253274110066_MC58_CY5_N10_01_CY3.mev.refIsIB.out


title: 253274110067_MC58_CY5_11_CY3.mev.refIsIB.out


title: 253274110055_MC58_CY5_M16917_CY3.mev.refIsIB.out


title: 253274110056_MC58_CY5_FAM18_CY3.mev.refIsIB.out


title: 253274110057_MC58_CY5_M13955_CY3.mev.refIsIB.out


title: 253274110066_MC58_CY5_C4505_CY3.mev.refIsIB.out


title: 253274110057_MC58_CY5_M12098_CY3.mev.refIsIB.out


title: 253274110056_MC58_CY5_M17643_CY3.mev.refIsIB.out


title: 253274110056_MC58_CY5_M15496_CY3.mev.refIsIB.out


title: 253274110055_MC58_CY5_M13519_CY3.mev.refIsIB.out


title: 253274110055_MC58_CY5_M06760_CY3.mev.refIsIB.out


title: 253274110056_MC58_CY5_M13410_CY3.mev.refIsIB.out


title: 253274110018_MC58_CY5_N57_01_CY3.mev.refIsIB.out


title: 253274110055_MC58_CY5_C1696_CY3.mev.refIsIB.out


title: 253274110054_MC58_CY5_M18774_CY3.mev.refIsIB.out


title: 253274110053_MC58_CY5_M17094_CY3.mev.refIsIB.out


title: 253274110017_MC58_CY5_HF117_CY3.mev.refIsIB.out


title: 253274110054_MC58_CY5_M15293_CY3.mev.refIsIB.out


title: 253274110054_MC58_CY5_M17058_CY3.mev.refIsIB.out


title: 253274110018_MC58_CY5_1076_CY3.mev.refIsIB.out

source_name: Genomic DNA purified from wild type bacteria.


title: 253274110066_MC58_CY5_02102_CY3.mev.refIsIB.out


title: 253274110054_MC58_CY5_M16239_CY3.mev.refIsIB.out


title: 253274110053_MC58_CY5_M00071_CY3.mev.refIsIB.out


title: 253274110052_MC58_CY5_M15905_CY3.mev.refIsIB.out


title: 253274110017_MC58_CY5_HF173_CY3.mev.refIsIB.out


title: 253274110053_MC58_CY5_M12394_CY3.mev.refIsIB.out


title: 253274110053_MC58_CY5_M15116_CY3.mev.refIsIB.out


title: 253274110052_MC58_CY5_M17661_CY3.mev.refIsIB.out


title: 253274110052_MC58_CY5_M14934_CY3.mev.refIsIB.out


title: 253274110051_MC58_CY5_M17062_CY3.mev.refIsIB.out


title: 253274110050_MC58_CY5_N32_02_CY3.mev.refIsIB.out


title: 253274110051_MC58_CY5_NG5_84_CY3.mev.refIsIB.out


title: 253274110051_MC58_CY5_M15451_CY3.mev.refIsIB.out


title: 253274110050_MC58_CY5_NmgNor19_CY3.mev.refIsIB.out


title: 253274110050_MC58_CY5_MK1302_03_CY3.mev.refIsIB.out


title: 253274110051_MC58_CY5_M12157_CY3.mev.refIsIB.out


title: 253274110052_MC58_CY5_M09261_CY3.mev.refIsIB.out


title: 253274110049_MC58_CY5_05107_CY3.mev.refIsIB.out


title: 253274110050_MC58_CY5_BF16_01_CY3.mev.refIsIB.out


title: 253274110049_MC58_CY5_MK1251_03_CY3.mev.refIsIB.out


title: 253274110049_MC58_CY5_MK110_03_CY3.mev.refIsIB.out


title: 253274110047_MC58_CY5_MK82_94_CY3.mev.refIsIB.out


title: 253274110049_MC58_CY5_MK18_2001_CY3.mev.refIsIB.out


title: 253274110048_MC58_CY5_M14518_CY3.mev.refIsIB.out


title: 253274110048_MC58_CY5_M16715_CY3.mev.refIsIB.out


title: 253274110046_MC58_CY5_N8_02_CY3.mev.refIsIB.out


title: 253274110048_MC58_CY5_M14614_CY3.mev.refIsIB.out


title: 253274110047_MC58_CY5_NmgNor20_CY3.mev.refIsIB.out


title: 253274110047_MC58_CY5_Kenya_1_06_CY3.mev.refIsIB.out


title: 253274110046_MC58_CY5_MK1187_03_CY3.mev.refIsIB.out


title: 253274110048_MC58_CY5_M11971_CY3.mev.refIsIB.out


title: 253274110059_MC58_CY5_HF159_CY3.mev.refIsIB.out


title: 253274110068_MC58_CY5_NGC28_CY3.mev.refIsIB.out


title: 253274110060_MC58_CY5_HF120_CY3.mev.refIsIB.out


title: 253274110069_MC58_CY5_238_YN_V1_CY3.mev.refIsIB.out


title: 253274110058_MC58_CY5_HF96_CY3.mev.refIsIB.out


title: 253274110058_MC58_CY5_M17189_CY3.mev.refIsIB.out


title: 253274110068_MC58_CY5_NGC16_CY3.mev.refIsIB.out


title: 253274110059_MC58_CY5_NGC94_CY3.mev.refIsIB.out


title: 253274110060_MC58_CY5_M16961_CY3.mev.refIsIB.out


title: 253274110059_MC58_CY5_HF149_CY3.mev.refIsIB.out


title: 253274110012_MC58_CY5_M14879_CY3.mev.refIsIB.out


title: 253274110013_MC58_CY5_M10372_CY3.mev.refIsIB.out


title: 253274110013_MC58_CY5_HF60.mev.refIsIB.out


title: 253274110059_MC58_CY5_C1878_CY3.mev.refIsIB.out


title: 253274110058_MC58_CY5_M39_CY3.mev.refIsIB.out


title: 253274110011_MC58_CY5_M15978_CY3.mev.refIsIB.out


title: 253274110058_MC58_CY5_HF109_CY3.mev.refIsIB.out


title: 253274110014_MC58_CY5_77215_CY3.mev.refIsIB.out


title: 253274110013_MC58_CY5_N17_04_CY3.mev.refIsIB.out


title: 253274110013_MC58_CY5_M11588_CY3.mev.refIsIB.out


title: 253274110012_MC58_CY5_M17084_CY3.mev.refIsIB.out


title: 253274110014_MC58_CY5_BB350_CY3.mev.refIsIB.out


title: 253274110011_MC58_CY5_M17140_CY3.mev.refIsIB.out


title: 253274110012_MC58_CY5_M17091_CY3.mev.refIsIB.out


title: 253274110011_MC58_CY5_M12695_CY3.mev.refIsIB.out


title: 253274110012_MC58_CY5_M11906_CY3.mev.refIsIB.out


title: 253274110011_MC58_CY5_M17859_CY3.mev.refIsIB.out


title: 253274110010_MC58_CY5_M16182_CY3.mev.refIsIB.out


title: 253274110010_MC58_CY5_M14418_CY3.mev.refIsIB.out


title: 253274110045_MC58_CY5_Niga12_96_CY3.mev.refIsIB.out


title: 253274110071_MC58_CY5_84216_CY3.mev.refIsIB.out


title: 253274110009_MC58_CY5_98_1101_118_CY3.mev.refIsIB.out


title: 253274110010_MC58_CY5_M08883_CY3.mev.refIsIB.out


title: 253274110046_MC58_CY5_98_1101_206_CY3.mev.refIsIB.out


title: 253274110010_MC58_CY5_M10574_CY3.mev.refIsIB.out


title: 253274110071_MC58_CY5_M00001_CY3.mev.refIsIB.out


title: 253274110009_MC58_CY5_07106_CY3.mev.refIsIB.out


title: 253274110008_MC58_CY5_N16_02_CY3.mev.refIsIB.out


title: 253274110065_MC58_CY5_NGC95_CY3.mev.refIsIB.out


title: 253274110064_MC58_CY5_L8039_CY3.mev.refIsIB.out


title: 253274110064_MC58_CY5_HF67_CY3.mev.refIsIB.out


title: 253274110065_MC58_CY5_EN3771_CY3.mev.refIsIB.out


title: 253274110009_MC58_CY5_589_JN_V1_CY3.mev.refIsIB.out


title: 253274110009_MC58_CY5_98_1101_134_CY3.mev.refIsIB.out


title: 253274110046_MC58_CY5_M900_CY3.mev.refIsIB.out


title: 253274110008_MC58_CY5_M05178_CY3.mev.refIsIB.out


title: 253274110065_MC58_CY5_BZ184_CY3.mev.refIsIB.out


title: AML 7324

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

description: AML

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and targeted intensity values at 100. Intensity values were log2 transformed.

