title: 9-cisRA 25365_1_4

city: Budapest

first: Zoltan

last: Nagy MD

state: Budapest

address: Szentkirályi str. 46.

department: 2nd Department of Medicine

country: Hungary

institute: Semmelweis University

description: Gene expression after 28 day 9-cisRA treatment

hyb_protocol: Labeled RNA was purified and hybridized to Agilent Human Gene Expression Microarray 4x44K  array slides, according to the manufacturer’s protocol.

scan_protocol: After washing, array scanning and feature extraction was performed with default scenario by Agilent DNA Microarray Scanner.

data_processing: Fluorescence intensities of spots were quantified, background subtracted, and dye normalized by Feature Extraction software, version 11.0.1 (Agilent Technologies).

label_protocol: Total RNA (200 ng) was labeled with Cy3 and amplified using Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.

extract_protocol: For the extraction of RNA Qiagen miRNeasy Kit was used according to the manufacturer's instructions.

treatment_protocol: SCID mice inoculated with H295R were treated for 28 day in four groups: I. mitotane, II. control, III, 9-cisRA, IV. combined(mitotane+9-cisRA).

value: H295R tumor

value: male


title: mitotane 25365_1_3

status: Public on Jun 07 2016

type: RNA

description: Gene expression after 28 day mitotane treatment

molecule: total RNA

organism: Mus musculus

source_name: mitotane

tag: tissue

tag: gender


title: BCR_T99_Probe35

city: Regensburg

first: Christian

middle: W

last: Kohler

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

scan_protocol: not provided

data_processing: Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260). Expression values of multiple probeIDs targeting the same gene where summarized into a single representative value by fitting a standard additive model using Tukey’s median polish procedure.

label: biotin

organism: Homo sapiens

label_protocol: cDNA was synthesized using 1 μg corresponding RNA and including Poly-A RNA controls with the help of the Affymetrix GeneChip® Poly-A RNA control Kit. Secondly, cRNA synthesis and cleanup was carried out using the Affymetrix GeneChip® IVT Labelling Kit. Subsequently, fragmentation and labeling for microarray hybridization was accomplished with the corresponding kits according to manufacturer’s instructions.

growth_protocol: 1x10^6 fresh CD10+ B cells were resuspended in RPMI 1640 (GIBCO, Paisley UK), 100 U/ml penicillin, 100 μg/ml streptomycin (Sigma-Aldrich, Dorset UK), 10 μg/ml ciprofloxacin (Bayer, Newbury UK) + 10% (v/v) FBS (Sigma-Aldrich, Dorset UK)

extract_protocol: Cells were harvested (10 min, 300 x g, 4°C) and washed with PBS containing 100 mM sodium orthovanadate. Samples were frozen at -80°C. RNA was isolated with the RNeasy Kit (Qiagen) for microarray analyses or with the NucleoSpin® RNA II Kit (Macherey-Nagel, Düren Germany)

treatment_protocol: In order to stimulate the cells, they were counted, centrifuged at 250 x g, 7 min and resuspended in fresh corresponding medium supplied with 10 mM Hepes (1x106 cells/ml) and supplemented with sCD40L (200ng/ml), anti human IgM/IgG F(ab)2 (13μg/ml), rhIL21 (100ng/ml), rhBAFF (100ng/ml and 200ng/ml) or LPS (1μM). Cells were incubated at 37°C, 5% CO2 for 3hrs for microarray analyses.

tag: experiment

value: BCR

tag: cell type

value: CD10+ B cells

value: faucial tonsil


title: O-7111525 (met)

type: genomic

city: Madrid

first: Silvana

last: Mouron

state: Madrid

address: Calle Melchor Fdez Almagro

department: Clinical Research

country: Spain

institute: CNIO

hyb_protocol: According to protocol, CGH arrays where hybrizdized 24 hours, at 65ºC and 20 rpm

scan_protocol: Agilent G2565CA scanner was used to scan slides at 3um resolution for both Cy5 and Cy3 channels

data_processing: Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench v5.0 (Agilent Technologies). CNA regions were detected using the ADM-2 (set as 6) statistic provided by DNA Analytics, with a minimum number of 10 consecutive probes. The segmentation process was carried out using the dnacopy Bioconductor package. Bioconductor´s CGHcall package was employed for determining the step, and CGHregions and CGHtest packages were used to estimate genomic regions and false discovery rate, respectively.

