title: Collagen 72hr Replicate 3

first: Helena

last: Morales Johansson

state: North Carolina

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: NCSU

description: Replicate 3

data_processing:
The data were average-normalized using Genome Studio version 1.6.0.

Raw data is unavailable.

source_name: Collagen 72hr

label_protocol: Biotinylated cRNA were preapred with Ambion Illumina Total prep RNA amplification kit

growth_protocol: AT2 cells were freshly isolated from human lung lobe and seeded onto collagen- or matrigel-coated dishes

extract_protocol: RNA was extracted with Trizol, followed by a clean-up with gDNA elimination column and QIAGEN Rneasy kit in accordance with the protocol provided with the kit. Quantification and quality control was performed with RiboGreen assay and Agilent Bioanalyzer.

treatment_protocol: Collagen- and matrigel-coated dishes

value: Lung lobe

value: Female

tag: age

value: Human alveolar epithelial type II (AT2) cells


title: Matrigel 72 hr Replicate 3

status: Public on Feb 01 2014

type: RNA

city: Raleigh

country: USA

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Matrigel 72 hr

tag: tissue

tag: gender

tag: cell type


title: Collagen 48 hr Replicate 3

description: Replicate 3

source_name: Collagen 48 hr


title: Collagen 48 hr Replicate 2

description: Replicate 2


title: Matrigel 24 hr Replicate 2

description: Replicate 2

source_name: Matrigel 24 hr


title: Collagen 12 hr Replicate 3

description: Replicate 3

source_name: Collagen 12 hr


title: Collagen 72hr Replicate 2

description: Replicate 2


title: Collagen 72hr Replicate 1

description: Replicate 1


title: Matrigel 24 hr Replicate 3

description: Replicate 3


title: Streptomycete_DB_1g_16.5d_rep1

city: Beijing

first: Huang

last: Bing

state: Chaoyang district

address: NO.1 Beichen West Road

department: State Key Laboratory of Microbial Resources

country: China

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression at 16.5d in colony cells exposed gravity control on ground

hyb_protocol: Cy3-labelled cRNA was fragmented at 60℃ for 30 minutes in a reaction volume of 250 ml following the manufacturers instructions. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent). After fragmentation, cRNA was hybridized at 65℃ for 17 h with a rotation at 10 rpm. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner System (G2565CA) using one color scan setting for 8*15k array slides with a resolution of 5 μm, 100% and 10% PTM respectively and the two data sets were combined automatically.

data_processing: The signal intensities were normalized using the Feature Extraction Software (Agilent). Data was analyzed using Genespring Software 5.0. Genes with all signals present (flag =P) were selected for analysis. Differentially expressed genes were selected with FC≥2.0 by T-test methods.

organism: Streptomyces coelicolor A3(2)

source_name: Streptomycete colonies,gravity control on ground,16.5d,replicate 1

label_protocol: 2 μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After RNAeasy column purification, 1.65 μg cRNA was labeled with Cy3 NHS ester and purified according to the manufacturer's instructions.

growth_protocol: The spores of Streptomyces coelicolor A3(2) wild type strain were incubated at 23±0.5℃ for 16.5-day in JCM42 agar medium inside the BIOBOX for spaceflight experiments during Shenzhou-8 space mission.

extract_protocol: Total RNA was extracted from colonies of Streptomyces coelicolor A3(2) wild type strain cultured in JCM42 agar medium for 16.5d using liquid nitrogen and Trizol (Invitrogen) according to the manufacturer’s recommendations. The whole process included the pestling, lysis and purification. At last the total RNA was purified using the Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: The spores of Streptomyces coelicolor A3(2) incubated in JCM42 agar medium were cultured and exposed to microgravity (μg) and simulated gravity (S-1g) environment during spaceflight with the corresponding static gravity control (1g) on ground.

tag: genotype

value: wild type

tag: strain form

value: colonies

tag: culture position

value: on ground (static1g position)

tag: culture temperature

tag: culture time


title: passage 28_H9 HESC_40Pb_acuteexposure

type: genomic

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

description:
Undifferentiated. Acute exposure to 40 µg/dl of Pb for 24 hours before DNA extraction.
Bisulphite treatment

hyb_protocol: Provided by Illumina™

scan_protocol: Background correction for array and raw beta value calculation done in Illumina Genome Studio™.

data_processing:
The background corrected raw data from Genome Studio™ was extracted in the form of a .txt file which contained complete annotation information, detection p-value, Average beta for all sample. The acute exposure and chronic exposure experiments were normalised seperately. Normalisation for Inf1/Inf2 probe was carried out using quantile normalization and peak based correction (PBC) poposed by Dedeurwaerder et al. 2011 in R (> 2.13.2) using R package Illumina methylation analyser. The normalised data was filtered using the detection p-value cut off of 0.05. All methylation sites located on sex chromosomes and localizing with SNP sites was removed (dbSNP v132). CpG sites/ probes was assigned to cluster based of correlation of beta values and base pair distance from each other using A-clustering (Sofer et al, 2012). Effect of exposure to increase concentrations of lead was carried out using generalised estimating equation model.
SIGNAL A (intensities of unmethylated probe as intergers), SIGNAL B (Intensities of methylated probe as integers)
Average Beta normalized for probe bias using quantile normalization and peak based correction using Illumina methylation analyser in R (>2.13.2)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: H9 Human embryonic stem cells, passage 28

label_protocol: Provided by Illumina™

growth_protocol: In these experiments, we used the WA09 hESC line (passages 26-34; WiCell Research Institute, Madison, WI, USA) (Thomson et al. 1998) that is NIH-approved and included in the National Stem Cell Registry.  Human ESCs were maintained on a feeder layer of irradiated mouse embryonic fibroblasts (GlobalStem, Rockville, MD, USA) in hESC medium. . Neural induction of hESCs was performed according to previously published protocols (Chang et al. 2010; Zhang et al. 2001). Briefly, hESC colonies were mechanically dissociated, transferred in 100 mm bacterial plates and maintained as aggregates (embryoid bodies, EBs) for 4 days in a medium composed of 50% hESC medium and 50% N2 medium. N2 medium was made of 1% N2 supplement (Life Technologies Corporation, Carlsbad, CA) and 1% penicillin/streptomycin in DMEM/F12.  On culture day 4, EBs were transferred to a new bacterial plate and cultured for an additional four days in N2 medium supplemented with 3 M retinoic acid (Sigma-Aldrich, St Louis, MO).  On day 8, and over the next 3 days, EBs were cultured in N2 medium, containing 20 ng/ml FGF-2 (N2/FGF-2; Peprotech, Rocky Hill, NJ).  EBs were subsequently transferred to 6-well plates coated with 20g/ml fibronectin (Life Technologies Corporation, Carlsbad, CA) and maintained in N2/FGF-2 medium for an additional 8 days.  Cells differentiating as neuroectodermal cells organized into neural-tube-like rosettes, which were then dissociated and plated in N2/FGF-2 medium on 10 g/ml polyornithine/5 g/ml laminin-coated dishes.  For neuronal differentiation, NPCs were passaged at a 5.105 cells/cm2 density in polyornithine/laminin-coated 12-well dishes and cultured in N2 medium supplemented with 10 ng/ml brain-derived neurotrophic factor (BDNF), 10 ng/ml glial cell-derived neurotrophic factor (GDNF), 10 ng/ml insulin-like growth factor (IGF) (all factors from Peprotech, Rocky Hill, NJ), 200 ng/ml ascorbic acid (Sigma-Aldrich, St Louis, MO) and 100 ng/ml cAMP (Sigma-Aldrich, St Louis, MO), according to a previously published protocol (Hu and Zhang 2010).

extract_protocol: DNA was isolated from control, Pb-exposed hESCs, and hESC-derived NPCs with Qiagen DNA kit. The Quantifiler Human DNA Quantification Kit® (Applied Biosystems) was used to determine the amount of amplifiable DNA.

treatment_protocol: The dose-response effects of Pb acetate on the generation of hESC-derived NPCs were determined in three different experimental paradigms. Paradigm A: hESCs were acutely exposed to the different concentrations of Pb or vehicle, 24 hours prior to DNA extraction.  Paradigm B: hESC colonies were mechanically dissociated into 150-200 pieces of homogeneous size that were randomly distributed into six-well plates.  The 24 hour acute exposure started at day 5 of the differentiation process, a day after initiation of neural induction with retinoic acid (day 5).  Cells then underwent the neural differentiation protocol until day 19.  Paradigm C: hESCs were chronically exposed to Pb during the whole neural differentiation procedure up to day 19 (days 0-19).

tag: differentiation state

value: Undifferentiated


title: Collagen 48 hr Replicate 1

description: Replicate 1


title: Collagen 12 hr Replicate 2

description: Replicate 2


title: Matrigel 72 hr Replicate 2

description: Replicate 2


title: Matrigel 48 hr Replicate 2

description: Replicate 2

source_name: Matrigel 48 hr


title: Collagen 12 hr Replicate 1

description: Replicate 1


title: Collagen 24 hr Replicate 1

description: Replicate 1

source_name: Collagen 24 hr


title: Collagen 24 hr Replicate 3

description: Replicate 3


title: Streptomycete_1G_96h_rep1

description: Gene expression at 96h in colony cells under gravity control

data_processing: The signal intensities were normalized using the Feature Extraction Software (Agilent). Data was analyzed using Genespring Software 5.0. Genes with all signals present (flag =P) were selected for analysis. Differentially expressed genes were selected with P＜0.05, FC≥2.0 by T-test methods.

source_name: Streptomycete colonies,gravity control,96h,replicate 1

label_protocol: 2 μg RNA was reverse-transcribed into cDNA and then transcribed into cRNA. After RNAeasy column purification, 4 μg cRNA was labeled with Cy3 NHS ester and purified according to the manufacturer's instructions.

growth_protocol: The spores of Streptomyces coelicolor A3(2) wild type strain were incubated at 28℃ for 96h in JCM42 agar medium.

extract_protocol: Total RNA was extracted from colonies of Streptomyces coelicolor A3(2) wild type strain cultured in JCM42 agar medium for 96h using liquid nitrogen and Trizol (Invitrogen) according to the manufacturer’s recommendations. The whole process included the pestling, lysis and purification. At last the total RNA was purified using the Qiagen RNeasy Mini Kit (Qiagen).

treatment_protocol: The spores of Streptomyces coelicolor A3(2) incubated in JCM42 agar medium were cultured and exposed to simulated microgravity condition by a rotating clinostat in the test group's samples; The same spores incubated in JCM42 agar medium were cultured and exposed to gravity condition on ground in the control group's samples.

value: under gravity control on ground


title: Matrigel 72 hr Replicate 1

description: Replicate 1


title: Matrigel 48 hr Replicate 3

description: Replicate 3


title: Matrigel 12 hr Replicate 3

description: Replicate 3

source_name: Matrigel 12 hr


title: Collagen 24 hr Replicate 2

description: Replicate 2


title: Matrigel 12 hr Replicate 2

description: Replicate 2


title: Matrigel 48 hr Replicate 1

description: Replicate 1


title: Tn5::4880 TR4 BR2, MHH1278, wild type

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

country: Germany

institute: Medical School Hannover

description:
MHH1278
14081223

Each Sample represents one channel of a dual-channel array.