label: Biotin

organism: Homo sapiens

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: cell type

value: mononuclear cells from bone marrow

tag: disease state

value: Acute myeloid leukemia


title: AML 7325

description: AML


title: 253274110008_MC58_CY5_07101_CY3.mev.refIsIB.out


title: 253274110047_MC58_CY5_BF12_03_CY3.mev.refIsIB.out


title: AML 7328

description: AML


title: AML 7326

description: AML


title: AML 7327

description: AML


title: AML 7323

description: AML


title: AML 7167

description: AML


title: AML 7322

description: AML


title: AML 7165

description: AML


title: AML 7321

description: AML


title: 253274110063_MC58_CY5_HF205_CY3.mev.refIsIB.out


title: AML 7176

description: AML


title: 253274110063_MC58_CY5_NG117_CY3.mev.refIsIB.out


title: AML 7161

description: AML


title: 253274110064_MC58_CY5_HF1_CY3.mev.refIsIB.out


title: 253274110064_MC58_CY5_HF13_CY3.mev.refIsIB.out


title: AML 7148

description: AML


title: AML 7146

description: AML


title: 253274110045_MC58_CY5_IHN5336_CY3.mev.refIsIB.out


title: 253274110008_MC58_CY5_500EA_V1_CY3.mev.refIsIB.out


title: 253274110007_MC58_CY5_M07182_CY3.mev.refIsIB.out


title: 253274110007_MC58_CY5_BZ78_CY3.mev.refIsIB.out


title: 253274110045_MC58_CY5_21_RA_V1_CY3.mev.refIsIB.out


title: AML 7136

description: AML


title: 253274110005_MC58_CY5_SM1166_CY3.mev.refIsIB.out


title: 253274110044_MC58_CY5_N22_06_CY3.mev.refIsIB.out


title: 253274110044_MC58_CY5_07107_CY3.mev.refIsIB.out


title: AML 7116

description: AML


title: AML 7117

description: AML


title: AML 7118

description: AML


title: 253274110045_MC58_CY5_01102_CY3.mev.refIsIB.out


title: 253274110007_MC58_CY5_M08377_CY3.mev.refIsIB.out


title: 253274110044_MC58_CY5_1068_CY3.mev.refIsIB.out


title: AML 7084

description: AML


title: AML 6463

description: AML


title: 253274110005_MC58_CY5_NGC44_CY3.mev.refIsIB.out


title: 253274110043_MC58_CY5_04103C_CY3.mev.refIsIB.out


title: 253274110043_MC58_CY5_MK208_2001_CY3.mev.refIsIB.out


title: AML 6457

description: AML


title: AML 6459

description: AML


title: AML 6455

description: AML


title: AML 6458

description: AML


title: 253274110044_MC58_CY5_01110_CY3.mev.refIsIB.out


title: 253274110005_MC58_CY5_MK43_03_CY3.mev.refIsIB.out


title: AML 6454

description: AML


title: 253274110043_MC58_CY5_07103_CY3.mev.refIsIB.out


title: 253274110043_MC58_CY5_MK580_03_CY3.mev.refIsIB.out


title: AML 6461

description: AML


title: 253274110042_MC58_CY5_N29_06_CY3.mev.refIsIB.out


title: AML 6453

description: AML


title: 253274110005_MC58_CY5_M07846_CY3.mev.refIsIB.out


title: AML 6456

description: AML


title: AML 6462

description: AML


title: 253274110004_MC58_CY5_M15535_CY3.mev.refIsIB.out


title: 253274110004_MC58_CY5_M14567_CY3.mev.refIsIB.out


title: 253274110042_MC58_CY5_115_CB_V1_CY3.mev.refIsIB.out


title: AML 6450

description: AML


title: 253274110042_MC58_CY5_98_1101_258_CY3.mev.refIsIB.out


title: AML 6451

description: AML


title: AML 6449

description: AML


title: AML 6452

description: AML


title: 253274110007_MC58_CY5_HF138_CY3.mev.refIsIB.out


title: 253274110042_MC58_CY5_MK17_2001_CY3.mev.refIsIB.out


title: AML 6357

description: AML


title: AML 5355

description: AML


title: 253274110041_MC58_CY5_Niga14_96_CY3.mev.refIsIB.out


title: 253274110041_MC58_CY5_N18_01_CY3.mev.refIsIB.out


title: AML 5354

description: AML


title: 253274110041_MC58_CY5_M7034_CY3.mev.refIsIB.out


title: 253274110017_MC58_CY5_HF29_CY3.mev.refIsIB.out


title: 253274110040_MC58_CY5_MK1233_03_CY3.mev.refIsIB.out


title: AML 5352

description: AML


title: AML 5353

description: AML


title: AML 5349

description: AML


title: AML 5350

description: AML


title: AML 5351

description: AML


title: 253274110038_MC58_CY5_04102B_CY3.mev.refIsIB.out


title: 253274110040_MC58_CY5_MK1178_03_CY3.mev.refIsIB.out


title: AML 5291

description: AML


title: 253274110041_MC58_CY5_06108BC_CY3.mev.refIsIB.out


title: AML 4342

description: AML


title: AML 5289

description: AML


title: AML 5348

description: AML


title: 253274110016_MC58_CY5_NG14_84_CY3.mev.refIsIB.out


title: 253274110040_MC58_CY5_161_DT_V1_CY3.mev.refIsIB.out


title: 253274110040_MC58_CY5_06107BC_CY3.mev.refIsIB.out


title: 253274110038_MC58_CY5_N28_00_CY3.mev.refIsIB.out


title: 253274110017_MC58_CY5_HF22_CY3.mev.refIsIB.out


title: 253274110038_MC58_CY5_BB393_CY3.mev.refIsIB.out


title: 253274110016_MC58_CY5_HF172_CY3.mev.refIsIB.out


title: AML 5287

description: AML


title: AML 5288

description: AML


title: AML 5290

description: AML


title: AML 5292

description: AML


title: 253274110038_MC58_CY5_232_LM_V1_CY3.mev.refIsIB.out


title: 253274110016_MC58_CY5_BB372_CY3.mev.refIsIB.out


title: 253274110004_MC58_CY5_M08854_CY3.mev.refIsIB.out


title: AML 3491

description: AML


title: AML 3493

description: AML


title: 253274110063_MC58_CY5_M14105_CY3.mev.refIsIB.out


title: AML 3488

description: AML


title: 253274110016_MC58_CY5_BI1068_CY3.mev.refIsIB.out


title: AML 3492

description: AML


title: AML 3489

description: AML


title: AML 3487

description: AML


title: 253274110037_MC58_CY5_04101_B_CY3.mev.refIsIB.out


title: AML 3485

description: AML


title: 253274110003_MC58_CY5_M14988_CY3.mev.refIsIB.out


title: AML 3332

description: AML


title: 253274110015_MC58_CY5_WDZ109_CY3.mev.refIsIB.out


title: 253274110004_MC58_CY5_M07194_CY3.mev.refIsIB.out


title: 253274110037_MC58_CY5_112_BK_V1_CY3.mev.refIsIB.out


title: AML 2704

description: AML


title: 253274110037_MC58_CY5_02106_CY3.mev.refIsIB.out


title: AML 3331

description: AML


title: 253274110003_MC58_CY5_M12885_CY3.mev.refIsIB.out


title: 253274110003_MC58_CY5_M09834_CY3.mev.refIsIB.out


title: 253274110037_MC58_CY5_N9_04_CY3.mev.refIsIB.out


title: AML 3330

description: AML


title: AML 3329

description: AML


title: AML 3486

description: AML


title: 253274110036_MC58_CY5_NmgNor11_CY3.mev.refIsIB.out


title: AML 1448

description: AML


title: 253274110003_MC58_CY5_M09035_CY3.mev.refIsIB.out


title: 253274110002_MC58_CY5_M14963_CY3.mev.refIsIB.out


title: Cells transfected with pCDNA3 and stimulated with TNFa, biological rep3

city: Stevenage

first: Jessica

last: Vamathevan

address: Gunnels Wood Road

department: R&D

country: United Kingdom

institute: GlaxoSmithKline

description: Gene expression data from HEK293 cells tranfected with with an pCDNA3 and stimulated with TNFa

hyb_protocol: Following fragmentation, 3.75 ug of cRNA were hybridized for 16-18 hr at 45C on GeneChip U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Fluorescence raw data of the hybridization were computed, RMA normalized, log2 transformed and statistically analyzed using ArrayStudio v4.0 (Omicsoft).

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

growth_protocol: HEK293 cells were plated at 0.4 x 106 cells per well in 6-well plates (Costar)

extract_protocol: Total cellular RNA was isolated, processed, and hybridized to the oligonucleotide microarray HG 133A Plus 2.0 Gene Chip arrays (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.

treatment_protocol: Cells were transfected with pCDNA3-Flag-SIRT6 WT, pCDNA3-Flag-SIRT6 H133W mutant, pCDNA3 alone or no DNA. Cells were grown in media containing transfection complexes for 24h prior to stimulation. Growth media was removed and replaced with fresh media containing TNFα (10ng/ml, R&D systems) or media containing equivalent volume of PBS/0.1% BSA as a control.

tag: cell line


title: Cells transfected with pCDNA3, biological rep3

description: Gene expression data from HEK293 cells tranfected with with an pCDNA3


title: Cells transfected with pCDNA3 and stimulated with TNFa, biological rep2

source_name: HEK293 cells tranfected with with an pCDNA3 and stimulated with TNFa


title: 253274110002_MC58_CY5_M15041_CY3.mev.refIsIB.out


title: 253274110036_MC58_CY5_N46_02_CY3.mev.refIsIB.out


title: Cells transfected with pCDNA3 and stimulated with TNFa, biological rep1


title: 253274110036_MC58_CY5_MK46_03_CY3.mev.refIsIB.out


title: 253274110036_MC58_CY5_01101_CY3.mev.refIsIB.out


title: Cells transfected with pCDNA3, biological rep2

source_name: HEK293 cells tranfected with with an pCDNA3


title: Cells transfected with H133W mutant sirtuin 6, biological rep2

description: Gene expression data from HEK293 cells transfected with H133W construct  and unstimulated


title: 53274110035_MC58_CY5_Sudan1_06_CY3.mev.refIsIB.out


title: 253274110001_MC58_CY5_M16600_CY3.mev.refIsIB.out


title: Cells transfected with H133W mutant sirtuin 6, biological rep3

source_name: HEK293 cells transfected with H133W construct  and unstimulated


title: 253274110035_MC58_CY5_MK15_2001_CY3.mev.refIsIB.out


title: Cells transfected with H133W mutant sirtuin 6 and stimulated with TNFa, biological rep2

description: Gene expression data from HEK293 cells transfected with H133W construct  and stimulated with TNFa


title: Cells transfected with pCDNA3, biological rep1


title: 253274110001_MC58_CY5_M18044_CY3.mev.refIsIB.out


title: Cells transfected with sirtuin 6 and stimulated with TNFa, biological rep2

description: Gene expression data from HEK293 cells transfected with SIRT6 construct  and stimulated with TNFa


title: 253274110001_MC58_CY5_M15040_CY3.mev.refIsIB.out


title: Cells transfected with H133W mutant sirtuin 6 and stimulated with TNFa, biological rep1

source_name: HEK293 cells transfected with H133W construct  and stimulated with TNFa


title: 253274110002_MC58_CY5_M11163_CY3.mev.refIsIB.out


title: 253274110035_MC58_CY5_BF6_06_CY3.mev.refIsIB.out


title: Cells transfected with sirtuin 6 and stimulated with TNFa, biological rep3

source_name: HEK293 cells transfected with SIRT6 construct  and stimulated with TNFa


title: 253274110002_MC58_CY5_M07044_CY3.mev.refIsIB.out


title: 253274110035_MC58_CY5_06104BC_CY3.mev.refIsIB.out


title: Cells transfected with sirtuin 6 and stimulated with TNFa, biological rep1


title: AML 3490

description: AML


title: Control cells stimulated with TNFa, biological rep3

description: Gene expression data from HEK293 cells stimulated with TNFa

source_name: HEK293 cells stimulated with TNFa


title: Cells transfected with sirtuin 6, biological rep2

description: Gene expression data from HEK293 cells transfected with SIRT6 construct  and unstimulated


title: 253274110034_MC58_CY5_MK16_2001_CY3.mev.refIsIB.out


title: Cells transfected with sirtuin 6, biological rep3

source_name: HEK293 cells transfected with SIRT6 construct  and unstimulated


title: 253274110034_MC58_CY5_MC58_CY3.mev.refIsIB.out


title: 253274110001_MC58_CY5_M13507_CY3.mev.refIsIB.out


title: Cells transfected with sirtuin 6, biological rep1


title: Control cells stimulated with TNFa, biological rep2


title: Control cells unstimulated, biological rep2

description: Gene expression data from HEK293 cells unstimulated

source_name: HEK293 cells unstimulated


title: 253274110028_MC58_CY5_M17070_CY3.mev.refIsIB.out


title: Control cells unstimulated, biological rep3


title: 253274110034_MC58_CY5_BT422_CY3.mev.refIsIB.out


title: 253274110033_MC58_CY5_02108_CY3.mev.refIsIB.out


title: VIHCC P_NY84

city: Dallas

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicate mesurements were averaged after removing outliers. After subtracting background signal intensities and applying a floor value of 0.01 was assigned to negative values, data were normalized using the cubic spline algorithm implemented in GenePattern IlluminaNormalizer module.

source_name: Human hepatocellular carcinoma

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, total RNA was extracted using TRIzol (Invitrogen).

tag: tissue

value: hepatocellular carcinoma

tag: vascular invasion

value: No


title: 253274110034_MC58_CY5_M14226_CY3.mev.refIsIB.out


title: 253274110033_MC58_CY5_98_1101_142_CY3.mev.refIsIB.out


title: 253274110033_MC58_CY5_05103_CY3.mev.refIsIB.out


title: Cells transfected with H133W mutant sirtuin 6, biological rep1


title: Control cells stimulated with TNFa, biological rep1


title: Control cells unstimulated, biological rep1


title: 253274110028_MC58_CY5_M15982_CY3.mev.refIsIB.out


title: Subject 3; two months before the beginning of heating experiment

city: Haga-Gun, Tochigi

first: Hidehiko

last: Kondo

address: 2606 Akabane, Ichikai-Machi

department: Biological Science Laboratories

institute: Kao Corporation

description: Image output files were inspected for hybridization artifacts, and based on the fluorescence intensity differences between perfect match and mismatch probes, the hybridization intensity was calculated for each transcript.

hyb_protocol: Following fragmentation, the 15 µg labeled cRNA hybridized for 16 hr at 45°C to Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions. After stringent washing in a fluidics station 450, cRNA was stained with R-phycoerythrin streptavidine and scanned after antibody amplification.

scan_protocol: Fluorescence intensities were measured with an Affymetrix Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Skeletal muscle

label_protocol: Preparation of labeled cRNA from the RNA was performed according to Affymetrix Two-Cycle Target Labeling Assay.

extract_protocol: Total RNA extraction was performed by using ISOGEN (Nippon Gene Co., LTD, Toyama, Japan) according to the manufacturer's instructions, and purified using an RNeasy Mini kit (Qiagen K.K, Tokyo, Japan).