hyb_protocol: Labelled cDNA was hybridzed following the manufacturer's instructions provided by Progenika.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Operation Software Version 1.4 (Affymetrix GeneChip Scanner GCS 30) and then processed with Agilent Scan Control and Feature Extraction Software. For Progenika arrays, the two channel gene expression feature was used. Signal intensity per spot was calculated by subtracting background from foreground and provided as median value of all measured pixel per spot. Progenika array data were normalized using the LOWESS (Locally weighted linear regression) algorithm to remove intensity-dependent effects that can appear by low signal intensities and to avoid a bias due to different label efficiencies of the fluorescent dyes (Quackenbush, 2002).

data_processing: Data were analyzed using the BRB ArrayTools Software (http://linus.nci.nih.gov/pilot/index.htm). Signal intensities were log2 transformed and median normalized over all arrays of one experiment, and an output file was generated providing mean signal intensities, P-value (two-sample t-test (with random variance model)), FDR (false discovery rate) and fold-change for all represented probe sets.

organism: Pseudomonas putida KT2440

source_name: bacterial culture wild type at 10°C

label_protocol: cDNA synthesis and labelling reactions were performed following the Progenika standard protocol.

growth_protocol: Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type or the respective Tn5 mutants, and incubated at 30°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30°C. For RNA extraction, the bacterial culture was inoculated in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8), the temperature was decreased from 30°C to 10°C. Three samples, each for parallel RNA extraction, were taken two hours after the medium had been cooled to 10°C.

extract_protocol: Total RNA extraction was performed according to the manufacturer's protocol provided by Qiagen for bacteria.

tag: strain

tag: growth condition


title: Tn5::4880 TR2 BR2, MHH1276, wild type

description:
MHH1276
14081221

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR3 BR2, MHH1277, wild type

description:
MHH1277
14081222

Each Sample represents one channel of a dual-channel array.


title: Matrigel 24 hr Replicate 1

description: Replicate 1


title: Tn5::4880 TR1 BR2, MHH1275, wild type

description:
MHH1275
14081220

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR1 BR2, MHH1279, wild type

description:
MHH1279
14081224

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR2 BR2, MHH1272, wild type

description:
MHH1272
14081217

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR3 BR2, MHH1273, wild type

description:
MHH1273
14081218

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR4 BR2, MHH1274, wild type

description:
MHH1274
14081219

Each Sample represents one channel of a dual-channel array.


title: Matrigel 12 hr Replicate 1

description: Replicate 1


title: Tn5::4696 TR3 BR2, MHH1269, wild type

description:
MHH1269
14081408

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR1 BR2, MHH1267, wild type

description:
MHH1267
14081406

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR2 BR2, MHH1268, wild type

description:
MHH1268
14081407

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR1 BR2, MHH1271, wild type

description:
MHH1271
14081410

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR4 BR2, MHH1270, wild type

description:
MHH1270
14081409

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR2 BR2, MHH1280, wild type

description:
MHH1280
14081225

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR4 BR2, MHH1298, wild type

description:
MHH1298
14081227

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR3 BR2, MHH1281, wild type

description:
MHH1281
14081226

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR3 BR2, MHH1265, wild type

description:
MHH1265
14081404

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR2 BR2, MHH1264, wild type

description:
MHH1264
14081403

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR4 BR2, MHH1266, wild type

description:
MHH1266
14081405

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR1 BR2, MHH1263, wild type

description:
MHH1263
14081402

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR4 BR1, MHH1262, wild type

description:
MHH1262
14081401

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR3 BR1, MHH1261, wild type

description:
MHH1261
14081400

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR2 BR1, MHH1256, wild type

description:
MHH1256
14081392

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR3 BR1, MHH1257, wild type

description:
MHH1257
14081393

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR2 BR1, MHH1260, wild type

description:
MHH1260
14081398

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR1 BR1, MHH1255, wild type

description:
MHH1255
14081391

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR1 BR1, MHH1259, wild type

description:
MHH1259
14081397

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR4 BR1, MHH1258, wild type

description:
MHH1258
14081396

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR3 BR1, MHH1253, wild type

description:
MHH1253
14081265

Each Sample represents one channel of a dual-channel array.


title: NPCs_passage26_24Pb_chronicexposure

description:
Neural precursor cells (NPCs) obtained from passage 26 H9 stem cells grown in medium containing 24µg/dl of Pb.
Bisulphite treatment

source_name: H9 Human embryonic stem cells, passage 26

value: Neural precursor cells (NPCs)


title: Tn5::4697 TR2 BR1, MHH1252, wild type

description:
MHH1252
14081264

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR4 BR1, MHH1254, wild type

description:
MHH1254
14081390

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR1 BR1, MHH1247, wild type

description:
MHH1247
14081215

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR2 BR1, MHH1248, wild type

description:
MHH1248
14081270

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR4 BR1, MHH1246, wild type

description:
MHH1246
14081214

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR4 BR1, MHH1250, wild type

description:
MHH1250
14081273

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR1 BR1, MHH1251, wild type

description:
MHH1251
14081263

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR3 BR1, MHH1249, wild type

description:
MHH1249
14081272

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR4 BR2, MHH1298, Tn5 mutant

description:
MHH1298
14081227

Each Sample represents one channel of a dual-channel array.

source_name: bacterial culture Tn5 mutant at 10°C


title: Tn5::4880 TR4 BR2, MHH1278, Tn5 mutant

description:
MHH1278
14081223

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR3 BR2, MHH1281, Tn5 mutant

description:
MHH1281
14081226

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR1 BR2, MHH1279, Tn5 mutant

description:
MHH1279
14081224

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR2 BR2, MHH1280, Tn5 mutant

description:
MHH1280
14081225

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR1 BR1, MHH1243, wild type

description:
MHH1243
13817569

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR3 BR1, MHH1245, wild type

description:
MHH1245
13817571

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR2 BR1, MHH1244, wild type

description:
MHH1244
13817570

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR1 BR2, MHH1275, Tn5 mutant

description:
MHH1275
14081220

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR4 BR2, MHH1274, Tn5 mutant

description:
MHH1274
14081219

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR3 BR2, MHH1277, Tn5 mutant

description:
MHH1277
14081222

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR2 BR2, MHH1276, Tn5 mutant

description:
MHH1276
14081221

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR3 BR2, MHH1265, Tn5 mutant

description:
MHH1265
14081404

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR2 BR2, MHH1264, Tn5 mutant

description:
MHH1264
14081403

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR2 BR2, MHH1272, Tn5 mutant

description:
MHH1272
14081217

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR3 BR2, MHH1273, Tn5 mutant

description:
MHH1273
14081218

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR1 BR2, MHH1263, Tn5 mutant

description:
MHH1263
14081402

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR1 BR2, MHH1267, Tn5 mutant

description:
MHH1267
14081406

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR1 BR2, MHH1271, Tn5 mutant

description:
MHH1271
14081410

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR4 BR2, MHH1266, Tn5 mutant

description:
MHH1266
14081405

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR2 BR2, MHH1268, Tn5 mutant

description:
MHH1268
14081407

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR4 BR2, MHH1270, Tn5 mutant

description:
MHH1270
14081409

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR3 BR2, MHH1269, Tn5 mutant

description:
MHH1269
14081408

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR3 BR1, MHH1261, Tn5 mutant

description:
MHH1261
14081400

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR2 BR1, MHH1260, Tn5 mutant

description:
MHH1260
14081398

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR1 BR1, MHH1259, Tn5 mutant

description:
MHH1259
14081397

Each Sample represents one channel of a dual-channel array.


title: Tn5::5044 TR4 BR1, MHH1262, Tn5 mutant

description:
MHH1262
14081401

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR4 BR1, MHH1258, Tn5 mutant

description:
MHH1258
14081396

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR1 BR1, MHH1255, Tn5 mutant

description:
MHH1255
14081391

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR2 BR1, MHH1256, Tn5 mutant

description:
MHH1256
14081392

Each Sample represents one channel of a dual-channel array.


title: Tn5::4880 TR3 BR1, MHH1257, Tn5 mutant

description:
MHH1257
14081393

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR3 BR1, MHH1253, Tn5 mutant

description:
MHH1253
14081265

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR4 BR1, MHH1254, Tn5 mutant

description:
MHH1254
14081390

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR4 BR1, MHH1246, Tn5 mutant

description:
MHH1246
14081214

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR2 BR1, MHH1248, Tn5 mutant

description:
MHH1248
14081270

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR3 BR1, MHH1249, Tn5 mutant

description:
MHH1249
14081272

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR1 BR1, MHH1247, Tn5 mutant

description:
MHH1247
14081215

Each Sample represents one channel of a dual-channel array.


title: Tn5::4697 TR2 BR1, MHH1252, Tn5 mutant

description:
MHH1252
14081264

Each Sample represents one channel of a dual-channel array.


title: Tn5::4696 TR4 BR1, MHH1250, Tn5 mutant

description:
MHH1250
14081273

Each Sample represents one channel of a dual-channel array.


title: steady states Benzoate I vs. Benzoate II - techn. repl. 2

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Operation Software Version 1.4 (Affymetrix GeneChip Scanner GCS 30) and data were processed using Agilent Scan Control and Feature Extraction Software

label_protocol: cDNA synthesis and labeling reactions were performed following the Progenika standard protocol.

growth_protocol: Pseudomonas putida strain KT2440 from -70°C glycerol stock was cultivated on LB agar plates at 30 °C for 24 hours. A single colony of P. putida KT2440 was inoculated into 5 mL of LB medium and incubated overnight. The LB-grown culture was further cultivated in two subsequent pre-cultures in M9 minimal medium (2 g/L Na2SO4 x 10 H2O; 2.68 g/L (NH4)2SO4; 1 g/L NH4Cl; 1.46 g/L K2HPO4; 0.4 g/L NaH2PO4 x 2H2O; 0.25 g/L MgSO4 x 7H2O; 22 mg/L CaCl2 x 2H2O; 0.27 mg/L ZnSO4 x 7H2O; 0.15 mg/L MnSO4 x H2O; 30.15 mg/L Na-EDTA; 0.24 mg/L CuSO4 x 5H2O; 24.1 mg/L FeCl3 x 6H2O and 0.27 mg/L CoCl2 x 6H2O) supplemented with Na-benzoate (1 g/L) in Erlenmeyer flasks (30°C, 150 rpm) and the final pre-culture was used to inoculate directly into the fermentor for chemostat experiments. The composition of the M9 medium for chemostat cultivations was calculated from elementary balancing for the production of 5 g dry weight biomass per liter: 15 g/L Na-benzoate or 20 g/L glucose or 15 g/L D-fructose. In order to maintain a constant biomass concentration during the substrate shift experiments, the concentration of C-source were changed according to the biomass growth yield on the respective substrates, with remaining components of the medium unchanged.Cultivation of Pseudomonas putida KT2440 was initiated with a batch mode of operation in benzoate minimal medium at 30 °C in a stirred tank bioreactor; with a working volume of 1.5 L.  The airflow was kept at 2 mL/min and the pH was controlled at 7.0 by the addition of 20 % H3PO4 and 2M NaOH. Batch cultivation was continuously monitored by changes in DO concentration and increase in OD450. Fed-batch operation was initiated with exponential feeding of benzoate solution (50 g/L), after complete consumption of benzoate in the growth medium, marked by steep increase in DO concentration. Exponential feeding was performed at a growth rate of 0.65 hr-1, controlled by a computer-aided feed-forward feedback control. After reaching the desired biomass concentration of 5 gDW per liter (corresponding to OD450 of ~30), continuous mode of operation was started with a dilution rate of 0.1 hr-1. Steady state conditions were confirmed when the optical density, dissolved oxygen, as well as the OTR and CTR from exhaust analysis, remained constant during five times the mean residence time.