tag: Gender

value: Male

tag: Tissue

value: vastus lateralis muscle


title: VIHCC P_NY673

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: VIHCC P_NY643

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: Subject 5; 1 day after the end of heating experiment


title: 253274110028_MC58_CY5_M15829_CY3.mev.refIsIB.out


title: Subject 4; 1 day after the end of heating experiment


title: Cells transfected with H133W mutant sirtuin 6 and stimulated with TNFa, biological rep3


title: VIHCC P_NY641


title: VIHCC P_NY633


title: VIHCC P_NY635

value: Yes


title: VIHCC P_NY637


title: VIHCC P_NY631


title: VIHCC P_NY639


title: 253274110015_MC58_CY5_NGC5_CY3.mev.refIsIB.out


title: 253274110014_MC58_CY5_HF129_CY3.mev.refIsIB.out


title: VIHCC P_NY615


title: Subject 2; 1 day after the end of heating experiment

description: Image output files were inspected for hybridization artifacts, and based on the fluorescence intensity differences between perfect match and mismatch probes.


title: 253274110015_MC58_CY5_HF76_CY3.mev.refIsIB.out


title: VIHCC P_NY619


title: VIHCC P_NY625


title: 253274110014_MC58_CY5_HF64_CY3.mev.refIsIB.out


title: 253274110033_MC58_CY5_02104_CY3.mev.refIsIB.out


title: Subject 5; two months before the beginning of heating experiment


title: Subject 1; 1 day after the end of heating experiment


title: 253274110028_MC58_CY5_M09554_CY3.mev.refIsIB.out


title: VIHCC P_NY627


title: Subject 3; 1 day after the end of heating experiment


title: VIHCC P_NY611


title: VIHCC P_NY609


title: VIHCC P_NY617


title: Subject 2; two months before the beginning of heating experiment


title: 253274110015_MC58_CY5_ETH2_CY3.mev.refIsIB.out


title: VIHCC P_NY607


title: Subject 1; two months before the beginning of heating experiment


title: VIHCC P_NY601


title: VIHCC P_NY599


title: Colon_UC_20

city: Stockholm

first: Linda

last: Gillberg

address: Gastro Research Lab M1:02

department: Medicine

country: Sweden

institute: Karolinska Institutet

description: The GEArray Q Series Human Nitric Oxide Gene Array contains 96 genes whose expression is controlled by or involved in signaling by the second messenger nitric oxide (NO).

hyb_protocol: Labeled RNA was hybridazed to a human nitric oxide gene array (GEArray Q; SuperArray Inc.) by incubation over-night at 60°C in accordance with the manufacturers protocol. Each sample was hybridized to its own individual membrane, while control samples were pooled and measured in quadruplicate. Also, washing was performed according to protocol.

scan_protocol: The array image was visualized using a phosphoimager (BAS-1500, Fujifilm Corp.) and TIFF documents created with the Image gauge software (version 3.45, Fujifilm Corp).

data_processing: Raw data were analysed with the GEArray Expression Analysis Suite software (version 2.0, SuperArray Inc.), with the parameters set to measure total intensity of brightness in a clover-shaped area surrounding each spot. All hybridization signals were corrected for local background of each spot, with negative values set to 0, and normalized according to the quantile normalization method using preprocessCore package in the R environment software. An mRNA transcript was regarded as being present if recovered in ≥ 50% of the samples examined in each group (i.e. n equal or more than 10); the intensity of its signal exceeding that of the lower 75th percentile of the local background.

source_name: colon mucosa, UC

label_protocol: Three mg of each sample of total RNA was reverse transcribed and labelled with 32P-dCTP (GE Heathcare) by PCR in accordance to the AmpoLabeling-LPR kit (SuperArray Inc.) protocol.

extract_protocol: Three biopsies (15-30 mg) were collected from each patient, immediately submerged in RNA stabilization reagent (RNAlater, Ambion), maintained at 4° C for 24 h and thereafter stored at –20° C. For isolation of total RNA biopsies were thawed and homogenized in RLT cell lysis buffer (Qiagen) with a rotor-stator knife (Ultra-Turrax T8, IKA), following which RNA was extracted with the RNeasy Mini kit (Qiagen). An enzymatic digestion step was included to remove traces of DNA (incubation at 37° C for 30 min with DNase I obtained from Promega).

value: colon mucosa

tag: ibd subtype

value: UC

tag: sex

value: female

tag: age

tag: duration of disease

value: 21 years


title: Colon_UC_8

value: male

value: 5 months


title: Colon_UC_9

value: diagnosed at inclusion


title: VIHCC P_NY605


title: Chromium + Ferrous sulfate treated rep4

city: Morgantown

first: Rajendran

last: Sellamuthu

state: WV

address: 1095 Willowdale Rd

department: HELD

description: The labeling and hybridization of microarray were performed at National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV and scanning was performed at the Center for Genomics Sciences, Alleghney-Singer Research Institute, Pittsburgh, PA.

hyb_protocol: Employing materials and protocols provided by Illumina, Inc, each labeled cRNA sample was hybridized to HumanRef-8 Sentrix BeadChip Array (Illumina, Inc, San Diego, CA) for 20 hrs at 580C. Following hybridization, micro arrays were washed to remove unbound and non-specifically hybridized target molecules and stained with Cy3-streptavidin conjugate (Illumina, Inc, San Diego, CA). This was followed by several non-stringent washing steps to remove unbound conjugate.

scan_protocol: The arrays were scanned with the Illumina BeadStation 500 platform, according to beadchip array manufacturer's protocol (Illumina, Inc, San Diego, CA).

data_processing: Array data were extracted using Illumina's BeadStudio software (Framework version 3.0.19.0). Normalization and statistical analysis of the beadarray expression data from the arrays were carried out in R/Bioconducter using the ‘lumi’ and ‘limma’ packages. The ‘lumi’ Bioconductor package covered the data input, quality control, varience stabilization, normalization and gene annotation (http://bioconductor.org/packagees/2.2/ bioc/vignettes/lumi/inst/doc/lumi.pdf). A linear model analysis using ‘limma’ package in R was conducted to identify differentially expressed genes. p values were calculated and log fold changes were converted to standard fold changes.  Resulting raw p-values were corrected for false discovery rate using the Benjamini-Hochberg method.

label: Biotin, Cy3-streptavidin

source_name: Human dermal fibroblast cell line (Catalogue No. CRL 2076, ATCC, Manassas, VA)

label_protocol: After the RNA quality measurement by the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), each RNA sample (375 ng) was amplified and biotin-labeled by employing the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc, Austin, TX).

extract_protocol: RNeasy Kit (Qiagen, Inc, Valencia, CA) with on-column DNA digestion following the manufacturer's instructions.

treatment_protocol: The human dermal fibroblasts were grown overnight in Iscove’s modified Dulbecco’s medium. Subsequently, the cells were treated with potassium dichromate in the presence or absence of ferrous sulfate for 24 hrs in serum free growth medium, followed by total RNA isolation.

value: fibroblast

tag: gender

value: newborn


title: Chromium + Ferrous sulfate treated rep3

institute: National Institute for Occupational Safety and Health


title: VIHCC P_NY591


title: Untreated Control rep4


title: VIHCC P_NY597


title: VIHCC P_NY593


title: Subject 4; two months before the beginning of heating experiment


title: VIHCC P_NY603


title: VIHCC P_NY589


title: Colon_UC_18

value: 2 years


title: Ferrous sulfate treated rep4


title: Colon_UC_17

value: 6 years


title: VIHCC P_NY587


title: Chromium treated rep4


title: Ferrous sulfate treated rep3


title: VIHCC P_NY595


title: VIHCC P_NY585


title: VIHCC P_NY583


title: Chromium treated rep3


title: Colon_UC_16

value: 16 years


title: VIHCC P_NY579

value: hepatocellular carcinoma


title: Untreated Control rep3


title: Colon_UC_19


title: VIHCC P_NY577

value: No


title: Colon_UC_15

value: 12 years


title: Colon_UC_10

value: 45 years


title: Colon_UC_1

value: 36 years


title: VIHCC P_NY575

value: Yes


title: Colon_UC_14

value: colon mucosa

value: UC


title: Chromium treated rep2


title: VIHCC P_NY573


title: Ferrous sulfate treated rep2


title: Chromium + Ferrous sulfate treated rep2


title: VIHCC P_NY567


title: Colon_UC_12

value: 28 years


title: Colon_UC_13

value: female


title: VIHCC P_NY559


title: VIHCC P_NY569


title: VIHCC P_NY565


title: VIHCC P_NY557


title: VIHCC P_NY561


title: Chromium + Ferrous sulfate treated rep1

value: male


title: Colon_UC_11

value: diagnosed at inclusion


title: VIHCC P_NY553


title: Colon_UC_7

value: 32 years


title: Chromium treated rep1

value: fibroblast

value: newborn


title: VIHCC P_NY551


title: Untreated Control rep1


title: VIHCC P_NY541


title: VIHCC P_NY549


title: Untreated Control rep2


title: VIHCC P_NY571


title: VIHCC P_NY547


title: Ferrous sulfate treated rep1


title: VIHCC P_NY537


title: VIHCC P_NY539


title: VIHCC P_NY531


title: VIHCC P_NY535


title: Colon_UC_6


title: VIHCC P_NY525


title: Colon_UC_5

value: 15 years


title: VIHCC P_NY529


title: Colon_UC_4


title: Colon_UC_2

value: 2 years


title: Telmisartan-treated 306

city: Nagoya

first: Satoru

last: Takahashi

state: Aichi

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Pathology

institute: Nagoya City University

hyb_protocol: The slides were hybridized with Cy3- or Cy5-labeled cRNA for 16-18 hr at 60°C, washed in 0.5 x SSC/0.01% SDS buffer for 5 min at room temperature, then 0.06 x SSC buffer for 2 min, and desiccated with a centrifuge.

scan_protocol: The slides were scanned with a DNA Microarray Scanner (Agilent Technologies) at two wavelengths to detect emission from both Cy3 and Cy5.

data_processing: Agilent Feature Extraction Software ver9.1 software was used to calculate the log10 (ventral prostate of TRAP rat/normal ventral prostate of F344 rat) ratios in the Sample data tables.

organism: Rattus norvegicus

source_name: Normal ventral prostate of F344 rat

label_protocol: Labeled using a Low RNA Input Fluorescent Linear Amplification kit (Agilent)

extract_protocol: Extracted using ISOGEN (Nippon Gene Co. Ltd., Toyama, Japan)

treatment_protocol: The rats in this group continuously received 2 or 10 mg/kg/day telmisartan in drinking water for 12 weeks, respectively.

value: 6 weeks

source_name: Ventral prostate of TRAP rat

value: SD

value: 15 weeks


title: VIHCC P_NY511

value: hepatocellular carcinoma

value: No


title: VIHCC P_NY527


title: Colon_UC_3

value: 14 years


title: Colon_CD_23

source_name: colon mucosa, CD

value: colon mucosa

value: CD

value: 31 years


title: VIHCC P_NY523

value: Yes


title: VIHCC P_NY521


title: Colon_CD_22

value: female

value: 19 years


title: VIHCC P_NY517


title: Telmisartan-treated 303

value: male


title: VIHCC P_NY501


title: Telmisartan-treated 305


title: VIHCC P_M77


title: Control 106

treatment_protocol: Rats in control group received basal diet and tap water.


title: Control 103


title: VIHCC P_NY505


title: Telmisartan-treated 302


title: VIHCC P_M487


title: VIHCC P_NY507


title: Colon_CD_26

value: diagnosed at inclusion


title: Control 102


title: VIHCC P_M479


title: Colon_CD_21

value: 23 years


title: Control 104


title: Colon_CD_20

value: 3 years


title: VIHCC P_M75


title: VIHCC P_M483


title: Colon_CD_14

value: 30 years


title: VIHCC P_M465


title: VIHCC P_M469


title: AsA PAT_rep2

city: Tukuba

first: Tadahiro

last: Suzuki

state: Ibaraki

address: kan-nondai 2-1-12

department: Applied Microbiology Division

institute: National Food Rsearch Institute

description:
Gene expression data from yeast
sod1_AsA PAT_2

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: CEL files were MAS5 normalized using Affymetrix GeneChip Operating Software Version 1.4

organism: Saccharomyces cerevisiae

source_name: SOD1 mutant strain processed by patulin and ascorbic acid

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated aRNA targets using Affymetrix 3'IVT Express Kit.

growth_protocol: S. cerevisiae BY 4743 (BY4743; MATa/α his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 lys2Δ0) derivative sod1 (SOD1 (YJR104C) knock-out strain) were grown in YPD medium at 25C for 2 days.

extract_protocol: Each sample of total RNA was extracted using FastRNA Pro Red kit (MP Biomedicals, US) according to the manufacturer’s instructions.

treatment_protocol: Yeast strain was grown in YPD medium with 25 ppm patulin and 10 mM ascorbic acid.

tag: genotype/variation

value: SOD1 mutant

tag: agent

value: patulin and ascorbic acid


title: AsA PAT_rep1

description:
Gene expression data from yeast
sod1_AsA PAT_1


title: VIHCC P_M443


title: AsA PAT_rep3

description:
Gene expression data from yeast
sod1_AsA PAT_3


title: Colon_CD_1

value: 9 years


title: VIHCC P_M431

value: hepatocellular carcinoma


title: VIHCC P_M441

value: No


title: VIHCC P_M461


title: Colon_CD_12

value: 14 years


title: VIHCC P_M423


title: VIHCC P_M415


title: PAT_rep3

description:
Gene expression data from yeast
sod1_PAT_3

source_name: SOD1 mutant strain processed by patulin

value: patulin


title: PAT_rep2

description:
Gene expression data from yeast
sod1_PAT_2


title: Colon_CD_18

value: colon mucosa

value: CD

value: 16 years


title: Colon_CD_17

value: 4 years


title: PAT_rep1

description:
Gene expression data from yeast
sod1_PAT_1


title: Colon_CD_16


title: VIHCC P_M411

value: Yes


title: Colon_CD_19

value: female

value: 8 years


title: VIHCC P_M409


title: AsA_rep3

description:
Gene expression data from yeast
sod1_AsA_3

source_name: SOD1 mutant strain processed by ascorbic acid

value: ascorbic acid


title: VIHCC P_M421


title: Colon_CD_15

value: 21 years


title: VIHCC P_M407


title: VIHCC P_M405


title: AsA_rep2

description:
Gene expression data from yeast
sod1_AsA_2


title: AsA_rep1

description:
Gene expression data from yeast
sod1_AsA_1


title: VIHCC P_M401


title: Colon_CD_11

value: male


title: VIHCC P_M395


title: Control_rep3

description:
Gene expression data from yeast
sod1_Con_3

source_name: SOD1 mutant strain

value: SOD1 mutant

value: control


title: Control_rep2

description:
Gene expression data from yeast
sod1_Con_2


title: VIHCC P_M403


title: VIHCC P_M377


title: VIHCC P_M397


title: Control_rep1

description:
Gene expression data from yeast
sod1_Con_1


title: Colon_CD_9

value: 38 years


title: VIHCC P_M345

value: hepatocellular carcinoma


title: VIHCC P_M383

value: No


title: VIHCC P_M381


title: Colon_CD_4


title: VIHCC P_M393


title: VIHCC P_M375


title: VIHCC P_M311


title: Colon_CD_6

value: 5 years


title: VIHCC P_M367


title: Colon_CD_2

value: 5 months


title: VIHCC P_M291


title: VIHCC P_M319


title: Colon_control_rep4

source_name: colon mucosa, control

value: colon mucosa

value: 2 males, 4 females


title: Colon_CD_3

value: CD

value: diagnosed at inclusion


title: 30 min UV-B vs 60 min UV-B, irradiated leaf Rep 1 uvb-short-30I_60I-Rep1-Cy3-60I

city: Stanford

middle: F

last: Fernandes

state: CA

address: 385 Serra Mall

department: Bio Sci

institute: Stanford University

hyb_protocol: 825 ng of each labeled target cRNA were hybridized for 17 h at 65C

scan_protocol: Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual.  Images were processed with the Agilent Feature Extraction software, version 10.

data_processing: Text files from Feature Extraction software were processed using the limma package of R.  After removal of spots flagged by Feature Extraction as below background or saturated or outliers, dye normalized values for each channel from Feature Extraction were normalized again to the median array intensity.  Average intensities were then calculated for probes with at least 3 of 4 good intensities.

organism: Zea mays

label_protocol: Total RNA (1000 ng) was amplified & labeled with Cy3 or Cy5 using Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: Plants were grown and dissected at the Stanford GREENHOUSES; tissues were collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA was extracted from 30 - 60  of frozen TISSUES with Invitrogen Purelink RNA Mini kit with DNase I treatment.

treatment_protocol: 0, 10, 30, or 60 min UV-B irradiation of top 2 leaves.

tag: sample type

value: 60 min UV-B, irradiated leaf

tag: tiime

value: 60 min

value: UV-B

value: irradiated leaf


title: VIHCC P_M309


title: 10 min UV-B vs 30 min UV-B, irradiated leaf Rep 1 uvb-short-10I_30I-Rep1-Cy3-30I

value: 30 min UV-B, irradiated leaf

value: 30 min

tag: treatment


title: VIHCC P_M315


title: VIHCC P_M289


title: Colon_control_rep3


title: 60 min UV-B vs 30 min UV-B, irradiated leaf Rep 2 uvb-short-30I_60I-Rep2-Cy3-30I


title: VIHCC P_M293


title: VIHCC P_M285


title: Colon_control_rep2


title: Colon_CD_10

value: male


title: VIHCC P_M275

value: Yes


title: VIHCC P_M271


title: VIHCC P_M287


title: VIHCC P_M267


title: VIHCC P_M261


title: 0 min UV-B vs 10 min UV-B, irradiated leaf Rep 1 uvb-short-0I_10I-Rep1-Cy3-10I

value: 10 min UV-B, irradiated leaf

value: 10 min


title: 30 min UV-B vs 10 min UV-B, irradiated leaf Rep 2 uvb-short-10I_30I-Rep2-Cy3-10I


title: Colon_control_rep1

value: control


title: 10 min UV-B vs 0 min UV-B, irradiated leaf Rep 2 uvb-short-0I_10I-Rep2-Cy3-0I

value: 0 min UV-B, irradiated leaf

value: 0 min


title: 0 min UV-B vs 30 min UV-B, irradiated leaf Rep 1 uvb-short-0I_30I-Rep1-Cy3-30I


title: VIHCC P_M269

value: hepatocellular carcinoma

value: No


title: VIHCC P_M251


title: VIHCC P_M229


title: VIHCC P_M207


title: VIHCC P_M225


title: VIHCC P_M255


title: VIHCC P_M235


title: VIHCC P_M217


title: 30 min UV-B vs 10 min UV-B, shielded ear Rep 2 uvb-short-10E_30E-Rep2-Cy3-10E

value: 10 min UV-B, shielded ear

value: shielded ear


title: 10 min UV-B vs 30 min UV-B, shielded ear Rep 1 uvb-short-10E_30E-Rep1-Cy3-30E

value: 30 min UV-B, shielded ear


title: H69_100uM Zebularine_SAMPLE 105

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: DMEM +10% fetal bovine serum, 2mM L-glutamine

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: mock, 100uM, or 200uM Zebularine for 7 days. Medium and drug was changed every 3 days

tag: drug sensitivity

value: cholangiocyte cell line H69

value: zebularine

tag: dose


title: H69_200uM zebularine_SAMPLE 108

description: replicate 3

tag: cell line


title: 30 min UV-B vs 0 min UV-B, irradiated leaf Rep 2 uvb-short-0I_30I-Rep2-Cy3-0I

value: UV-B

tag: tissue

value: irradiated leaf


title: 0 min UV-B vs 10 min UV-B, shielded ear Rep 1 uvb-short-0E_10E-Rep1-Cy3-10E


title: VIHCC P_M211

tag: vascular invasion


title: 0 min UV-B vs 30 min UV-B, shielded ear Rep 1 uvb-short-0E_30E-Rep1-Cy3-30E

value: 30 min


title: VIHCC P_M219


title: VIHCC P_M227


title: H69_200uM zebularine_SAMPLE 107

description: replicate 2


title: VIHCC P_M209


title: 10 min UV-B vs 0 min UV-B, shielded ear Rep 2 uvb-short-0E_10E-Rep2-Cy3-0E

value: 0 min UV-B, shielded ear


title: H69_200uM zebularine_SAMPLE 106

description: replicate 1


title: 30 min UV-B vs 10 min UV-B, shielded leaf Rep 2 uvb-short-10S_30S-Rep2-Cy3-10S

value: 10 min UV-B, shielded leaf

value: shielded leaf


title: VIHCC P_M203


title: 30 min UV-B vs 0 min UV-B, shielded ear Rep 2 uvb-short-0E_30E-Rep2-Cy3-0E


title: H69_100uM Zebularine_SAMPLE 103

description: replicate 1


title: VIHCC P_B221


title: VIHCC P_B213


title: VIHCC P_M201


title: H69_Mock_SAMPLE 102

description: replicate 3

value: mock


title: VIHCC P_B211


title: H69_Mock_SAMPLE 101

description: replicate 2


title: 10 min UV-B vs 0 min UV-B, shielded leaf Rep 2 uvb-short-0S_10S-Rep2-Cy3-0S

value: 0 min UV-B, shielded leaf


title: 0 min UV-B vs 10 min UV-B, shielded leaf Rep 1 uvb-short-0S_10S-Rep1-Cy3-10S

value: 10 min


title: VIHCC P_B209

value: Yes


title: VIHCC P_B219

value: hepatocellular carcinoma


title: 10 min UV-B vs 30 min UV-B, shielded leaf Rep 1 uvb-short-10S_30S-Rep1-Cy3-30S

value: 30 min UV-B, shielded leaf


title: VIHCC P_B181

value: No


title: H69_100uM Zebularine_SAMPLE 104

description: replicate 2


title: VIHCC P_B201


title: THLE-3_200uM zebularine_SAMPLE 99

description: replicate 3

value: Non-transformed Liver cell line THLE-3


title: 0 min UV-B vs 30 min UV-B, shielded leaf Rep 1 uvb-short-0S_30S-Rep1-Cy3-30S


title: H69_Mock_SAMPLE 100

description: replicate 1


title: VIHCC P_B161


title: THLE-3_200uM zebularine_SAMPLE 98

description: replicate 2


title: 60 min UV-B vs 30 min UV-B, irradiated leaf Rep 2 uvb-short-30I_60I-Rep2-Cy5-60I

value: 60 min UV-B, irradiated leaf

value: 60 min


title: VIHCC P_B173


title: VIHCC P_B207


title: VIHCC P_B157


title: 30 min UV-B vs 0 min UV-B, shielded leaf Rep 2 uvb-short-0S_30S-Rep2-Cy3-0S

value: 0 min


title: VIHCC P_B175


title: 30 min UV-B vs 60 min UV-B, irradiated leaf Rep 1 uvb-short-30I_60I-Rep1-Cy5-30I

value: 30 min UV-B, irradiated leaf

value: UV-B


title: THLE-3_200uM zebularine_SAMPLE 97

description: replicate 1

value: zebularine


title: VIHCC P_B171


title: THLE-3_100uM Zebularine_SAMPLE 96

description: replicate 3


title: 30 min UV-B vs 10 min UV-B, irradiated leaf Rep 2 uvb-short-10I_30I-Rep2-Cy5-30I

value: 30 min

value: irradiated leaf


title: VIHCC P_B149


title: VIHCC P_B129


title: VIHCC P_B072


title: VIHCC P_B179


title: VIHCC P_B007


title: VIHCC P_B151


title: 10 min UV-B vs 30 min UV-B, irradiated leaf Rep 1 uvb-short-10I_30I-Rep1-Cy5-10I

value: 10 min UV-B, irradiated leaf


title: VIHCC P_B005


title: THLE-3_100uM Zebularine_SAMPLE 95

description: replicate 2


title: 10 min UV-B vs 0 min UV-B, irradiated leaf Rep 2 uvb-short-0I_10I-Rep2-Cy5-10I


title: THLE-3_Mock_SAMPLE 93

description: replicate 3

value: mock


title: ssm065

city: Seattle

first: David

middle: K

last: Pritchard

state: WA

address: 815 Mercer Street Rm.  418

institute: University of Washington

data_processing: Data was quantile normalized without background subtraction using Bioconductor packages

source_name: Male Subject with Carotid Disease

label_protocol: Labeled cRNAs were generated using the Illumina TotalPrep RNA Amplification Kit from Ambion (Cat number IL1791) following the manufacturer’s specifications.