extract_protocol: Total RNA extraction was performed according the manufacturer's protocol provided by Qiagen for bacteria.

treatment_protocol: For transcriptome analysis, 1 mL of bio-suspension from the reactor is withdrawn into 4 mL of RNA protect solution in 15 mL falcon tubes. The diluted sample is vortexed immediately and incubated at room temperature for 5 minutes. The sample is then centrifuged at 5000 g for 10 minutes at room temperature. The supernatant is discarded and the pellet is frozen at -70 °C until analysis.

value: steady state benzoate I

source_name: bacterial culture, steady state benzoate II

value: steady state benzoate II


title: steady states Benzoate I vs. Benzoate II - techn. repl. 1

source_name: bacterial culture, steady state benzoate I


title: steady states Benzoate I vs. Benzoate II - techn. repl. 3


title: Tn5::4695 TR3 BR1, MHH1245, Tn5 mutant

description:
MHH1245
13817571

Each Sample represents one channel of a dual-channel array.


title: steady states Fructose vs. Benzoate II - techn. repl. 4

source_name: bacterial culture, steady state fructose

value: steady state fructose


title: Tn5::4697 TR1 BR1, MHH1251, Tn5 mutant

description:
MHH1251
14081263

Each Sample represents one channel of a dual-channel array.


title: DMSO p53 ChIP

city: Montpellier

first: Michael

last: Girardot

state: France

address: 1919 route de Mende

country: France

institute: IGMM CNRS UMR5535

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

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

data_processing: Arrays were processed using NimbleGen's standard protocol for NimbleScan 2.4 ChIP data extraction.

source_name: p53 ChIP from DMSO-treated HEL cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: RPMI 1640 + 10% FBS + 1mM pyruvate + 2 mM Glutamine.

extract_protocol: 10e6 cells were fixed for 10 min in 1% Formaldehyde and quenched with 125mM Glycine for 5 min. Chromatin immunoprecipitations were performed following Diagenode's OneDay ChIP protocol.

treatment_protocol: DMSO

tag: cell line

value: HEL

tag: treatment

value: DMSO

tag: chip antibody

tag: antibody vendor

value: Active Motif

tag: antibody catalog #

source_name: Input DNA from DMSO-treated HEL cells


title: steady states Fructose vs. Benzoate II - techn. repl. 2


title: Tn5::4695 TR2 BR1, MHH1244, Tn5 mutant

description:
MHH1244
13817570

Each Sample represents one channel of a dual-channel array.


title: Tn5::4695 TR1 BR1, MHH1243, Tn5 mutant

description:
MHH1243
13817569

Each Sample represents one channel of a dual-channel array.


title: steady states Fructose vs. Benzoate II - techn. repl. 3


title: steady states  Glucose vs. Fructose - techn. repl. 4

source_name: bacterial culture, steady state glucose

value: steady state glucose


title: INC STAT5B ChIP

source_name: STAT5B ChIP from ruxolitinib-treated cells

treatment_protocol: Ruxolitinib (1 µM, 16h).

value: ruxolitinib

value: Millipore

source_name: Input DNA from ruxolitinib-treated HEL cells


title: steady states  Glucose vs. Fructose - techn. repl. 3


title: FFPE_breast_cancer_DNA10082.009.CEL

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description:
For ER status, 1 represents ER-pos and 0 ER-neg.
FFPE primary breast cancer samples profiled using Affymetrix HG-U133 Plus 2.0 microarray platform after RNA amplification with the Nugen WT-Ovation FFPE System

hyb_protocol: Hybridization was performed according with the manufacturer's intructions

scan_protocol: Scanning was performed according with the manufacturer's intructions

data_processing: Using the altcdenvsf Bioconductor package we created an alternative Chip Description Filewhere only probes univocally mapping RefSeq transcripts (hg19, GRCh37) were retained. For genes with multiple RefSeq transcripts, the longest isoform was considered. Summarization and normalization were carried out using the fRMA method.

source_name: breast cancer

label_protocol: 5 µg of aDNAss were labeled using the Encore Biotin Module essentially according to manufacturer's inststructions

extract_protocol: Total RNA was extracted using a non commercially available kit by Roche. 100 ng of total RNA were amplified using the WT Ovation FFPE amplification system V2

value: breast cancer

tag: er status


title: DMSO STAT5B ChIP

source_name: STAT5B ChIP from DMSO-treated HEL cells


title: steady states  Glucose vs. Fructose - techn. repl. 2


title: FFPE_breast_cancer_DNA10082.012.CEL

tag: tissue


title: FFPE_breast_cancer_DNA10082.011.CEL


title: steady states Fructose vs. Benzoate II - techn. repl. 1


title: FFPE_breast_cancer_DNA10082.010.CEL


title: steady states  Glucose vs. Fructose - techn. repl. 1


title: steady states Benzoate I vs. Glucose - techn. repl. 4


title: FFPE_breast_cancer_DNA10082.008.CEL


title: FFPE_breast_cancer_DNA10082.007.CEL


title: Floral_mix-conditioned bees compared to air exposure (no odor association)

city: Brisbane

first: Alexandre

middle: Santos

last: Cristino

state: Queensland

address: 79 QBI Building

department: The Queensland Brain Institute

country: Australia

institute: The University of Queensland

description: The analysis used Air group (no odor learning) as control sample for comparison to two groups of floral mix-conditioned bees.

hyb_protocol: Pairs of RNA samples were labeled with Cy3 or Cy5 fluorophores and hybridized to the same slide following the experimental design: (1) linalool versus air; (2) floral mix versus air. Dye swaps were done for each comparison. Prior to pre-hybridization, each slide was UV cross-linked and plunged into 0.2% SDS, washed with water, plunged into ethanol and centrifuged at 2000 g for 3 min. Pre-hybridizations were done for 1-2 h in a warm solution (42°C) containing 20% Formamide, 10% Denhardt’s solution (50x), 33.2% SSC 20x, 0.1% SDS and 0.5% tRNA (10 mg/mL) and then rinsed in Milli-Q water, plunged into isopropyl alcohol and dried by centrifugation at 2000 g for 3 min. Probes (in 60 µL of 49% formamide, 49% SSC 20x and 0.2% SDS) were preheated at 50°C for 3 min and then transferred to slides and covered with lifter-slip cover glasses (22×60, 31.25 µL). Slides were subsequently placed in single-slide hybridization chambers (CLS2551, Corning) and incubated in a water bath to allow hybridization to occur for 17 h at 42°C. Washing procedure included the following steps: 2× SSC and 0.1% SDS; 2× SSC; 0.1× SSC and bi-distilled water. Each step was conducted for 3 min at room temperature, except for the first step, which consisted of 10 sec at 42°C. Slides were dried by centrifugation at 2000 g for 2 min previous scanning.

scan_protocol: The microarray slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) at a 10 micron resolution, during which Cy3 was excited with a green laser (532 nm) and Cy5 with a red laser (635 nm).. For images quantitation we used GenePix® Pro 6.0 software with default parameters.

data_processing: Background correction was performed to avoid the correction of negative or zero intensities (offset correction) by adding to the background-corrected intensities a positive constant of 50. It reduces spurious variation in log-ratios, particularly at low intensity spots. The print-tip loess normalization was used to correct for within-array dye and spatial effects, and single channel normalization was used to facilitate comparison between arrays. As the bEST_9000 array has duplicates for each probe, the normalization procedure also considered the variation among their values 55. After normalization we determined a log2 ratio for each probe on each array. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data. A Bayesian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene

organism: Apis mellifera

source_name: Air

label_protocol: Twenty micrograms of amplified RNA were labeled with Cy3 or Cy5 dye (RPN5661, GE Healthcare). Probe purification was done using MinElute PCR Purification Kit (QIAGEN).

growth_protocol: Foraging honeybees (Apis mellifera) were captured at the entrance of an outdoor hive located on campus of The University of Queensland, Brisbane, Australia. .

extract_protocol: Total RNA was extracted from the pooled brains for each group using TRizol protocol (Invitrogen) combined with column purification (RNeasy Mini Kit, QIAGEN). cDNA synthesis (from 1 μg total RNA), RNA amplification and probe preparation  were done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

treatment_protocol: Groups of 60 bees were odor-conditioned to linalool and floral mix using the standard Pproboscis extension reflex assay (PER) assay. A group of 60 bees were carried on under the same experimental paradigm but with no odor learning (air).

value: brain


title: Linalool-conditioned bees compared to air exposure (no odor learning)

description: The analysis used Air group (no odor learning) as control sample for comparison to two groups of linalool-conditioned bees.

source_name: Linalool


title: steady states Benzoate I vs. Glucose - techn. repl. 3


title: Linalool-conditioned bees compared to floral mix-conditioned bees

description: The analysis used Floral mix group as control sample for comparison to Linalool-conditioned bees.


title: FFPE_breast_cancer_DNA10082.005.CEL


title: INC p53 ChIP

source_name: p53 ChIP from ruxolitinib-treated cells


title: AM HAM3 adherent 0h

city: St Lucia

first: ronan

last: kapetanovic

state: QLD

address: The University of Queensland

institute: Institute for Molecular Bioscience

description:
Re-analysis of GSM1098004
Gene expression data from adherent alveolar macrophages from Hampshire pigs.

hyb_protocol: The fragmented and biotin labelled cDNA was hybridized to the Snowball arrays, using the Affymetrix HybWashStain Kit and Affymetrix standard protocols.

scan_protocol: GeneChips were scanned using the Affymetrix 7G scanner.

data_processing: A total of 10 Affymetrix SNOWBALLs520824F_v1 arrays were QC analyzed. Normalization of the 47845 features across all arrays was achieved using the robust multi-array average (RMA) expression measure (Partek Genomic Suite, Partek, St. Louis, USA). Statistical anlysis was performed by Partek and using Biolayout Express 3D.

organism: Sus scrofa

label_protocol: 500 ng of total RNA was amplified using the Ambion WT Expression Kit (Affymetrix). 5µg of the resulting cDNA was fragmented and labelled using the Affymetrix Terminal Labelling Kit.

growth_protocol: Cells were recovered from -155°C by quickly thawing them at 37 °C, then slowly diluting the freezing medium by dropwise addition of 40 ml of warm PBS over 2-3 min to avoid the shock of sudden dilution of DMSO. Cells were seeded at 1x10e6 cells/ml in 6-wells plates in complete medium (RPMI-1640, Glutamax supplement (35050-61; Invitrogen), 10% heat-inactivated FCS (PAA Laboratories), penicillin/streptomycin (15140; Invitrogen, Paisley, U.K.)) with rhCSF-1 and left overnight.

extract_protocol: RNA extraction was carried out using RNA-Bee (Fischer) following manual instruction and RNA quantified using a Nanodrop (Nanodrop, USA). RNA quality was assessed using Agilent nanochip (Agilent)

treatment_protocol: The next day, adherent cells were removed, fresh complete medium was added and cells were stimulated with LPS from Salmonella enterica serotype minnesota Re 595 (100 ng/ml; L9764; Sigma-Aldrich).