growth_protocol: Monocytes were isolated in a two step process. First, peripheral blood mononuclear cell (PBMC) populations were isolated using a modified density gradient centrifugation.using CPT tubes.  Next monocytes were isolated using a negative selection system with magnetic beads coupled to CD3, CD7, CD16, CD19, CD56, CD123 and CD235a (Miltenyi - Monocyte Isolation Kit II)

extract_protocol: The total RNA from enriched monocytes was extracted from purified cells using mini RNeasy kits from QIAGEN.

value: male

tag: cell type

value: Monocytes


title: ssm167


title: THLE-3_Mock_SAMPLE 92

description: replicate 2


title: THLE-3_Mock_SAMPLE 91

description: replicate 1


title: THLE-3_100uM Zebularine_SAMPLE 94

description: replicate 1


title: 0 min UV-B vs 30 min UV-B, irradiated leaf Rep 1 uvb-short-0I_30I-Rep1-Cy5-0I

value: 0 min UV-B, irradiated leaf


title: ssm230


title: 0 min UV-B vs 10 min UV-B, irradiated leaf Rep 1 uvb-short-0I_10I-Rep1-Cy5-0I


title: ssm170


title: WITT_200uM zebularine_SAMPLE 88

description: replicate 1

source_name: WITT

value: resistant

value: Liver cancer cell line WITT


title: ssm211


title: 10 min UV-B vs 30 min UV-B, shielded ear Rep 1 uvb-short-10E_30E-Rep1-Cy5-10E

value: 10 min UV-B, shielded ear

value: 10 min

value: shielded ear


title: ssm079


title: ssm212


title: 30 min UV-B vs 10 min UV-B, shielded ear Rep 2 uvb-short-10E_30E-Rep2-Cy5-30E

value: 30 min UV-B, shielded ear


title: WITT_200uM zebularine_SAMPLE 89

description: replicate 2


title: Macrophage_WTvsMD2_PBS_Mouse2_Rep1

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

institute: Lund University

hyb_protocol: Pretreatment of arrays, hybridization, and post-hybridization washes was carried out according to manufacturers’ instructions (Corning ChipShot™ labeling system).

scan_protocol: Hybridized microarrays were imaged using an Agilent G2565AA microarray scanner (Agilent Technologies). Fluorescence intensities were extracted using Gene Pix Pro 4.0 software (Axon Instruments Inc., Foster City, CA).

data_processing: All microarray data were stored, filtered and normalized in the BioArray Software Environment (BASE; http://base.thep.lu.se/). T test statistics with Benjamini-Hochberg correction for multiple testing were calculated in the R software environment for statistical computing (http://www.r-project.org/).

organism: Mus musculus

source_name: Bone marrow derived macrophages

label_protocol: Fluorescence-labeled cRNA target was prepared from 500 ng total RNA using Agilent Low Linear amplification kit (Agilent Technologies, Santa Clara, CA, USA) according to manufacturers’ instructions.

growth_protocol: Bone marrows were harvested from femur and tibia of 6- to 8-week-old mice. Bone marrow (BM)-derived macrophages were differentiated from bone marrow cells cultured in DMEM medium (Mediatech, Herndon, VA) supplemented with 10% heat-inactivated FBS, 20% L929-conditioned media and 10µg/ml ciprofloxacin (Bayer, West Haven, CT). Ex vivo cultured macrophages were collected at day 8.

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Macrophages were treated with 10 ng/ml PGN-free LPS, 100 ng/ml synthetic Lipid A, 10 nM Pam2CSK4 or PBS for 2 hours before RNA isolation.

tag: strain

tag: genotype

value: WT

value: PBS


title: WITT_200uM zebularine_SAMPLE 90

description: replicate 3


title: Macrophage_MD2_LPS_Mouse1_Rep1

value: 10 ng LPS /mL


title: ssm120


title: 0 min UV-B vs 10 min UV-B, shielded ear Rep 1 uvb-short-0E_10E-Rep1-Cy5-0E

value: 0 min UV-B, shielded ear

value: 0 min

value: UV-B


title: ssm210


title: WITT_100uM Zebularine_SAMPLE 87

description: replicate 3

value: zebularine


title: 30 min UV-B vs 0 min UV-B, irradiated leaf Rep 2 uvb-short-0I_30I-Rep2-Cy5-30I

value: 30 min UV-B, irradiated leaf

value: 30 min

value: irradiated leaf


title: Macrophage_WTvsMD2_PBS_Mouse2_Rep2


title: 10 min UV-B vs 0 min UV-B, shielded ear Rep 2 uvb-short-0E_10E-Rep2-Cy5-10E


title: Macrophage_MD2_LPS_Mouse1_Rep2


title: Macrophage_WT_LPS_Mouse1_Rep2


title: Macrophage_WT_LPS_Mouse1_Rep1


title: 30 min UV-B vs 0 min UV-B, shielded ear Rep 2 uvb-short-0E_30E-Rep2-Cy5-30E


title: ssm119

value: male

value: Monocytes


title: ssm118


title: WITT_100uM Zebularine_SAMPLE 86

description: replicate 2

value: resistant

value: Liver cancer cell line WITT


title: ssm097


title: WITT_100uM Zebularine_SAMPLE 85

description: replicate 1


title: WITT_Mock_SAMPLE 84

description: replicate 3

value: mock


title: 0 min UV-B vs 30 min UV-B, shielded ear Rep 1 uvb-short-0E_30E-Rep1-Cy5-0E

value: shielded ear


title: Macrophage_WTvsMD2_PBS_Mouse1_Rep1


title: 30 min UV-B vs 10 min UV-B, shielded leaf Rep 2 uvb-short-10S_30S-Rep2-Cy5-30S

value: 30 min UV-B, shielded leaf

value: shielded leaf


title: Macrophage_MD2_Pam2_Mouse1_Rep1

value: 10 nM Pam2

value: PBS


title: WITT_Mock_SAMPLE 83

description: replicate 2


title: 10 min UV-B vs 0 min UV-B, shielded leaf Rep 2 uvb-short-0S_10S-Rep2-Cy5-10S

value: 10 min UV-B, shielded leaf

value: 10 min


title: ssm131


title: ssm122


title: 10 min UV-B vs 30 min UV-B, shielded leaf Rep 1 uvb-short-10S_30S-Rep1-Cy5-10S

value: UV-B


title: ssm121


title: Macrophage_WTvsMD2_PBS_Mouse1_Rep2

value: WT


title: ssm130


title: 0 min UV-B vs 10 min UV-B, shielded leaf Rep 1 uvb-short-0S_10S-Rep1-Cy5-0S

value: 0 min UV-B, shielded leaf

value: 0 min


title: Macrophage_WT_Pam2_Mouse1_Rep1


title: KMBC_200uM zebularine_SAMPLE 80

description: replicate 2

source_name: KMBC

value: sensitive

value: Liver cancer cell line KMBC

value: zebularine


title: Macrophage_WT_Pam2_Mouse2_Rep1


title: KMBC_200uM zebularine_SAMPLE 81

description: replicate 3


title: Macrophage_MD2_Pam2_Mouse2_Rep1


title: ssm127

value: male

value: Monocytes


title: 30 min UV-B vs 0 min UV-B, shielded leaf Rep 2 uvb-short-0S_30S-Rep2-Cy5-30S

value: 30 min


title: KMBC_200uM zebularine_SAMPLE 79

description: replicate 1


title: Macrophage_WT_LipidA_Mouse1_Rep1

value: 100 ng Lipid A /mL


title: WITT_Mock_SAMPLE 82

description: replicate 1

value: Liver cancer cell line WITT

value: mock


title: ssm146


title: Macrophage_MD2_LipidA_Mouse1_Rep1


title: KMBC_100uM Zebularine_SAMPLE 78

description: replicate 3


title: 0 min UV-B vs 30 min UV-B, shielded leaf Rep 1 uvb-short-0S_30S-Rep1-Cy5-0S

value: shielded leaf


title: ssm145


title: ssm144


title: KMBC_100uM Zebularine_SAMPLE 77

description: replicate 2


title: Macrophage_MD2_Pam2_Mouse1_Rep2

value: 10 nM Pam2

value: PBS


title: KMBC_100uM Zebularine_SAMPLE 76

description: replicate 1


title: KMBC_Mock_SAMPLE 75

description: replicate 3


title: Macrophage_MD2_LipidA_Mouse1_Rep2


title: ssm134


title: ssm150


title: KMCH_200uM zebularine_SAMPLE 72

description: replicate 3

source_name: KMCH

value: Liver cancer cell line KMCH


title: ssm153


title: KMCH_200uM zebularine_SAMPLE 71

description: replicate 2


title: KMBC_Mock_SAMPLE 73

description: replicate 1


title: ssm088


title: Macrophage_MD2_Pam2_Mouse2_Rep2


title: KMBC_Mock_SAMPLE 74

description: replicate 2


title: Macrophage_MD2_LPS_Mouse2_Rep1

value: 10 ng LPS /mL


title: ssm069


title: ssm171


title: ssm161


title: KMCH_100uM Zebularine_SAMPLE 69

description: replicate 3


title: Macrophage_MD2_LipidA_Mouse2_Rep2


title: Macrophage_WT_Pam2_Mouse1_Rep2

value: WT


title: Macrophage_WT_LipidA_Mouse1_Rep2


title: KMCH_200uM zebularine_SAMPLE 70

description: replicate 1


title: KMCH_100uM Zebularine_SAMPLE 68

description: replicate 2


title: Macrophage_MD2_LipidA_Mouse2_Rep1


title: Macrophage_WT_Pam2_Mouse2_Rep2


title: Macrophage_MD2_LPS_Mouse2_Rep2


title: ssm163


title: Macrophage_WT_LipidA_Mouse2_Rep2


title: ssm160


title: KMCH_100uM Zebularine_SAMPLE 67

description: replicate 1


title: ssm159


title: KMCH_Mock_SAMPLE 65

description: replicate 2


title: Macrophage_WT_LipidA_Mouse2_Rep1


title: ssm202


title: Macrophage_WT_LPS_Mouse2_Rep2


title: KMCH_Mock_SAMPLE 64

description: replicate 1


title: KMCH_Mock_SAMPLE 66

description: replicate 3


title: stem pulvini Upper Side: 24.0 Hours: rep1

city: Glen Osmond

first: Qisen

last: Zhang

state: South Australia

address: Waite Campus

department: School of Agriculture, Food and Wine

country: Australia

institute: University Of Adelaide

hyb_protocol: Standard Agilent Hybridization protocol.

scan_protocol: After hybridization, the microarray slides were washed and scanned immediately with Agilent’s G2505B DNA Microarray Scanner at two laser power settings (100% and 10%). The images were inspected visually for image artifacts, and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v 9.5.1).

data_processing: The data were then normalized using quantile normalization (BOLSTAD http://www.ncbi.nlm.nih.gov/pubmed/12538238) and passed forward for periodicity determination. Further quality control and downstream analysis were performed using data analysis tools in Rosetta’s Resolver Database and in the statistical program R.

source_name: stem pulvini_24hr_rep1_Upper Side

label_protocol: Each mRNA sample was made into double-stranded DNA, amplified by an in-vitro transcription reaction, and labeled with Cy3 or Cy5 fluorescent dye, all using Agilent’s Low RNA Linear Amp kit. Biological replicates were labeled alternately using Cy3 or Cy5 to guard against dye-bias.

growth_protocol: Maize plants (O9B) were grown in a glass house at 17/27C.

extract_protocol: Total RNA was isolated from frozen ground tissue (SQ Tissue Kit, Omega Biotek), followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for the 108 samples. The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: The maize plants were subjected to gravistimulation when the tip of primary cob was first visible (60 – 65 days from sowing) by placing on floors at approximately 20 degree angle.  The maize plants were placed on the floor with leaves protruding from both sides.  Stem pulvini were dissected and frozen in liquid nitrogen immediately for RNA preparation.

value: stem pulvini Upper Side

tag: time point

value: 24.0 Hours

tag: replicate


title: stem pulvini Upper Side: 24.0 Hours: rep3

source_name: stem pulvini_24hr_rep3_Upper Side


title: Macrophage_TLR4-/-_LipidA_Exp2_Rep2

description: Exp2 TLR4_KO LipidA cy5_cy3 s24

hyb_protocol: Labeled samples were hybridized overnight using Genomic Solutions GeneTAC Hybridization Station (Perkin-Elmer, Boston, MA) to the PGA mouse v1.1 oligonucleotide array (Massachusetts General Hospital (MGH), Cambridge, MA).

scan_protocol: Fluorescent images from the arrays were acquired using a microarray scanner and its accompanying software (GenePix 4000B microarray scanner; Axon Instruments, Union City, CA).

label_protocol: Eight µg RNA of both test and reference samples was reverse transcribed and differentially labeled with monoreactive Cy3 and Cy5 Dyes (Amersham, Piscataway, NJ) using the Atlas Powerscript Fluorescent Labeling Kit (Clontech, Mountain View, CA). Labeled samples were purified with Cyscribe GFX Purification Kit (Amersham).

extract_protocol: Total RNA was isolated using the RNeasy kit (Qiagen, Valencia, CA). RNA integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Macrophages were treated with 10 ng/ml PGN-free LPS, 100 ng/ml synthetic Lipid A or 10 nM Pam2CSK4 for 2 hours before RNA isolation.