tag: breed

value: Hampshire

value: adherent alveolar macrophage

tag: sample group

value: untreated

tag: time


title: FFPE_breast_cancer_DNA10082.002.CEL


title: FFPE_breast_cancer_DNA10082.006.CEL


title: FFPE_breast_cancer_DNA10082.003.CEL


title: FFPE_breast_cancer_DNA10082.004.CEL


title: AM HAM4 adherent 0h

description:
Re-analysis of GSM1098002
Gene expression data from adherent alveolar macrophages from Hampshire pigs.

tag: cell type


title: FFPE_breast_cancer_DNA10082.001.CEL


title: AM HAM2 adherent 0h

description:
Re-analysis of GSM1098005
Gene expression data from adherent alveolar macrophages from Hampshire pigs.


title: steady states Benzoate I vs. Glucose- techn. repl. 2


title: Benzoate shift T7 90' - techn. repl. 4

source_name: bacterial culture, 90 min after benzoate shift

value: benzoate shift

value: 90 min


title: AM HAM5 adherent 0h

description:
Re-analysis of GSM1098003
Gene expression data from adherent alveolar macrophages from Hampshire pigs.


title: steady states Benzoate I vs. Glucose - techn. repl. 1


title: AM HAM5 non adherent 0h

description:
Gene expression data from non-adherent alveolar macrophages from Hampshire pigs.
AM_HAM5_NONadherent.CEL

treatment_protocol: The next day, non-adherent cells were harvested and cells with high size and granularity were sorted by cytometry. Cells were then lysed in 1ml of RNA-bee and kept in -80°C.

value: non-adherent alveolar macrophage


title: AM HAM1 adherent 0h

description:
Re-analysis of GSM1098001
Gene expression data from adherent alveolar macrophages from Hampshire pigs.


title: Benzoate shift T7 90' - techn. repl. 3


title: FFPE_breast_cancer_DNA10064.017.CEL


title: AM HAM1 non adherent 0h

description:
Gene expression data from non-adherent alveolar macrophages from Hampshire pigs.
AM_HAM1_NONadherent.CEL


title: AM HAM4 non adherent 0h

description:
Gene expression data from non-adherent alveolar macrophages from Hampshire pigs.
AM_HAM4_NONadherent.CEL


title: AM HAM2 non adherent 0h

description:
Gene expression data from non-adherent alveolar macrophages from Hampshire pigs.
AM_HAM2_NONadherent.CEL


title: FFPE_breast_cancer_DNA10064.018.CEL


title: Benzoate shift T7 90' - techn. repl. 2


title: AM HAM3 non adherent 0h

description:
Gene expression data from non-adherent alveolar macrophages from Hampshire pigs.
AM_HAM3_NONadherent.CEL


title: FFPE_breast_cancer_DNA10064.015.CEL


title: Benzoate shift T7 90' - techn. repl. 1


title: Male_75ppmPB_Day7_Rep3

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

hyb_protocol: For each array, 15 μg of amplified biotin-cRNAs were fragmented and hybridized to the array for 16 h at 45°C in a rotating hybridization oven using the Affymetrix eukaryotic target hybridization controls and protocol.  Hybridized probe sets on the array were stained with streptavidin/phycoerythrin using a double-antibody staining procedure and washed using the EukGE-WS2v5 protocol of the Affymetrix fluidics station FS450 for antibody amplification.

scan_protocol: Arrays were scanned with an Affymetrix scanner 3000

data_processing: The raw signal intensities from each scan (.cel files) were imported into the gene expression analysis software Rosetta Resolver version 7.2 (Rosetta Inpharmatics, Kirkland, WA, USA).  This software was used to determine which probe sets in a treatment group differed from the control group.  The scans were converted into profiles within this software and the data were normalized using Rosetta error model (Weng et al., 2006).

organism: Mus musculus

label_protocol: Total RNA (4 μg) for each sample was amplified and labeled by the Enzo BioArray RNA Amplification and Biotin labeling System (Enzo Life Sciences, Farmingdale, NY, USA).

growth_protocol: dietary in vivo exposure

extract_protocol: conventional Trizol RNA extraction

value: liver


title: Benzoate shift T4 30' - techn. repl. 3

source_name: bacterial culture, 30 min after benzoate shift

value: 30 min


title: Benzoate shift T4 30' - techn. repl. 4

value: steady state fructose


title: Male_75ppmPB_Day7_Rep2


title: Male_75ppmPB_Day2_Rep4


title: Male_75ppmPB_Day2_Rep3


title: Male_75ppmPB_Day7_Rep4


title: Benzoate shift T4 30' - techn. repl. 2


title: FFPE_breast_cancer_DNA10064.014.CEL


title: Male_150ppmPB_Day7_Rep4


title: Male_75ppmPB_Day2_Rep2


title: FFPE_breast_cancer_DNA10064.011.CEL


title: Benzoate shift T4 30' - techn. repl. 1


title: Male_75ppmPB_Day2_Rep1


title: FFPE_breast_cancer_DNA10064.009.CEL


title: Male_75ppmPB_Day7_Rep1


title: Benzoate shift T2 10' - techn. repl. 4

source_name: bacterial culture, 10 min after benzoate shift

value: 10 min


title: FFPE_breast_cancer_DNA10064.010.CEL


title: FFPE_breast_cancer_DNA10064.012.CEL


title: FFPE_breast_cancer_DNA10064.016.CEL


title: Male_150ppmPB_Day7_Rep1


title: Benzoate shift T2 10' - techn. repl. 3


title: Male_150ppmPB_Day7_Rep2


title: Male_150ppmPB_Day7_Rep3


title: FFPE_breast_cancer_DNA10064.008.CEL


title: Benzoate shift T2 10' - techn. repl.2


title: Male_150ppmPB_Day2_Rep2


title: Benzoate shift T2 10' - techn. repl. 1


title: Male_150ppmPB_Day2_Rep4


title: Fructose shift T8 120' - techn. repl. 4

source_name: bacterial culture, 120 min after fructose shift

value: fructose shift

value: 120 min


title: FFPE_breast_cancer_DNA10064.006.CEL


title: FFPE_breast_cancer_DNA10064.007.CEL


title: Male_150ppmPB_Day2_Rep1


title: Male_15ppmPB_Day7_Rep4


title: FFPE_breast_cancer_DNA10064.004.CEL


title: Male_15ppmPB_Day2_Rep3


title: Male_150ppmPB_Day2_Rep3


title: Male_15ppmPB_Day7_Rep1


title: Fructose shift T8 120' - techn. repl. 3

value: steady state glucose


title: Male_15ppmPB_Day2_Rep1


title: Male_15ppmPB_Day7_Rep3


title: Male_15ppmPB_Day2_Rep2


title: Male_15ppmPB_Day2_Rep4


title: Male_15ppmPB_Day7_Rep2


title: Male_1.5ppmPB_Day7_Rep3


title: FFPE_breast_cancer_DNA10064.005.CEL


title: Fructose shift T8 120' - techn. repl. 2


title: Male_1.5ppmPB_Day7_Rep4


title: Fructose shift T8 120' - techn. repl. 1


title: FFPE_breast_cancer_DNA10064.002.CEL


title: Fructose shift T3 30' - techn. repl. 4

source_name: bacterial culture, 30 min after fructose shift


title: Male_1.5ppmPB_Day7_Rep2


title: Male_1.5ppmPB_Day7_Rep1


title: Male_1.5ppmPB_Day2_Rep4


title: FFPE_breast_cancer_DNA10051.018.CEL


title: FFPE_breast_cancer_DNA10051.017.CEL


title: Male_1.5ppmPB_Day2_Rep2


title: FFPE_breast_cancer_DNA10051.014.CEL


title: Male_0ppmPB_Day7_Rep3


title: FFPE_breast_cancer_DNA10051.015.CEL


title: FFPE_breast_cancer_DNA10064.001.CEL


title: Male_0ppmPB_Day7_Rep2


title: Male_1.5ppmPB_Day2_Rep1


title: Male_0ppmPB_Day7_Rep4


title: Male_0ppmPB_Day2_Rep4


title: Male_0ppmPB_Day7_Rep1


title: Fructose shift T3 30' - techn. repl. 3


title: Fructose shift T1 10' - techn. repl. 4

source_name: bacterial culture, 10 min after fructose shift


title: Fructose shift T3 30' - techn. repl. 1


title: Male_0ppmPB_Day2_Rep1


title: Male_0ppmPB_Day2_Rep2


title: FFPE_breast_cancer_DNA10051.013.CEL


title: Male_0ppmPB_Day2_Rep3


title: Fructose shift T1 10' - techn. repl. 3


title: FFPE_breast_cancer_DNA10051.016.CEL


title: Male_0.15ppmPB_Day7_Rep3


title: FFPE_breast_cancer_DNA10051.012.CEL


title: Fructose shift T1 10' - techn. repl. 2


title: Male_0.15ppmPB_Day7_Rep4


title: Glucose shift T7 105' - techn. repl. 3

source_name: bacterial culture, 105 min after glucose shift

value: glucose shift

value: 105 min

source_name: bacterial culture, steady state benzoate I

value: steady state benzoate I


title: Male_0.15ppmPB_Day7_Rep1


title: Glucose shift T7 105' - techn. repl. 2


title: FFPE_breast_cancer_DNA10051.011.CEL

value: breast cancer


title: FFPE_breast_cancer_DNA10051.010.CEL


title: Fructose shift T1 10' - techn. repl. 1


title: Male_0.15ppmPB_Day2_Rep4


title: Glucose shift T7 105' - techn. repl. 1


title: Male_0.15ppmPB_Day2_Rep2


title: FFPE_breast_cancer_DNA10051.008.CEL


title: Glucose shift T2 20' - techn. repl. 3

source_name: bacterial culture, 20 min after glucose shift

value: 20 min


title: Male_0.15ppmPB_Day2_Rep1


title: Female_75ppmPB_Day2_Rep2


title: Female_75ppmPB_Day7_Rep1


title: Female_75ppmPB_Day7_Rep3


title: Male_0.15ppmPB_Day2_Rep3


title: Female_75ppmPB_Day7_Rep4


title: FFPE_breast_cancer_DNA10051.005.CEL


title: FFPE_breast_cancer_DNA10051.006.CEL


title: Glucose shift T2 20' - techn. repl. 2


title: Glucose shift T2 20' - techn. repl. 4


title: Female_75ppmPB_Day7_Rep2


title: Female_75ppmPB_Day2_Rep1


title: Female_75ppmPB_Day2_Rep3


title: Female_150ppmPB_Day7_Rep4


title: FFPE_breast_cancer_DNA10051.002.CEL


title: Female_75ppmPB_Day2_Rep4


title: FFPE_breast_cancer_DNA10051.007.CEL


title: Glucose shift T2 20' - techn. repl. 1


title: FFPE_breast_cancer_DNA10051.004.CEL


title: Female_150ppmPB_Day7_Rep3


title: Glucose shift T1 10' - techn. repl. 4

source_name: bacterial culture, 10 min after glucose shift


title: FFPE_breast_cancer_DNA10051.001.CEL


title: Glucose shift T1 10' - techn. repl. 3


title: Glucose shift T1 10' - techn. repl. 2


title: Glucose shift T1 10' - techn. repl. 1


title: Female_150ppmPB_Day7_Rep1


title: Female_150ppmPB_Day7_Rep2


title: Female_150ppmPB_Day2_Rep4


title: Female_150ppmPB_Day2_Rep3


title: Female_150ppmPB_Day2_Rep1


title: Female_15ppmPB_Day7_Rep4


title: Female_15ppmPB_Day7_Rep1


title: Female_15ppmPB_Day2_Rep2


title: Female_15ppmPB_Day2_Rep1


title: Female_15ppmPB_Day2_Rep4


title: Female_150ppmPB_Day2_Rep2


title: Female_15ppmPB_Day2_Rep3


title: Female_15ppmPB_Day7_Rep3


title: mouse mammary tumor [F21T2]

city: Berkeley

first: Jian-Hua

last: Mao

state: CA

address: One Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: Gene expression data from mammary tumor.