value: 100 ng Lipid A/mL

tag: experiment

value: Experiment 2


title: ssm200

tag: gender


title: WRL68_200uM zebularine_SAMPLE 62

description: replicate 2

value: resistant

value: Liver cancer cell line WRL68

value: zebularine


title: Macrophage_WT_LPS_Mouse2_Rep1


title: stem pulvini Upper Side: 6.0 Hours: rep3

source_name: stem pulvini_6hr_rep3_Upper Side

value: 6.0 Hours


title: stem pulvini Upper Side: 24.0 Hours: rep2

source_name: stem pulvini_24hr_rep2_Upper Side


title: stem pulvini Upper Side: 6.0 Hours: rep2

source_name: stem pulvini_6hr_rep2_Upper Side


title: WRL68_200uM zebularine_SAMPLE 61

description: replicate 1


title: Macrophage_TLR4-/-_LipidA_Exp2_Rep3

description: Exp2 TLR4_KO LipidA cy3_cy5 s17


title: ssm219

value: male

value: Monocytes


title: stem pulvini Upper Side: 6.0 Hours: rep4

source_name: stem pulvini_6hr_rep4_Upper Side


title: WRL68_200uM zebularine_SAMPLE 63

description: replicate 3


title: Macrophage_TLR4-/-_LipidA_Exp2_Rep4

description: Exp2 TLR4_KO LipidA cy3_cy5 s18


title: ssm216


title: ssm213


title: Macrophage_TLR4-/-_LipidA_Exp2_Rep1

description: Exp2 TLR4_KO LipidA cy5_cy3 s23


title: stem pulvini Upper Side: 1.0 Hours: rep4

source_name: stem pulvini_1hr_rep4_Upper Side

value: 1.0 Hours


title: ssm194


title: ssm193


title: ssm074


title: WRL68_100uM Zebularine_SAMPLE 60

description: replicate 3


title: stem pulvini Upper Side: 6.0 Hours: rep1

source_name: stem pulvini_6hr_rep1_Upper Side


title: ssm071


title: Macrophage_TLR4-/-_LPS_Exp2_Rep3

description: Exp2 TLR4_KO LPS cy5_cy3 s25

value: 10 ng LPS/mL


title: WRL68_100uM Zebularine_SAMPLE 58

description: replicate 1


title: stem pulvini Upper Side: 1.0 Hours: rep1

source_name: stem pulvini_1hr_rep1_Upper Side


title: WRL68_100uM Zebularine_SAMPLE 59

description: replicate 2


title: Macrophage_TLR4-/-_LPS_Exp2_Rep4

description: Exp2 TLR4_KO LPS cy5_cy3 s26


title: ssm186


title: Macrophage_TLR4-/-_LPS_Exp2_Rep2

description: Exp2 TLR4_KO LPS cy3_cy5 s16


title: stem pulvini Lower Side: 24.0 Hours: rep4

source_name: stem pulvini_24hr_rep4_Lower Side

value: stem pulvini Lower Side


title: WRL68_Mock_SAMPLE 56

description: replicate 2

value: mock


title: ssm068


title: WRL68_Mock_SAMPLE 57

description: replicate 3


title: ssm188


title: Macrophage_TLR4-/-_Pam2_Exp2_Rep4

description: Exp2 TLR4_KO Pam2 cy5_cy3 s30

value: 10 nM Pam2

value: PBS


title: Macrophage_TLR4-/-_Pam2_Exp2_Rep3

description: Exp2 TLR4_KO Pam2 cy5_cy3 s29


title: stem pulvini Lower Side: 24.0 Hours: rep1

source_name: stem pulvini_24hr_rep1_Lower Side


title: stem pulvini Upper Side: 1.0 Hours: rep2

source_name: stem pulvini_1hr_rep2_Upper Side


title: Macrophage_TLR4-/-_LPS_Exp2_Rep1

description: Exp2 TLR4_KO LPS cy3_cy5 s15


title: stem pulvini Lower Side: 6.0 Hours: rep4

source_name: stem pulvini_6hr_rep4_Lower Side


title: stem pulvini Lower Side: 24.0 Hours: rep3

source_name: stem pulvini_24hr_rep3_Lower Side


title: Hep3B_200uM zebularine_SAMPLE 53

description: replicate 2

value: Liver cancer cell line Hep3B


title: ssm182

source_name: Male Subject with Carotid Disease


title: ssm185


title: stem pulvini Lower Side: 6.0 Hours: rep3

source_name: stem pulvini_6hr_rep3_Lower Side


title: WRL68_Mock_SAMPLE 55

description: replicate 1


title: Macrophage_TLR4-/-_Pam2_Exp2_Rep2

description: Exp2 TLR4_KO Pam2 cy3_cy5 s28

source_name: Bone marrow derived macrophages


title: Hep3B_200uM zebularine_SAMPLE 54

description: replicate 3


title: Macrophage_TLR4-/-_Pam2_Exp2_Rep1

description: Exp2 TLR4_KO Pam2 cy3_cy5 s27


title: Hep3B_200uM zebularine_SAMPLE 52

description: replicate 1


title: stem pulvini Lower Side: 6.0 Hours: rep1

source_name: stem pulvini_6hr_rep1_Lower Side


title: stem pulvini Lower Side: 6.0 Hours: rep2

source_name: stem pulvini_6hr_rep2_Lower Side


title: ssm181


title: Macrophage_WT_LipidA_Exp2_Rep4

description: Exp2 WT LipidA cy5_cy3 s10

value: WT


title: Hep3B_100uM Zebularine_SAMPLE 51

description: replicate 3


title: Hep3B_100uM Zebularine_SAMPLE 49

description: replicate 1


title: ssm172


title: stem pulvini Lower Side: 1.0 Hours: rep1

source_name: stem pulvini_1hr_rep1_Lower Side


title: ssm229


title: stem pulvini Lower Side: 1.0 Hours: rep4

source_name: stem pulvini_1hr_rep4_Lower Side


title: stem pulvini Lower Side: 1.0 Hours: rep2

source_name: stem pulvini_1hr_rep2_Lower Side


title: ssm166


title: Hep3B_Mock_SAMPLE 48

description: replicate 3


title: Macrophage_WT_LipidA_Exp2_Rep3

description: Exp2 WT LipidA cy5_cy3 s9


title: ssm173


title: Macrophage_WT_LipidA_Exp2_Rep2

description: Exp2 WT LipidA cy3_cy5 s6


title: Macrophage_WT_LPS_Exp2_Rep3

description: Exp2 WT LPS cy5_cy3 s13


title: Macrophage_WT_LPS_Exp2_Rep4

description: Exp2 WT LPS cy5_cy3 s14


title: ssm222


title: stem pulvini Lower Side: 1.0 Hours: rep3

source_name: stem pulvini_1hr_rep3_Lower Side


title: stem pulvini: 24.0 Hours: rep4

source_name: stem pulvini_24hr_rep4

value: stem pulvini

value: 24.0 Hours


title: Hep3B_Mock_SAMPLE 47

description: replicate 2


title: ssm162


title: Hep3B_100uM Zebularine_SAMPLE 50

description: replicate 2


title: Macrophage_WT_LipidA_Exp2_Rep1

description: Exp2 WT LipidA cy3_cy5 s5

value: 100 ng Lipid A/mL

value: Experiment 2


title: stem pulvini: 24.0 Hours: rep2

source_name: stem pulvini_24hr_rep2


title: ssm154


title: Hep3B_Mock_SAMPLE 46

description: replicate 1


title: FOCUS_200uM zebularine_SAMPLE 45

description: replicate 3

source_name: FOCUS

value: resistant

value: Liver cancer cell line FOCUS


title: Macrophage_WT_LPS_Exp2_Rep2

description: Exp2 WT LPS cy3_cy5 s4


title: stem pulvini: 24.0 Hours: rep1

source_name: stem pulvini_24hr_rep1


title: ssm078


title: Macrophage_WT_Pam2_Exp2_Rep4

description: Exp2 WT Pam2 cy5_cy3 s22


title: ssm147


title: FOCUS_100uM Zebularine_SAMPLE 42

description: replicate 3

value: zebularine


title: FOCUS_200uM zebularine_SAMPLE 44

description: replicate 2


title: stem pulvini: 6.0 Hours: rep3

source_name: stem pulvini_6hr_rep3

value: 6.0 Hours


title: stem pulvini: 6.0 Hours: rep2

source_name: stem pulvini_6hr_rep2


title: Macrophage_WT_Pam2_Exp2_Rep1

description: Exp2 WT Pam2 cy3_cy5 s19


title: Macrophage_WT_LPS_Exp2_Rep1

description: Exp2 WT LPS cy3_cy5 s3


title: stem pulvini: 1.0 Hours: rep3

source_name: stem pulvini_1hr_rep3


title: ssm075

value: male

value: Monocytes


title: FOCUS_100uM Zebularine_SAMPLE 41

description: replicate 2


title: FOCUS_100uM Zebularine_SAMPLE 40

description: replicate 1


title: stem pulvini: 6.0 Hours: rep1

source_name: stem pulvini_6hr_rep1


title: Macrophage_WT_Pam2_Exp2_Rep3

description: Exp2 WT Pam2 cy5_cy3 s21


title: ssm080

source_name: Male Subject with Carotid Disease


title: stem pulvini: 1.0 Hours: rep1

source_name: stem pulvini_1hr_rep1

value: 1.0 Hours


title: Macrophage_WTvsTLR4-/-_PBS_Exp2_Rep4

description: Exp2 WT_vs_TLR4_KO Ctrl cy3_cy5 s8

source_name: Bone marrow derived macrophages


title: FOCUS_200uM zebularine_SAMPLE 43

description: replicate 1


title: Macrophage_WT_Pam2_Exp2_Rep2

description: Exp2 WT Pam2 cy3_cy5 s20


title: ssm135


title: FOCUS_Mock_SAMPLE 38

description: replicate 2


title: FOCUS_Mock_SAMPLE 39

description: replicate 3


title: ssm201


title: ssm143


title: stem pulvini: 1.0 Hours: rep2

source_name: stem pulvini_1hr_rep2


title: FOCUS_Mock_SAMPLE 37

description: replicate 1


title: stem pulvini: 0.0 Hours: rep2

source_name: stem pulvini_0hr_rep2

value: 0.0 Hours


title: Macrophage_WTvsTLR4-/-_PBS_Exp2_Rep2

description: Exp2 WT_vs_TLR4_KO Ctrl cy5_cy3 s12


title: leaf sheath pulvini Upper Side: 24.0 Hours: rep4

source_name: leaf sheath pulvini_24hr_rep4_Upper Side

value: leaf sheath pulvini Upper Side


title: ssm098


title: Macrophage_WTvsTLR4-/-_PBS_Exp1_Rep3

description: Exp1 WT_vs_TLR4_KO Ctrl cy5_cy3 s26

value: Experiment 1


title: ssm250


title: ssm192


title: Macrophage_WTvsTLR4-/-_PBS_Exp1_Rep4

description: Exp1 WT_vs_TLR4_KO Ctrl cy5_cy3 s28

value: PBS


title: Huh7_200uM zebularine_SAMPLE 36

description: replicate 3

value: sensitive

value: Liver cancer cell line Huh7


title: Macrophage_WTvsTLR4-/-_PBS_Exp2_Rep1

description: Exp2 WT_vs_TLR4_KO Ctrl cy5_cy3 s11

value: WT


title: Macrophage_WTvsTLR4-/-_PBS_Exp2_Rep3

description: Exp2 WT_vs_TLR4_KO Ctrl cy3_cy5 s7


title: Macrophage_WTvsTLR4-/-_PBS_Exp1_Rep1

description: Exp1 WT_vs_TLR4_KO Ctrl cy3_cy5 s6


title: Huh7_100uM Zebularine_SAMPLE 33

description: replicate 3


title: ssm239


title: ssm204


title: Huh7_100uM Zebularine_SAMPLE 32

description: replicate 2


title: leaf sheath pulvini Upper Side: 6.0 Hours: rep3

source_name: leaf sheath pulvini_6hr_rep3_Upper Side


title: Macrophage_TLR4-/-_LipidA_Exp1_Rep4

description: Exp1 TLR_KO LipidA cy3_cy5 s8


title: leaf sheath pulvini Upper Side: 24.0 Hours: rep2

source_name: leaf sheath pulvini_24hr_rep2_Upper Side

value: 24.0 Hours


title: stem pulvini: 0.0 Hours: rep1

source_name: stem pulvini_0hr_rep1

value: stem pulvini


title: ssm238


title: Macrophage_WTvsTLR4-/-_PBS_Exp1_Rep2

description: Exp1 WT_vs_TLR4_KO Ctrl cy3_cy5 s32


title: Huh7_100uM Zebularine_SAMPLE 31

description: replicate 1


title: Huh7_200uM zebularine_SAMPLE 34

description: replicate 1


title: leaf sheath pulvini Upper Side: 24.0 Hours: rep3

source_name: leaf sheath pulvini_24hr_rep3_Upper Side


title: stem pulvini: 0.0 Hours: rep4

source_name: stem pulvini_0hr_rep4


title: Macrophage_TLR4-/-_LipidA_Exp1_Rep2

description: Exp1 TLR_KO LipidA cy5_cy3 s9

value: 100 ng Lipid A/mL


title: Huh7_Mock_SAMPLE 30

description: replicate 3

value: mock


title: Sk-Hep1_200uM zebularine_SAMPLE 26

description: replicate 2

value: Liver cancer cell line Sk-Hep1


title: leaf sheath pulvini Upper Side: 6.0 Hours: rep1

source_name: leaf sheath pulvini_6hr_rep1_Upper Side


title: leaf sheath pulvini Upper Side: 6.0 Hours: rep2

source_name: leaf sheath pulvini_6hr_rep2_Upper Side


title: Macrophage_TLR4-/-_LipidA_Exp1_Rep3

description: Exp1 TLR_KO LipidA cy3_cy5 s11


title: leaf sheath pulvini Upper Side: 1.0 Hours: rep2

source_name: leaf sheath pulvini_1hr_rep2_Upper Side


title: ssm249


title: Huh7_Mock_SAMPLE 29

description: replicate 2


title: leaf sheath pulvini Upper Side: 1.0 Hours: rep4

source_name: leaf sheath pulvini_1hr_rep4_Upper Side


title: ssm234


title: Huh7_Mock_SAMPLE 28

description: replicate 1


title: ssm237


title: Sk-Hep1_100uM Zebularine_SAMPLE 24

description: replicate 3

value: zebularine


title: leaf sheath pulvini Lower Side: 24.0 Hours: rep4

source_name: leaf sheath pulvini_24hr_rep4_Lower Side

value: leaf sheath pulvini Lower Side


title: ssm233

value: male


title: leaf sheath pulvini Lower Side: 24.0 Hours: rep3

source_name: leaf sheath pulvini_24hr_rep3_Lower Side


title: ssm235

source_name: Male Subject with Carotid Disease

value: Monocytes


title: ssm277


title: Sk-Hep1_200uM zebularine_SAMPLE 25

description: replicate 1


title: Macrophage_TLR4-/-_LipidA_Exp1_Rep1

description: Exp1 TLR_KO LipidA cy5_cy3 s33


title: Macrophage_TLR4-/-_LPS_Exp1_Rep3

description: Exp1 TLR_KO LPS cy3_cy5 s29

value: 10 ng LPS/mL


title: Macrophage_TLR4-/-_LPS_Exp1_Rep4

description: Exp1 TLR_KO LPS cy3_cy5 s30


title: Huh7_200uM zebularine_SAMPLE 35

description: replicate 2


title: Sk-Hep1_200uM zebularine_SAMPLE 27

description: replicate 3


title: ssm232


title: ssm245


title: Macrophage_TLR4-/-_LPS_Exp1_Rep2

description: Exp1 TLR_KO LPS cy5_cy3 s13


title: ssm199


title: Macrophage_TLR4-/-_Pam2_Exp1_Rep4

description: Exp1 TLR_KO Pam2 cy3_cy5 s7

value: 10 nM Pam2


title: Macrophage_TLR4-/-_LPS_Exp1_Rep1

description: Exp1 TLR_KO LPS cy5_cy3 s10


title: leaf sheath pulvini Lower Side: 24.0 Hours: rep1

source_name: leaf sheath pulvini_24hr_rep1_Lower Side


title: Macrophage_TLR4-/-_Pam2_Exp1_Rep3

description: Exp1 TLR_KO Pam2 cy3_cy5 s31

source_name: Bone marrow derived macrophages


title: leaf sheath pulvini Lower Side: 6.0 Hours: rep4

source_name: leaf sheath pulvini_6hr_rep4_Lower Side

value: 6.0 Hours


title: ssm191


title: leaf sheath pulvini Lower Side: 6.0 Hours: rep1

source_name: leaf sheath pulvini_6hr_rep1_Lower Side


title: ssm266

source_name: Male Control


title: ssm218


title: Macrophage_WT_LipidA_Exp1_Rep4

description: Exp1 WT LipidA cy3_cy5 s17

value: Experiment 1


title: Macrophage_TLR4-/-_Pam2_Exp1_Rep1

description: Exp1 TLR_KO Pam2 cy5_cy3 s12

value: PBS


title: Sk-Hep1_100uM Zebularine_SAMPLE 22

description: replicate 1

value: sensitive


title: Macrophage_TLR4-/-_Pam2_Exp1_Rep2

description: Exp1 TLR_KO Pam2 cy5_cy3 s27


title: Sk-Hep1_100uM Zebularine_SAMPLE 23

description: replicate 2


title: leaf sheath pulvini Lower Side: 6.0 Hours: rep2

source_name: leaf sheath pulvini_6hr_rep2_Lower Side


title: Sk-Hep1_Mock_SAMPLE 21

description: replicate 3


title: Sk-Hep1_Mock_SAMPLE 19

description: replicate 1


title: Macrophage_WT_LipidA_Exp1_Rep3

description: Exp1 WT LipidA cy3_cy5 s14


title: Sk-Hep1_Mock_SAMPLE 20

description: replicate 2


title: HLE_200uM zebularine_SAMPLE 18

description: replicate 3

source_name: HLE

value: Liver cancer cell line HLE


title: ssm264


title: leaf sheath pulvini Lower Side: 1.0 Hours: rep2

source_name: leaf sheath pulvini_1hr_rep2_Lower Side

value: 1.0 Hours


title: leaf sheath pulvini Lower Side: 1.0 Hours: rep4

source_name: leaf sheath pulvini_1hr_rep4_Lower Side


title: HLE_200uM zebularine_SAMPLE 17

description: replicate 2


title: ssm263


title: ssm255


title: Macrophage_WT_LipidA_Exp1_Rep2

description: Exp1 WT LipidA cy5_cy3 s24

value: WT


title: leaf sheath pulvini Lower Side: 1.0 Hours: rep1

source_name: leaf sheath pulvini_1hr_rep1_Lower Side


title: Macrophage_WT_LPS_Exp1_Rep4

description: Exp1 WT LPS cy3_cy5 s20


title: leaf sheath pulvini: 24.0 Hours: rep3

source_name: leaf sheath pulvini_24hr_rep3

value: leaf sheath pulvini

value: 24.0 Hours


title: Macrophage_WT_LipidA_Exp1_Rep1

description: Exp1 WT LipidA cy5_cy3 s16

value: 100 ng Lipid A/mL


title: HLE_200uM zebularine_SAMPLE 16

description: replicate 1


title: HLE_100uM Zebularine_SAMPLE 15

description: replicate 3


title: leaf sheath pulvini: 24.0 Hours: rep2

source_name: leaf sheath pulvini_24hr_rep2


title: Macrophage_WT_LPS_Exp1_Rep2

description: Exp1 WT LPS cy5_cy3 s23


title: ssm252


title: Macrophage_WT_LPS_Exp1_Rep3

description: Exp1 WT LPS cy3_cy5 s15


title: HLE_100uM Zebularine_SAMPLE 14

description: replicate 2


title: leaf sheath pulvini: 6.0 Hours: rep4

source_name: leaf sheath pulvini_6hr_rep4


title: ssm260


title: Macrophage_WT_LPS_Exp1_Rep1

description: Exp1 WT LPS cy5_cy3 s22


title: ssm267


title: ssm254


title: HLE_Mock_SAMPLE 12

description: replicate 3

value: mock


title: ssm246


title: HLE_100uM Zebularine_SAMPLE 13

description: replicate 1

value: zebularine


title: leaf sheath pulvini: 6.0 Hours: rep3

source_name: leaf sheath pulvini_6hr_rep3


title: HLE_Mock_SAMPLE 11

description: replicate 2


title: leaf sheath pulvini: 24.0 Hours: rep1

source_name: leaf sheath pulvini_24hr_rep1


title: Macrophage_WT_Pam2_Exp1_Rep4

description: Exp1 WT Pam2 cy3_cy5 s25


title: ssm265


title: HLE_Mock_SAMPLE 10

description: replicate 1


title: leaf sheath pulvini: 6.0 Hours: rep2

source_name: leaf sheath pulvini_6hr_rep2


title: Macrophage_WT_Pam2_Exp1_Rep3

description: Exp1 WT Pam2 cy3_cy5 s19


title: leaf sheath pulvini: 6.0 Hours: rep1

source_name: leaf sheath pulvini_6hr_rep1


title: Huh1_200uM zebularine_SAMPLE 9

description: replicate 3

value: Liver cancer cell line Huh1


title: ssm269

value: male


title: Huh1_200uM zebularine_SAMPLE 8

description: replicate 2


title: leaf sheath pulvini: 1.0 Hours: rep4

source_name: leaf sheath pulvini_1hr_rep4


title: leaf sheath pulvini: 1.0 Hours: rep3

source_name: leaf sheath pulvini_1hr_rep3


title: ssm257

value: Monocytes


title: ssm268


title: Macrophage_WT_Pam2_Exp1_Rep2

description: Exp1 WT Pam2 cy5_cy3 s21

source_name: Bone marrow derived macrophages


title: Macrophage_WT_Pam2_Exp1_Rep1

description: Exp1 WT Pam2 cy5_cy3 s18


title: ssm256


title: leaf sheath pulvini Upper Side: 6.0 Hours: rep4

source_name: leaf sheath pulvini_6hr_rep4_Upper Side

value: leaf sheath pulvini Upper Side


title: Huh1_100uM Zebularine_SAMPLE 6

description: replicate 3


title: Huh1_100uM Zebularine_SAMPLE 4

description: replicate 1


title: leaf sheath pulvini: 1.0 Hours: rep2

source_name: leaf sheath pulvini_1hr_rep2


title: Huh1_200uM zebularine_SAMPLE 7

description: replicate 1


title: ssm261

source_name: Male Control


title: ssm282


title: ssm262


title: Huh1_100uM Zebularine_SAMPLE 5

description: replicate 2


title: Huh1_Mock_SAMPLE 3

description: replicate 3


title: leaf sheath pulvini: 1.0 Hours: rep1

source_name: leaf sheath pulvini_1hr_rep1


title: ssm279


title: ssm271


title: Huh1_Mock_SAMPLE 2

description: replicate 2


title: day 4 post-exposure to S. mansoni (6)

status: Public on Jul 30 2011

city: Albuquerque

first: Michelle

middle: A.

last: Forys

state: NM

address: MSC03 2020, 1 University of New Mexico

department: Biology

institute: University of New Mexico

description: Each array was probed with a mixture of total RNA converted to cDNA of one Cy3 labeled IRR-only snail and one Cy5 labeled IRR-CH snail from the same time point. There are six from each time point (2dpe and 4dpe) for each treatment type.