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

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

data_processing: The data were analyzed with by Robust Multi-array Analysis (RMA).

source_name: mouse mammary tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: spontaneous mammary tumors from genetically diverse MMTV-ErbB2 mice

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

value: mammary tumor

tag: genotype

tag: genetic background

value: F1:C57BL/6 x FVB/N


title: Female_1.5ppmPB_Day7_Rep1


title: Female_15ppmPB_Day7_Rep2


title: Female_1.5ppmPB_Day2_Rep4


title: Female_1.5ppmPB_Day7_Rep3


title: mouse mammary tumor [F21T4]


title: Female_1.5ppmPB_Day7_Rep4


title: Fructose shift T3 30' - techn. repl. 2

source_name: bacterial culture, steady state glucose


title: Female_1.5ppmPB_Day2_Rep3


title: mouse mammary tumor [F21T3]


title: mouse mammary tumor [F18T1]


title: Female_1.5ppmPB_Day2_Rep2


title: mouse mammary tumor [056T1]

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: Female_0ppmPB_Day7_Rep4


title: Female_0ppmPB_Day7_Rep3


title: Female_1.5ppmPB_Day2_Rep1


title: Female_1.5ppmPB_Day7_Rep2


title: Female_0ppmPB_Day7_Rep2


title: Male_1.5ppmPB_Day2_Rep3


title: mouse mammary tumor [F15T2]


title: Female_0ppmPB_Day2_Rep3


title: mouse mammary tumor [F14T2]


title: Female_0ppmPB_Day2_Rep2


title: Female_0ppmPB_Day2_Rep4


title: mouse mammary tumor [F17T1]


title: Female_0ppmPB_Day7_Rep1


title: Female_0.15ppmPB_Day7_Rep4


title: mouse mammary tumor [F11T1]


title: Female_0ppmPB_Day2_Rep1


title: Female_0.15ppmPB_Day2_Rep3


title: mouse mammary tumor [F14T1]


title: Female_0.15ppmPB_Day2_Rep4


title: Female_0.15ppmPB_Day7_Rep2


title: Female_0.15ppmPB_Day7_Rep3


title: Female_0.15ppmPB_Day2_Rep1


title: mouse mammary tumor [051T1]


title: Female_0.15ppmPB_Day2_Rep2


title: mouse mammary tumor [F10T2]


title: con-2 (DFW)

city: kawasaki

first: Akihito

last: Yasuoka

state: kanagawa

address: kawasaki-ku, tonomachi 3-25-13

department: project of health and anti-aging

country: Japan

institute: kanagawa academy of science and technology

hyb_protocol: anti-sense RNA probe was fragmented, and hybridized with GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Japan) for 16 hr.

scan_protocol: The chip was washed, stained, and scanned with Affymetrix GeneChip Command Console software (Affymetrix, Japan).

data_processing: The probe signals were normalized by the Factor Analysis for Robust Microarray Summarization (qFARMS) on the R 2.12. platform, and the probes were selected according to the false discovery rate (FDR) values obtained by comparisons of expression levels among the experimental groups. The selected gene sets were analyzed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http//david.abcc.ncifcrf.gov/) for their significant representation in certain Gene Ontology (GO) terms.

source_name: Five-week-old C3H/HeN female CAR deficient mice liver

label_protocol: A biotin-labeled anti-sense RNA probe was synthesized from cDNA using a GeneChip® 3' IVT Express Kit (Affymetrix, Japan),

growth_protocol: Five-week-old C3H/HeN female mice (CLEA, Japan) were acclimated to the maintenance condition (25°C, 8:00-20:00 day / 20:00-8:00 night cycle and 35~40 % humidity), fed a CE-2 diet (CLEA, Japan), and given water ad libitum for one week.

extract_protocol: Total RNA was isolated from 50 mg of mouse liver using ISOGEN (Nippon gene, Japan) and purified using an RNeasy Mini Kit (Qiagen, USA). The quality of the purified RNA was examined by the Agilent RNA 6000 Nano Assay protocol (Agilent technologies, Japan) and reverse-transcribed into cDNA using a One-Cycle cDNA Synthesis Kit (Affymetrix, Japan).

treatment_protocol: Each group of mice (n=4 for wild type mice analysis and n=3 for CAR decficient mice analysis) was fed Lieber's isocaloric diet (Oriental yeast, Japan) containing water, containing ethanol, containing ethanol and ellagic acid (Fluka Biochemika, Switzerland), or containing ethanol and trans-resveratrol (Sigma, USA) (Supplementary Table 1) for one week at 10:00 ad libitum. Then, the mice were fed each diet at 12 g / day for four weeks (Supplementary Fig. 1A). The approximate intake of each polyphenol was 50 mg / kg body weight / day. At 10:00 of the final day of the experimental period, the animals were anesthetized by diethyl ether, sacrificed by cervial fracture, and the heart blood, and the liver were collected.

tag: gender

value: female

tag: genotype/variation

value: CAR deficient

tag: age

value: Five-weeks-old

tag: agent

value: control


title: Male_0.15ppmPB_Day7_Rep2

value: liver

tag: strain


title: Female_0.15ppmPB_Day7_Rep1


title: mouse mammary tumor [F06T1]


title: Et-3 (DFW)

value: EtOH


title: mouse mammary tumor [F10T1]


title: Et+ella-3 (DFW)

value: Et+ella


title: mouse mammary tumor [F01T1]


title: con-3 (DFW)


title: Et-1 (DFW)


title: con-1 (DFW)


title: Et-2 (DFW)


title: Et+ella-1 (DFW)


title: mouse mammary tumor [299T6]


title: Et+res-1 (DFW)

value: Et+res


title: mouse mammary tumor [F09T1]


title: mouse mammary tumor [F04T1]


title: mouse mammary tumor [299T4]


title: Et+res-3 (DFW)


title: mouse mammary tumor [299T2]


title: Et+ella-2 (DFW)


title: mouse mammary tumor [299T1]


title: Et+res-2 (DFW)


title: WT-control-3 (DFW)

source_name: Five-week-old C3H/HeN female mice liver

value: WT


title: WT-control-1 (DFW)


title: WT-Et+res-1 (DFW)


title: WT-control-2 (DFW)


title: WT-control-4 (DFW)


title: WT-Et+res-2 (DFW)


title: WT-Et+ella-1 (DFW)


title: mouse mammary tumor [050T2]


title: mouse mammary tumor [298T2]


title: WT-Et+ella-3 (DFW)


title: WT-Et+res-4 (DFW)


title: mouse mammary tumor [298T3]


title: WT-EtOH-3 (DFW)


title: WT-Et+res-3 (DFW)


title: mouse mammary tumor [292T2]


title: WT-EtOH-4 (DFW)


title: mouse mammary tumor [298T1]


title: mouse mammary tumor [292T3]


title: WT-EtOH-1 (DFW)


title: Postnatal 12 weeks mutant heart biological rep2

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

hyb_protocol: After purification and fragmentation, 15ug of cRNA was used in a 300 ul hybridization mixture containing spiked IVT controls. Approximately 200 ul of mixture was hybridized on chips for 16 h at 45°C. Standard posthybridization wash and double-stain protocols used an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned by GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biontin

source_name: postnatal 12 weeks pitx2 cko heart

label_protocol: 8 ug of total RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first-strand cDNA. After second-strand synthesis, double-strand cDNA was used in an in vitro transcription (IVT) reaction to generate biotinylated cRNA.

extract_protocol: Total RNA was extracted by using Trizol (GIBCOyBRL). RNA pellets were resuspended at 1 ug RNA/ul diethyl pyrocarbonate-treated water.

value: 12 wk

value: whole heart

value: MCKcre Pitx2 Flox/Flox


title: mouse mammary tumor [292T1]


title: Postnatal 12 weeks mutant heart biological rep3


title: mouse mammary tumor [291T1]


title: WT-EtOH-5 (DFW)


title: mouse mammary tumor [289T1]


title: mouse mammary tumor [288T1]


title: Postnatal 6 weeks mutant heart biological rep2

source_name: postnatal 6 weeks pitx2 cko heart

value: 6 wk


title: Postnatal 12 weeks mutant heart biological rep1


title: Postnatal 6 weeks control heart biological rep1

source_name: postnatal 6 weeks control heart

value: Pitx2 Flox/Flox


title: Postnatal 12 weeks control heart biological rep3

source_name: postnatal 12 weeks control heart


title: Postnatal 6 weeks mutant heart biological rep1


title: Postnatal 12 weeks control heart biological rep2


title: mouse mammary tumor [287T1]

value: mammary tumor


title: mouse mammary tumor [290T1]


title: mouse mammary tumor [282T1]


title: Postnatal 3 weeks control heart biological rep3

source_name: postnatal 3 weeks control heart

value: 3 wk


title: Postnatal 6 weeks mutant heart biological rep3


title: Postnatal 3 weeks control heart biological rep2


title: mouse mammary tumor [284T2]

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: Postnatal 12 weeks control heart biological rep1


title: Postnatal 6 weeks control heart biological rep2


title: Postnatal 6 weeks control heart biological rep3


title: mouse mammary tumor [047T1]


title: Postnatal 3 weeks mutant heart biological rep3

source_name: postnatal 3 weeks pitx2 cko heart


title: Postnatal 3 weeks mutant heart biological rep2


title: Postnatal 3 weeks mutant heart biological rep1


title: mouse mammary tumor [278T2]


title: Subject 226

city: Maastricht

first: Simone

middle: G

last: van Breda

state: Limburg

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization according to Agilent instructions on 4x44K human whole genome microarrays.

scan_protocol: Slides were scanned on a GenePix® 4000B Microarray Scanner (Molecular Devices, Sunnyvale, USA). Cy3 was excited at a wavelengths of 532 nm. Laser power was set to 100%. The photo multiplier tube gain was set to a saturation tolerance of 0.02% to minimize background and saturated spots. Photomultiplier gain was set to 522 (Cy3), based on automatic establishment of ideal scan settings. Images were subsequently saved (resolution 5 micron, 16 bit tiff image).

data_processing: Bad and empty spots were flagged using the GenePix Pro software (version 6.0, Molecular Devices, Sunnyvale, CA). Quality control was performed in the statistical software environment R (version 2.10.1, The R Foundation for Statistical Computing, Vienna, Austria). Quantile normalization and subsequent data processing including background subtraction and Log2 transformation of spot intensities was performed in ArrayTrack (version 3.4, NCTR, Jefferson, AR).

source_name: Lymphocytes isolated from blood after the intervention

label_protocol: Cyanine 3 (Cy3)- and Cyanine 5 (Cy5)-labeled cRNA probes were generated using the Two-Color Microarray-Based Gene Expression Analysis kit from Agilent Technologies (Amstelveen, the Netherlands) according to the manufacturer's protocol.