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 100 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 3.0 h at 42°C in hybridization buffer prior to hybridization with labeled probes. Labeled cDNA was hybridized overnight at 42°C.

scan_protocol: Microarray slides were scanned with a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon and colleagues.

data_processing: A preloaded grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians to Alien control spots. SAM was used to determine significiantly differentially regulated genes with a cut of of 2-fold and a false positive rate of less then 10%

organism: Biomphalaria glabrata

source_name: 4-8mm Biomphalaria glabrata exposed to irradiated E. paraensei miracidia only

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis and colleagues. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1.0 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µL 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2.0 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3 and Cy5 labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Snails and trematodes used in this study were maintained at the University of New Mexico

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

treatment_protocol: B. glabrata snails were placed in well plates with artificial spring water and exposed to 25-30 irradiated E. paraensei miricidia for 24 hours on day 0. On day 4, they were split into two separate groups, one half that would be left as the irradiated only group and the other half would be exposed to 15-20 S. mansoni miracidia. Samples were collected on 1, 2, and 4 days post-exposure to E. paraensei, and 1, 2, 4, and 8 days post exposure to S. mansoni for RNA extraction, but only samples from 2 and 4 dpe to S. mansoni were used for this microarray experiment, which correspond with the sample names (i.e. 2-1 means day 2 post-exposure to S. mansoni- snail 1 from that group). The controls from this experiment including the BS-90 snails exposed to only S. mansoni and the M-line snails exposed to only S. mansoni were treated under the same conditions and sampled at the same time points, but were not used for this microarray experiment.

tag: developmental stage

value: exposed to 25-30 irradiated E. paraensei miracidia only

value: whole organism

source_name: 4-8mm Biomphalaria glabrata exposed to irradiated E. paraensei and 4 days later challenged with S. mansoni

value: exposed to 25-30 irradiated E. paraensei miracidia and then 4 days later exposed to 15-20 S. mansoni miracidia

tag: time

value: day 4 post exposure


title: day 2 post-exposure to S. mansoni (5)

value: exposed to 25-30 irradiated E. paraensei miracidia and then 2 days later exposed to 15-20 S. mansoni miracidia

value: day 2 post exposure


title: day 4 post-exposure to S. mansoni (5)


title: day 4 post-exposure to S. mansoni (3)


title: day 4 post-exposure to S. mansoni (4)


title: day 4 post-exposure to S. mansoni (1)


title: Huh1_Mock_SAMPLE 1

description: replicate 1

tag: agent


title: day 4 post-exposure to S. mansoni (2)


title: day 2 post-exposure to S. mansoni (4)


title: day 2 post-exposure to S. mansoni (1)


title: day 2 post-exposure to S. mansoni (6)


title: day 2 post-exposure to S. mansoni (2)


title: 600bp TC6372 dsRNA injected adult female ticks 2 rep 2

city: Brisbane

first: Ala

last: Lew-Tabor

state: Queensland

address: 306 Carmody Rd, St Lucia

department: Queensland Alliance for Agriculture and Food Innovation

institute: The University of Queensland

description: dsRNA injected adult female ticks

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

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

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

organism: Rhipicephalus microplus

source_name: Rhipicephalus (Boophilus) microplus (N strain)

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

growth_protocol: NFRS (non-resistant field strain) adult female ticks were collected from infested cattle from the Department of Employment, Economic Development & Innovation’s (formerly Dept. of Primary Industries & Fisheries) Biosecurity tick colony kindly provided by Dr Louise Jackson (Stewart et al., 1982). Fresh adult female ticks were collected at 21 days fed to repletion and were utilised on the day of collection in microinjection experiments. The 600bp dsRNA targeting TC6372 (R. microplus Ubiquitin-63E homologue) was prepared as described previously (Kurscheid et al 2009) using PCR amplification and T7 RNA transcription as per manufacturer’s instructions (Ambion MEGAScript RNAi kit, Applied Biosystems, CA, USA). Thirty ticks were utilised to obtain RNA for each microarray slide. Adult female ticks were injected via the spiracle with 5µL of 3330nM of dsRNA and  PBS injected controls (30 ticks per experimental duplicate, total 120 ticks). All ticks were incubated in a humidified incubator at 28oC (Kurscheid et al., 2009).  Ticks were inspected daily for mortalities and oviposition and after 5 days were removed for RNA processing. After rinsing in 0.1% DEPC-treated water, ticks were dissected in an 8cm culture dish (Nalgene) kept in a tray of wet ice. Sterile scalpel blades and forceps were pre-treated with RNaseZAP (Ambion, CA, USA). An incision was made with a sterile razor blade just above the right spiracle, starting at the right side of the capitulum and cutting around to the left side of the capitulum. The dorsal cuticle was then lifted with a pair of dissection forceps. Viscera were individually transferred into 2mL screw-cap microfuge tubes containing 1.5mL ice-cold TRIzol reagent (Invitrogen, CA, USA) and 100mg of 1mm sterile glass beads. The viscera were then homogenized using a bead beater for 5 minutes prior to RNA extraction.

extract_protocol: Total RNA was isolated using the TRIzol® reagent according to the manufacturer’s protocol (GibcoBRL, USA). The RNA pellet was re-suspended in 400µL 0.1% DEPC-treated water. The total RNA was examined for integrity using gel electrophoresis, and subsequently stored at -80°C until further use. cDNA was prepared from the RNA extracted from un-treated controls and the injected Ubiquitin-63E (TC6372) 600bp dsRNA treated ticks above (prepared in duplicate from 30 ticks treated and un-treated).  mRNA was prepared using the SuperScriptTM Double-Stranded cDNA Synthesis Kit (Invitrogen, USA) as recommended by the manufacturer with the exception that after the second strand cDNA synthesis was terminated by the addition of 0.5 M EDTA, and, prior to the phenol:chloroform:isoamyl alcohol extraction, a RNase A treatment step was included as recommended in the NimbleGen cDNA protocol (NimbleGen, USA) (Rodriguez Valle et al., 2010). After this RNase A treatment the Superscript double stranded cDNA Synthesis protocol was followed as described in the technical manual. cDNA median size was verified by 1% agarose electrophoresis in TAE 1X, and 2 g of each cDNA sample were sent to NimbleGen Systems Inc. (Madison, WI, USA) for microarray hybridization using the R. microplus custom array (NimbleGen Custom Design name: 2006-05-22_B_microplus_50mer_exp).

value: Wild-type

tag: phenotype

value: Tick Field strain not resistant to acaricide

tag: treatment group

value: dsRNA injected

value: adult

tag: Sex

value: female


title: 600bp TC6372 dsRNA injected adult female ticks 2 rep 1

description: dsRNA injected adult female ticks


title: day 2 post-exposure to S. mansoni (3)

tag: treatment


title: Decay Oxi mutant t=50

city: Rehovot

first: Ophir

last: Shalem

address: Hertzel

country: Israel

institute: Weizmann Inst.

description: Reference decay profile

data_processing: RMA algorithms using bioconductor software implemented in R for mRNA abundance. For decay experiments data was scaled as described in the materials and methods of the accompanied manuscript. For mRNA abundnce (MA) Fold change: log2 of the intesity value divided by the intensity value at time point zero. For Decay data: the precentage of decrease from time point zero, e.g. 0.4 means 40% of the initial mRNA amount. These data are presented on the Series record.

source_name: Decay Oxi mutant t=50

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacture instructions.

growth_protocol: cells were grown in YPD to mid log phase in 30 degrees

extract_protocol: Total RNA was extracted using MasterPure™ (EPICENTER Biotechnologies)

treatment_protocol: At time 0 cells were treated with 0.3mM of H2O2 or 0.1% of MMS for mRNA abundance measurements. For decay experiments cells were treated with 1,10-phenanthroline (100mg/ml) either with (Oxi) or without (Ref) adding H2O2 (0.3mM) 7 minutes before 1,10-phenanthroline.


title: Decay Oxi mutant t=0

description: Reference decay profile

hyb_protocol: GeneChip system according to manufacture instructions.

source_name: Decay Oxi mutant t=0


title: Decay Oxi mutant t=40

description: Reference decay profile

scan_protocol: GeneChip system according to manufacture instructions.

source_name: Decay Oxi mutant t=40


title: Decay Oxi mutant t=20

description: Reference decay profile

source_name: Decay Oxi mutant t=20


title: 600bp TC6372 dsRNA injected adult female ticks 1 rep 2

description: dsRNA injected adult female ticks


title: Decay Oxi mutant t=5

description: Reference decay profile

source_name: Decay Oxi mutant t=5


title: 600bp TC6372 dsRNA injected adult female ticks 1 rep 1

description: dsRNA injected adult female ticks


title: Untreated adult female ticks 2 rep 2

description: untreated control adult female ticks

value: untreated control


title: Decay Oxi mutant t=30

description: Reference decay profile

source_name: Decay Oxi mutant t=30


title: Decay Oxi mutant t=10

description: Reference decay profile

source_name: Decay Oxi mutant t=10


title: Decay Ref mutant t=50

description: Reference decay profile

source_name: Decay Ref mutant t=50


title: Untreated adult female ticks 1 rep 2

description: untreated control adult female ticks


title: Decay Ref mutant t=40

description: Reference decay profile

source_name: Decay Ref mutant t=40


title: Untreated adult female ticks 2 rep 1

description: untreated control adult female ticks


title: Untreated adult female ticks 1 rep 1

description: untreated control adult female ticks


title: Decay Ref mutant t=0

description: Reference decay profile

source_name: Decay Ref mutant t=0


title: Decay Oxi wt t=30

description: Reference decay profile

source_name: Decay Oxi wt t=30


title: Decay Oxi wt t=50

description: Reference decay profile

source_name: Decay Oxi wt t=50


title: Decay Oxi wt t=20

description: Reference decay profile

source_name: Decay Oxi wt t=20


title: Decay Ref mutant t=5

description: Reference decay profile

source_name: Decay Ref mutant t=5


title: Decay Oxi wt t=5

description: Reference decay profile

source_name: Decay Oxi wt t=5


title: Decay Oxi wt t=10

description: Reference decay profile

source_name: Decay Oxi wt t=10


title: Decay Ref wt t=40

description: Reference decay profile

source_name: Decay Ref wt t=40


title: Decay Ref mutant t=20

description: Reference decay profile

source_name: Decay Ref mutant t=20


title: Decay Oxi wt t=0

description: Reference decay profile

source_name: Decay Oxi wt t=0


title: Decay Ref wt t=30

description: Reference decay profile

source_name: Decay Ref wt t=30


title: Decay Ref wt t=10

description: Reference decay profile

source_name: Decay Ref wt t=10


title: Decay Ref wt t=0

description: Reference decay profile

source_name: Decay Ref wt t=0


title: Decay Ref wt t=5

description: Reference decay profile

source_name: Decay Ref wt t=5


title: Decay Ref wt t=50

description: Reference decay profile

source_name: Decay Ref wt t=50


title: MA MMS mutant t=140

description: mRNA abundance following treatment of 0.1% of MMS

source_name: MA MMS mutant t=140


title: Decay Ref wt t=20

description: Reference decay profile

source_name: Decay Ref wt t=20


title: Decay Oxi wt t=40

description: Reference decay profile

source_name: Decay Oxi wt t=40


title: MA MMS mutant t=120

source_name: MA MMS mutant t=120


title: MA MMS mutant t=180

source_name: MA MMS mutant t=180


title: MA MMS mutant t=80

source_name: MA MMS mutant t=80


title: MA MMS mutant t=40

source_name: MA MMS mutant t=40


title: MA MMS mutant t=100

source_name: MA MMS mutant t=100


title: MA MMS mutant t=20

source_name: MA MMS mutant t=20


title: MA MMS mutant t=0

source_name: MA MMS mutant t=0