extract_protocol: Lymphocytes isolated from the blood drawn from each participant before and after the intervention were lysed with TRIzol® reagent (Invitrogen) and stored at -80C until RNA extraction. Total RNA extracted using Trizol following manufacturer's instructions. The RNeasy® Mini Kit was used to purify total RNA from salts and residual DNA (Qiagen).

treatment_protocol: Healthy volunteer consumed 1 litre of blueberry/apple juice per day for four weeks. Before and after the intervention lymphocytes were isolated from blood drawn from which RNA was isolated for transcriptomic analyses. Each subject acted as its own control.

value: male

tag: age (yrs)

source_name: Lymphocytes isolated from blood before the intervention


title: Postnatal 3 weeks control heart biological rep1


title: mouse mammary tumor [276T2]


title: Subject 221

value: female


title: mouse mammary tumor [275T2]


title: Subject 219


title: Subject 217


title: Subject 223


title: Subject 216


title: Subject 215


title: Subject 222


title: Subject 218


title: a/alpha WT cells_PDA_30 hours_rep4

city: Providence

first: Christine

last: Scaduto

state: RI

address: 171 Meeting Street

department: Molecular Microbiology and Immunology

institute: Brown University

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 30 hours vs. WT C. lusitaniae cells on YPD for 2 hours

hyb_protocol: 300ng of Cy3 and Cy5 samples were mixed together in a total volume of 25uL ddH2O, heated to 95C for 3 min, and cooled to room temperature. 25uL GE hybridization buffer was added to samples, mixed, and spun down. 40uL of hybridization sample was loaded onto slide, slide sealed, and incubated at 65C rotating at 10rpm for ~17 hours. Slide washed using Agilent Wash Buffers and Drying and Stabilization Solution.

scan_protocol: Scanned using Axon 4000b scanner, pixel size = 5 um, Lines to average = 2, Focus position = 15. Scanned for count ratio = 1.

data_processing: Data normalized using Goulphar. Mnorm log2 values were averaged for each spot.

organism: Clavispora lusitaniae

source_name: WT a/alpha cells, PDA, 30 hours

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy3 (reference) or Cy5 (experimental). Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: Cells grown overnight in liquid YPD media, 3 OD600 of cells plated onto PDA plates or YPD at the appropriate time points. Cells spun scraped off plates and flash frozen in liquid nitrogen at the given time points.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

source_name: a/alpha WT cells, YPD, 2 hours


title: mouse mammary tumor [270T2]


title: mouse mammary tumor [275T1]


title: mouse mammary tumor [276T1]


title: mouse mammary tumor [268T5]


title: Subject 213


title: Subject 212


title: a/alpha WT cells_PDA_24 hours_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 24 hours vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpha cells, PDA, 24 hours


title: mouse mammary tumor [268T3]


title: Subject 211


title: Subject 210


title: Subject 214


title: a/alpha WT cells_PDA_18 hours_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 18 hours vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpha cells, PDA, 18 hours


title: Subject 206


title: Subject 224


title: Subject 208


title: a/alpha WT cells_PDA_12 hours_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 12 hours vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpha cells, PDA, 12 hours


title: WT-Et+ella-4 (DFW)

value: Five-weeks-old


title: a/alpha WT cells_PDA_8 hours_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 8 hours vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpha cells, PDA, 8 hours


title: mouse mammary tumor [046T1]

source_name: mouse mammary tumor


title: Subject 185


title: mouse mammary tumor [268T1]


title: Subject 196


title: mouse mammary tumor [266T1]


title: a/alpha WT cells_ PDA_ 4 hours_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 4 hours vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpa cells, PDA, 4 hours


title: Subject 194


title: Subject 184


title: Subject 189


title: Subject 200


title: Subject 199


title: a/alpha WT cells_PDA_30 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 30 hours vs. WT C. lusitaniae cells on YPD for 2 hours


title: Subject 197


title: a/alpha WT cells_ PDA_ 30minutes_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 30 minutes vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpha cells, PDA, 30 minutes


title: mouse mammary tumor [265T4]


title: a/alpha WT cells_ PDA_ 2 hours_rep4

description: Biological Replicate 4 of 4. WT C. lusitaniae cells on PDA for 2 hours vs. WT C. lusitaniae on YPD for 2 hours

source_name: WT a/alpha cells, PDA, 2 hours


title: Subject 198


title: mouse mammary tumor [265T2]


title: Subject 179


title: mouse mammary tumor [267T2]


title: Subject 180


title: Subject 183


title: Subject 182


title: mouse mammary tumor [266T2]


title: WT-Et+ella-2 (DFW)

source_name: Five-week-old C3H/HeN female mice liver


title: Subject 188


title: a/alpha WT cells_PDA_24 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 24 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 192


title: Subject 181


title: mouse mammary tumor [259T2]


title: Subject 167


title: Subject 174


title: Subject 177


title: mouse mammary tumor [261T1]


title: Subject 172


title: Subject 166


title: Subject 170


title: mouse mammary tumor [264T3]


title: a/alpha WT cells_PDA_18 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 18 hours vs. WT C. lusitaniae on YPD for 2 hours


title: mouse mammary tumor [265T1]


title: Subject 164


title: mouse mammary tumor [040T2]


title: Subject 162


title: Subject 163


title: Subject 171


title: a/alpha WT cells_ PDA_ 2 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 2 hours vs. WT C. lusitaniae on YPD for 2 hours


title: mouse mammary tumor [259T1]


title: Subject 165


title: Subject 159


title: a/alpha WT cells_ PDA_ 4 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 4 hours vs. WT C. lusitaniae on YPD for 2 hours


title: a/alpha WT cells_PDA_8 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 8 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 160


title: mouse mammary tumor [258T2]


title: a/alpha WT cells_ PDA_ 30minutes_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 30 minutes vs. WT C. lusitaniae on YPD for 2 hours


title: a/alpha WT cells_PDA_8 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 8 hours vs. WT C. lusitaniae on YPD for 2 hours


title: a/alpha WT cells_ PDA_ 4 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 4 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 154


title: a/alpha WT cells_PDA_12 hours_rep3

description: Biological Replicate 3 of 4. WT C. lusitaniae cells on PDA for 12 hours vs. WT C. lusitaniae on YPD for 2 hours


title: mouse mammary tumor [253T4]

description: Gene expression data from mammary tumor.


title: mouse mammary tumor [251T5]


title: Subject 145


title: mouse mammary tumor [257T1]


title: Subject 153


title: Subject 156


title: Subject 146


title: a/alpha WT cells_PDA_18 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 18 hours vs. WT C. lusitaniae on YPD for 2 hours


title: a/alpha WT cells_PDA_30 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 30 hours vs. WT C. lusitaniae cells on YPD for 2 hours


title: Subject 161


title: a/alpha WT cells_PDA_24 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 24 hours vs. WT C. lusitaniae on YPD for 2 hours


title: mouse mammary tumor [252T1]


title: Subject 151


title: Subject 157


title: mouse mammary tumor [253T3]


title: Subject 152


title: mouse mammary tumor [251T3]


title: Subject 150


title: a/alpha WT cells_ PDA_ 30minutes_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 30 minutes vs. WT C. lusitaniae on YPD for 2 hours


title: a/alpha WT cells_PDA_12 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 12 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 140


title: Subject 148


title: a/alpha WT cells_ PDA_ 2 hours_rep2

description: Biological Replicate 2 of 4. WT C. lusitaniae cells on PDA for 2 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 155


title: Subject 158


title: Subject 143


title: Subject 141


title: mouse mammary tumor [258T1]


title: a/alpha WT cells_PDA_30 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 30 hours vs. WT C. lusitaniae cells on YPD for 2 hours


title: mouse mammary tumor [253T1]


title: a/alpha WT cells_PDA_24 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 24 hours vs. WT C. lusitaniae on YPD for 2 hours


title: mouse mammary tumor [251T1]


title: Subject 138


title: Subject 136


title: Subject 132


title: Subject 133


title: Subject 130


title: a/alpha WT cells_PDA_18 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 18 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 129


title: Subject 127


title: a/alpha WT cells_ PDA_ 4 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 4 hours vs. WT C. lusitaniae on YPD for 2 hours


title: a/alpha WT cells_ PDA_ 2 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 2 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 131


title: a/alpha WT cells_PDA_8 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 8 hours vs. WT C. lusitaniae on YPD for 2 hours


title: mouse mammary tumor [040T1]


title: a/alpha WT cells_PDA_12 hours_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 12 hours vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 123


title: Subject 120


title: PC3 5

city: New York

first: Dingcheng

last: Gao

state: NY

address: 1300 York Ave

department: CT Surgery

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip (MoGene-1_0-st-v1). GeneChips were washed and stained using the Affymetrix Fluidics Station 400.

data_processing: RMA protocol for normalization of signal between microarray chips

source_name: Lung, PC3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: 8 week old B6 mice were treated i.p. with tumor cell conditioned media

extract_protocol: Lungs were explanted, minced to aproximatedly 1mm^2 pieces and subjected to RNA extraction using QIAgen RNEasy kit

treatment_protocol: Daily injections of 100 uL of tumor cell-derived conditioned medium were administered during 7 days

value: Lung


title: Subject 121


title: Beta-catenin deficient macrophage

city: Toronto

first: Saeid

last: Amini-Nik

state: ON

address: 101 College St

country: Canada

institute: Hospital For Sick Children

description: Bone marrow derived macrophage

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix mouse 1.0 ST gene array

data_processing: Data normalized using Robust Multichip Average (RMA) algoritm

source_name: B-Cat KO macrophage

label_protocol: Affymetrix protocol

growth_protocol: Breifly, bone marrow was flushed using lymphocyte medium (RPMI-1640 +10% fetal bovine serum+1% penicillin-streptomycin) supplemented with 20 mM HEPES. Cells were then seeded at the concentration of 2 x 106 cells/ml.  Condition medium from L929 cells (ATCC: CCL-1, macrophage media) was used to facilitate the growth of macrophages

extract_protocol: Qiagen RNA extraction kit

value: 8 weeks


title: LN4 1

source_name: Lung, LN4


title: Subject 124


title: Control Macrophage

description: Bone marrow derived macrophage

source_name: Control Macrophage

treatment_protocol: Condition medium from L929 cells (ATCC: CCL-1, macrophage media) was used to facilitate the growth of macrophages


title: a/alpha WT cells_ PDA_ 30minutes_rep1

description: Biological Replicate 1 of 4. WT C. lusitaniae cells on PDA for 30 minutes vs. WT C. lusitaniae on YPD for 2 hours


title: Subject 126

source_name: Lymphocytes isolated from blood after the intervention


title: Subject 116

source_name: Lymphocytes isolated from blood before the intervention


title: PC3 4


title: a/alpha ste12 deletion mutants on PDA 24h replicate 1

description: Biological replicate 1 of 1, ste12 24h PDA vs WT 2h YPD

source_name: a/alpha ste12 deletion mutants

source_name: a/alpha WT cells


title: LN4 3


title: Subject 119


title: a/alpha ste12 deletion mutants on PDA 12h replicate 1

description: Biological replicate 1 of 1, ste12  12h PDA vs. WT 2h YPD


title: a/alpha ste12 deletion mutants on PDA 18h replicate 1

description: Biological replicate 1 of 1, ste12 18h PDA vs WT 2h YPD


title: Control 4

source_name: Lung, RPMI Control


title: Subject 115


title: Subject 112


title: Subject 111


title: Control 2


title: Subject 114


title: Subject 113


title: Subject 106


title: Subject 102


title: Subject 101


title: WT a_PDA_24h_rep 2

description: Biological Replicate 2 of 2. C. lusitaniae WT a cells incubated on PDA for 24 hours vs. C.lusitaniae WT a cells incubated on YPD for 2 hours

source_name: WT a cells, PDA, 24 hours

source_name: WT a cells, YPD, 2 hours


title: WT alpha_PDA_24h_rep 2

description: Biological Replicate 2 of 2. C. lusitaniae WT alpha cells incubated on PDA for 24 hours vs. C. lusitaniae WT alpha cells incubated on YPD for 2 hours

source_name: WT alpha cells, PDA, 24 hours

source_name: Wt alpha cells, YPD, 24 hours


title: TAE LFD-Vehicle

city: Lille

first: kassem

last: makki

address: 1, rue du Pr Calmette

institute: CNRS UMR8199

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using cubic spline normalization with GenomeStudio (Illumina).

source_name: mouse visceral white adipose tissue

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin-aRNA Labeling for Illumina System.

extract_protocol: RNA was extracted with Trizol reagent with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Rapamycin was weekly administrated to HFD-fed C57BL/6 mice for 22 weeks.

value: 28 weeks

value: visceral white adipose tissue

tag: obesity status

value: lean


title: Subject 108


title: Subject 99


title: WT alpha_PDA_30m_rep 2

description: Biological Replicate 2 of 2. C. lusitaniae WT alpha cells incubated on PDA for 30 minutes vs. C. lusitaniae WT alpha cells incubated on YPD for 2 hours

source_name: WT alpha cells, PDA, 30 minutes

source_name: Wt alpha cells, YPD, 2 hours


title: Subject 105


title: Subject 109


title: TAE HFD-Vehicle

value: obese


title: TAE HFD-Rapamycin


title: Subject 100


title: a/alpha ste12 deletion mutants on PDA 0h replicate 1

description: Biological replicate 1 of 1, ste12 0h on PDA vs WT on YPD 2h


title: Normal mouse mammary gland [NormalF1B6FVBwt3]

description: Gene expression data from normal mammary gland.

source_name: Normal mouse mammary gland

value: Normal mammary gland

value: Wild type

value: F1:C57BL/6 x FVB/N


title: WT alpha_PDA_2h_rep 1

description: Biological Replicate 1 of 1. C. lusitaniae WT alpha cells incubated on PDA for 2 hours vs. C. lusitaniae WT alpha cells incubated on YPD for 2 hours

source_name: WT alpha cells, PDA, 2 hours


title: WT alpha_PDA_24h_rep 1

description: Biological Replicate 1 of 2. C. lusitaniae WT alpha cells incubated on PDA for 24 hours vs. C. lusitaniae WT alpha cells incubated on YPD for 2 hours


title: Subject 94


title: Subject 96


title: WT a_PDA_30m_rep 2

description: Biological Replicate 2 of 2. C. lusitaniae WT a cells incubated on PDA for 30 minutes vs. C.lusitaniae WT a cells incubated on YPD for 2 hours

source_name: WT a cells, PDA, 30 minutes


title: Subject 98


title: Subject 92


title: Normal mouse mammary gland [NormalF1B6FVBwt2]


title: Subject 88


title: Subject 97


title: Subject 93


title: Subject 91


title: Subject 86


title: Normal mouse mammary gland [NormalF1B6FVBwt1]


title: Subject 89


title: Subject 137


title: Subject 87


title: WT a_PDA_2h_rep 1

description: Biological Replicate 1 of 1. C. lusitaniae WT a cells incubated on PDA for 2 hours vs. C.lusitaniae WT a cells incubated on YPD for 2 hours

source_name: WT a cells, PDA, 2 hours


title: Subject 84


title: WT alpha_PDA_30m_rep 1

description: Biological Replicate 1 of 2. C. lusitaniae WT alpha cells incubated on PDA for 30 minutes vs. C. lusitaniae WT alpha cells incubated on YPD for 2 hours


title: Normal mouse mammary gland [NormalFVBneu1]

value: FVB/N


title: Subject 85


title: Subject 81


title: Subject 80


title: Normal mouse mammary gland [NormalFVBneu2]


title: WT a_PDA_30m_rep 1

description: Biological Replicate 1 of 2. C. lusitaniae WT a cells incubated on PDA for 30 minutes vs. C.lusitaniae WT a cells incubated on YPD for 2 hours


title: ime2Δ/ime2Δ a/alpha_ PDA_ 12 hours_rep 3

description: Biological Replicate 3 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 12h vs. WT C. lusitaniae on YPD for 4 hours

source_name: ime2Δ/ime2Δ a/alpha cells, PDA, 12 hours

source_name: a/alpha WT cells, YPD, 4 hours


title: ime2Δ/ime2Δ a/alpha_ PDA_ 24 hours_rep 3

description: Biological Replicate 3 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 24h vs. WT C. lusitaniae on YPD for 4 hours

source_name: ime2Δ/ime2Δ a/alpha cells, PDA, 24 hours


title: Normal mouse mammary gland [NormalFVBneu3]


title: Subject 72

source_name: Lymphocytes isolated from blood before the intervention

source_name: Lymphocytes isolated from blood after the intervention


title: WT a_PDA_24h_rep 1

description: Biological Replicate 1 of 2. C. lusitaniae WT a cells incubated on PDA for 24 hours vs. C.lusitaniae WT a cells incubated on YPD for 2 hours


title: Normal mouse mammary gland [NormalF1B6FVBneu1]


title: ime2Δ/ime2Δ a/alpha_ PDA_ 18 hours_rep 3

description: Biological Replicate 3 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 18h vs. WT C. lusitaniae on YPD for 4 hours

source_name: ime2Δ/ime2Δ a/alpha cells, PDA, 18 hours


title: mouse mammary tumor [F1_6T1]

description: Gene expression data from mammary tumor.

source_name: mouse mammary tumor


title: Normal mouse mammary gland [NormalF1B6FVBneu2]


title: ime2Δ/ime2Δ a/alpha_ PDA_ 0 hours_rep 3

description: Biological Replicate 3 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 0h vs. WT C. lusitaniae on YPD for 4 hours

source_name: ime2Δ/ime2Δ a/alpha cells, PDA, 0 hours


title: D. shibae 5 h in the light vs. 5 h in the dark after 12 days in co-culture with P. minimum, LD2

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

hyb_protocol: Hybridization of 500 ng labelled RNA was performed according to the Agilent two-color microarray protocol.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray scanner. Raw data was collected using the Agilent Feature Extraction software v10.7.

data_processing: Median values of Cy3 and Cy5 channels were processed in the R environment using the limma package. Background correction was performed using the normexp method, Cy3 and Cy5 channels were loess normalized, Quantile-normalization was used for separate microarrays.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: D. shibae 5 h in the light

label_protocol: 2 µg RNA were labelled with Cy3 or Cy5 using the Universal Linker System (Kreatech) according to the manufacturer's protocol.

growth_protocol: Co-cultures were obtained by adding 10E7 cells ml-1 bacteria cells to cultures of P. minimum immediately after subculturing them in fresh medium with an initial density of approximately 2000 cells ml-1. Cultures were grown in 100-ml batches in 300-ml Erlenmeyer flasks at 22°C under a 12:12 h light-dark cycle with a light intensity of about 40 µmol photons m-2s-1.

extract_protocol:
RNA isolation: For RNA extraction, the samples were thawed at room temperature then transferred to a cryotube filled with 0.3 g acid-washed glass beads. The cells were homogenized using FastPrep-24 instrument (MP Biomedicals, California, USA) at 6.0 m/s for 3 min and then incubated for 5 min at room temperature. Samples were centrifuged at 12,000 x g for 10 min at 4°C and the supernatants were transferred to fresh tubes, followed by the addition of 100 µl of 1-bromo-3-chloropropane (BCP, Sigma, Germany) and incubation for 10 min at room temperature. Samples were centrifuged at 12,000 x g for 10 min at 4°C, after which the aqueous phase was transferred to new tubes and mixed with 500 µl of absolute ethanol. Extracts were applied to RNeasy spin columns (RNeasy mini kit, Qiagen, Hilden, Germany) and processed according to the manufacturer's instructions. In addition, samples were treated with DNase I (Qiagen, Hilden, Germany). Removal of genomic DNA was verified via PCR. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA).
Ribosomal RNA depletion: Oligotex mRNA kit (Qiagen, Hilden, Germany) was used to isolate the algal mRNA. For isolation of D. shibae mRNA, MICROBEnrich kit (Ambion, Life Technologies, Darmstadt, Germany) was used to remove the eukaryotic rRNA and MICROBExpress kit (Ambion, Life Technologies, Darmstadt, Germany) to remove the prokaryotic rRNA, according to the manufacturer's instructions.

treatment_protocol: For transcriptome analysis of the co-culture in the light and in the dark, sampling was achieved at day 12, as the algae reached the late exponential growth phase. To the time point 5 hours growth in the light or in the dark, 50 ml cultures were pelleted in 2 ml EPs and covered with 1 ml Trizol reagent and then snap frozen in liquid nitrogen and stored at -70° C until RNA isolation.

tag: strain/background

tag: light/dark condition

value: light

tag: days in co-culture with p. minimum

source_name: D. shibae 5 h in the dark

value: dark


title: Steer #411 - 13.5 months

city: Edmonton

first: Josue

middle: Moura

last: Romao

state: Alberta

address: 116 St. and 85 Ave.

department: AFNS

institute: University of Alberta

hyb_protocol: The labeled RNA was hybridized with array slides with hybridization buffer and 10X GE blocking agent, and were incubated at 55ºC for ~20 hours. Finally, the arrays were washed with GE wash buffers.

scan_protocol: The arrays were scanned at 5 μM resolution on an Agilent G2565CA High Resolution Scanner (Agilent Technologies). Data was processed through Agilent’s Feature Extraction software version 10.7.3.1  using the protocol miRNA_107_Sep09

data_processing: The data was normalized to the 75th percentile using GeneSpring GX 11.5 (Agilent Technologies)

organism: Bos taurus

source_name: Subcutaneous fat tissue

label_protocol: Total RNA (100 ng/sample) was firstly labeled with the AGILENT miRNA Complete Labeling and Hyb Kit (Version 2.1) by dephosphorylation with Calf Intestinal Phosphatase followed by denaturing and ligation with Cyanine3-pCp to the 3’ end.

extract_protocol: Total RNA extraction was performed by homogenizing the fat tissue samples with TRIZOL® (TRI reagent, Invitrogen, Carlsbad, CA, USA) following the manufactures instructions for samples with high fat content.

tag: tissue

value: Subcutaneous fat

tag: diet

value: High fat diet (7.1% fat)

value: 13.5 months


title: Steer #411 - 15 months

value: 15 months


title: mouse mammary tumor [F1_27T1]

value: mammary tumor


title: D. shibae 5 h in the light vs. 5 h in the dark after 12 days in co-culture with P. minimum, LD1


title: Subject 69

value: female


title: Subject 70

value: male


title: Subject 68


title: Steer #202 - 15 months


title: Subject 71


title: ime2Δ/ime2Δ a/alpha_ PDA_ 12 hours_rep 2

description: Biological Replicate 2 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 12h vs. WT C. lusitaniae on YPD for 4 hours


title: ime2Δ/ime2Δ a/alpha_ PDA_ 24 hours_rep 2

description: Biological Replicate 2 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 24h vs. WT C. lusitaniae on YPD for 4 hours


title: Steer #411 - 12 months

value: 12 months


title: Subject 67


title: Steer #202 - 12 months


title: Steer #202 - 13.5 months


title: mouse mammary tumor [F1_24T1]


title: Subject 64


title: mouse mammary tumor [F1_22T1]


title: Steer #109 - 15 months


title: ime2Δ/ime2Δ a/alpha_ PDA_ 0 hours_rep 2

description: Biological Replicate 2 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 0h vs. WT C. lusitaniae on YPD for 4 hours


title: ime2Δ/ime2Δ a/alpha_ PDA_ 24 hours_rep 1

description: Biological Replicate 1 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 24h vs. WT C. lusitaniae on YPD for 4 hours


title: mouse mammary tumor [F1_25T1]


title: mouse mammary tumor [241T1]

value: F1Bx:(C57BL/6 x FVB/N) x FVB/N


title: Subject 65


title: ime2Δ/ime2Δ a/alpha_ PDA_ 18 hours_rep 1

description: Biological Replicate 1 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 18h vs. WT C. lusitaniae on YPD for 4 hours


title: mouse mammary tumor [246T1R]


title: Subject 62


title: mouse mammary tumor [F1_26T1]


title: Steer #109 - 13.5 months


title: ime2Δ/ime2Δ a/alpha_ PDA_ 18 hours_rep 2

description: Biological Replicate 2 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 18h vs. WT C. lusitaniae on YPD for 4 hours


title: ime2Δ/ime2Δ a/alpha_ PDA_ 12 hours_rep 1

description: Biological Replicate 1 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 12h vs. WT C. lusitaniae on YPD for 4 hours


title: Subject 61


title: mouse mammary tumor [231T1]


title: Subject 60


title: ime2Δ/ime2Δ a/alpha_ PDA_ 0 hours_rep 1

description: Biological Replicate 1 of 3. ime2Δ/ime2Δ C. lusitaniae cells on PDA for 0h vs. WT C. lusitaniae on YPD for 4 hours


title: Steer #109 - 12 months


title: Steer #103 - 15 months


title: ime2Δ cells_PDA_12h_rep3

description: Biological replicate 3 of 3. ime2Δ a and alpha cells mixed for 12h on PDA vs. a cells on YPD for 4 hours

source_name: ime2Δ a and alpha cells, 12h, PDA

value: RSY406 and RSY410

source_name: WT a cells, 4 hours, YPD


title: mouse mammary tumor [182T1]


title: mouse mammary tumor [171T2]


title: Steer #103 - 13.5 months


title: Steer #405 - 15 months

value: Control diet (2.7% fat)


title: Steer #405 - 13.5 months


title: Steer #103 - 12 months


title: Subject 59


title: a and alpha cells_PDA_12h_rep3

description: Biological replicate 3 of 3. WT a and alpha cells mixed for 12h on PDA vs. a cells on YPD for 4 hours

source_name: WT a and alpha cells, 12h, PDA

value: RSY284 and RSY411


title: Steer #405 - 12 months


title: a and alpha cells_PDA_0h_rep3

description: Biological replicate 3 of 3. WT a and alpha cells mixed for 0h on PDA vs. a cells on YPD for 4 hours

source_name: WT a and alpha cells, 0h, PDA


title: Subject 56


title: Subject 58


title: a and alpha cells_PDA_4h_rep3

description: Biological replicate 3 of 3. WT a and alpha cells mixed for 4h on PDA vs. a cells on YPD for 4 hours

source_name: WT a and alpha cells, 4h, PDA


title: mouse mammary tumor [152T1]


title: a and alpha cells_PDA_12h_rep2

description: Biological replicate 2 of 3. WT a and alpha cells mixed for 12h on PDA vs. a cells on YPD for 4 hours


title: Subject 55


title: Subject 53


title: ime2Δ cells_PDA_12h_rep2

description: Biological replicate 2 of 3. ime2Δ a and alpha cells mixed for 12h on PDA vs. a cells on YPD for 4 hours


title: Subject 51


title: Steer #211 - 13.5 months


title: mouse mammary tumor [149T1]


title: a and alpha cells_PDA_4h_rep2

description: Biological replicate 2 of 3. WT a and alpha cells mixed for 4h on PDA vs. a cells on YPD for 4 hours


title: Steer #209 - 15 months


title: Steer #211 - 15 months


title: mouse mammary tumor [092T1]

description: Gene expression data from mammary tumor.


title: mouse mammary tumor [159T1]


title: ime2Δ a and alpha cells_PDA_12h_rep1

description: Biological replicate 1 of 3. ime2Δ a and alpha cells mixed for 12h on PDA vs. a cells on YPD for 4 hours


title: a and alpha cells_PDA_12h_rep1

description: Biological replicate 1 of 3. WT a and alpha cells mixed for 12h on PDA vs. a cells on YPD for 4 hours


title: a and alpha cells_PDA_0h_rep2

description: Biological replicate 2 of 3. WT a and alpha cells mixed for 0h on PDA vs. a cells on YPD for 4 hours


title: Subject 47


title: Steer #211 - 12 months


title: Steer #209 - 13.5 months


title: mouse mammary tumor [114T1]


title: mouse mammary tumor [076T1]


title: Steer #209 - 12 months


title: Subject 46


title: mouse mammary tumor [098T1]


title: Subject 44


title: a and alpha cells_PDA_0h_rep1

description: Biological replicate 1 of 3. WT a and alpha cells mixed for 0h on PDA vs. a cells on YPD for 4 hours


title: a and alpha cells_PDA_4h_rep1

description: Biological replicate 1 of 3. WT a and alpha cells mixed for 4h on PDA vs. a cells on YPD for 4 hours


title: Subject 45


title: mouse under NASH diet, biological replicate 4

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

institute: University of Regensburg

description: Gene expression data from liver of a mouse under NASH diet

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST 16-array plate consists of 16 single Gene 1.1 ST arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (Rev. 2).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: The intensities of the CEL files were normalized with the VSN algorithm (Huber, 2002) and summarized to gene expression levels based on entrez gene identifiers using the chip description file from brainarray (Dai, 2005)

source_name: liver of a 26-week old mouse fed with NASH-inducing diet

label_protocol: The Ambion WT Expression Kit Protocol (Rev. C) was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (Rev. 2).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Mini Kit, Qiagen, Hilden, Germany)

tag: treatment

value: NASH-inducing diet

value: liver

value: 26 weeks


title: mouse mammary tumor [073T2]


title: mouse mammary tumor [074T1]


title: Steer #111 - 15 months


title: mouse mammary tumor [035T1R]


title: mouse mammary tumor [010T1]


title: mouse mammary tumor [037T1]


title: Subject 43


title: Steer #111 - 13.5 months


title: Subject 41


title: Steer #111 - 12 months


title: Subject 40


title: mouse under NASH diet, biological replicate 3


title: mouse mammary tumor [025T1]


title: Subject 39


title: mouse under NASH diet, biological replicate 1


title: mouse under NASH diet, biological replicate 2


title: mouse under regular diet, biological replicate 4

description: Gene expression data from liver of a mouse under regular diet

source_name: liver of a 26-week old mouse fed with regular diet

value: regular diet


title: mouse mammary tumor [004T1]


title: mouse mammary tumor [007T1]


title: Subject 32


title: mouse mammary tumor [249T1]


title: Subject 31


title: Subject 37


title: mouse mammary tumor [247T3]


title: mouse under regular diet, biological replicate 3


title: mouse mammary tumor [247T1]


title: mouse mammary tumor [247T2]


title: Subject 27


title: MCF7 TFAP2C knockdown, technical rep 1

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

hyb_protocol: Biotin-cRNA was mixed with Illumina hybridization buffer and placed onto Illumina Human HT-12 v4 BeadChips (Part No. BD-103-0204, Illumina, San Diego, CA, USA). Hybridization was performed at 58 ºC for 17h with rocking in an Illumina Hybridization Oven (Cat# SE-901-1001, Illumina, San Diego, CA, USA). The arrays were washed, blocked, and then stained with streptavidin-Cy3 (Cat# PA43001, Amersham/GE Healthcare, Piscataway, NJ, USA) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.

scan_protocol: BeadChips were scanned with the Illumina iScan System (ID #N054, Illumina, San Diego, CA, USA).

data_processing: The data was collected and analyzed using the GenomeStudio software v2011.1 (Illumina, San Diego, CA, USA).

source_name: MCF7 cell line, TFAP2C knockdown

label_protocol: Briefly, 200 ng total RNA was converted to amplified biotin-cRNA using the Ambion TotalPrep RNA Amplification Kit (Cat# AMIL1791, Ambion, Austin, TX, USA).

growth_protocol: The MCF7 cell line was obtained from the American Type Culture Collection and grown in appropriate medium at 37 oC in a humidified 5% CO2 incubator.

extract_protocol: For RNA isolation, the mirVana Isolation kit № AM1560 (Ambion, USA) was used without enrichment. All procedures were done according to the manufacturer's protocol. All required RNA sample preparations, the subsequent hybridization and performing microarray analysis were done at the University of Iowa DNA Facility according to the manufacturer's recommended protocols.

treatment_protocol: In order to constantly knockdown TFAP2C expression in the MCF7 cell line, commercially available MISSION shRNA Lentiviral Particles based on pLKO.1-puro vector containing shRNA targeting TFAP2C (Cat# TRCN0000019745) and Non-Mammalian shRNA Control (Cat# SHC002) were used (Sigma-Aldrich, St. Louis, MO, USA).

tag: cell line

tag: shRNA


title: Subject 29


title: MCF7 TFAP2C knockdown, technical rep 3


title: Subject 33


title: mouse mammary tumor [246T1]

tag: genotype


title: mouse under regular diet, biological replicate 1


title: MCF7 TFAP2C knockdown, technical rep 2


title: MCF7 TFAP2C knockdown, rep 2


title: mouse mammary tumor [246T3]

tag: genetic background


title: mouse mammary tumor [246T2]


title: Subject 26

tag: gender


title: MCF7 TFAP2C knockdown, rep 3


title: TAX1BP1_16w_WT_mitral valves_3

city: Oita

first: Satoko

last: Nakano

address: 1-1 Idaigaoka Yufu

institute: Oita University

description: Laser capture microdissection from mitral valves of 16w WT mouse3

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Version 10.7.3.1, Agilent Technologies) with the manufacturer's recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed R statistical package ((Version 1.15.1). The strategy adopted in Agi4x44Preproces is to produce, for each set of replicated probes, a unique probe value obtained by computing the median of the intensities of the probes belonging to the replicated probe set. This has been implemented in the summarize.probe function. This function uses an RGList as an input and it produces another RGList where each set of replicated non-control probes have been collapsed into a single value.

source_name: 16w,WT,mitral valves,3

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit (Agilent Technologies).

extract_protocol: Mitral valves from 8 and 16 weeks age of male TAX1BP1-KO mice and their wild-type litter mates were collected by Arcturus XT laser capture microdissection system according to a manufacture's directions. Total RNA was purified from the mitral valves by using the RNeasy mini kit (Qiagen)

value: mitral valves

tag: background strain


title: MCF7 TFAP2C knockdown, rep 1


title: TAX1BP1_16w_WT_mitral valves_2

description: Laser capture microdissection from mitral valves of 16w WT mouse2

source_name: 16w,WT,mitral valves,2

tag: age