molecule: genomic DNA

source_name: Epithelial tissue (breast cancer)

label_protocol: Labeling protocol was done according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, ULS labeling for FFPE sections v3.2 (G4410-90020)

extract_protocol: 10um tissue sections were deparaffined using heated Xylol and rehidratation was conducted with subsequent lowered EtOH (00%,80%, 50%, H20). Tissue was then treated with sodium thiocyanate. DNA then was extracted with DNA was extracted a tissue protocol from Qiagen Dneasy blood and tissue kit, using EtOH 80% instead of Wash Buffer 2 (according to ULS protocols)

tag: disease state

value: HRPBC

tag: tumor pair

value: O

tag: tumor state

value: Metastasis

tag: age

tag: Sex

value: Female

source_name: reference

tag: reference

value: PROMEGA CONTROL DNA

value: Male


title: M-7111521 (met)

value: M


title: L-071100401-2 (prim)

value: L

value: Primary Tumor


title: L-7111494 (met)


title: M-71200066 (prim)


title: control 25364_1_3

description: Gene expression after 28 day control corn oil treatment

source_name: control


title: 9-cisRA 25364_1_4


title: combined 25364_1_2

description: Gene expression after 28 day mitotane+9cisRA treatment

source_name: combined


title: combined 25365_1_1


title: K-7111492 (met)

value: K


title: mitotane 25364_1_1


title: K-7111493 (prim)


title: 9-cisRA 25363_1_4


title: prostate_cancer_biopsy_sample_15

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathological re-review by an expert genitourinary pathologist, tumor was macrodissected from surrounding stroma from 3–4 10 µm tissue sections from a region with maximum tumor content for total RNA extraction.

treatment_protocol: Not Applicable

tag: gs

tag: psa

tag: t-category

value: prostate biopsy


title: control 25365_1_2


title: J-7111490 (met)

value: J


title: Mb1 Infected monocytes BioRep3

type: protein

city: Saskatoon

first: Erin

last: Scruten

state: Saskatchewan

address: 120 Veterinary Road

institute: VIDO-Intervac

scan_protocol: Arrays were read using a GenePix Professional 4200A microarray scanner at 532-560 nm with a 580 nm filter to detect dye fluorescence.  Images were collected using the GenePix 6.0 software and the spot intensity signal collected as the mean of pixel intensity using local feature background intensity background calculation with the default scanner saturation level.

data_processing: Foreground signal mean of pixel intensity.  Background intensity for each spot as the average of pixels from four regions in the immediate vicinity of each spot.  Perform global normalization to the 50th percentile on the raw data, using GeneSpring software.  Evaluate reproducibility of the signal by comparing peptide signals to a baseline value of 1 for the normalized data from the replicates, using a sample t test.

label: Green fluorescence

molecule: protein

organism: Bos taurus

source_name: Bovine monocytes infected with Mb1

label_protocol: Slides were submerged in phospho-specific fluorescent ProQ Diamond Phosphoprotein Stain with agitation for 1 hour.  Arrays were then washed three times in destain containing 20% acetonitrile and 50 mM sodium acetate at pH 4.0 for 10 minutes.  A final wash was done with distilled deionized water.

growth_protocol: Blood samples (300 ml from each animal) were obtained from 6 clinically healthy animals with no history of M. bovis infection. Buffy coat fraction (containing PBMC) was purified by Ficoll gradients (GE Healthcare, Mississauga, ON, Canada) as described by (11).   Magnetic activated cells sorting (MACS) was used to purify monocytes (CD14+ cells) by direct labeling with mouse monoclonal anti human CD14 microbeads (Miltenyi Biotec, Gladbach, Germany) and positive selection through an LS column (Miltenyi) according to the instructions of the manufacturer.  Briefly, purified PBMC were enumerated using a coulter counter and viability was determined by trypan-blue exclusion.  PBMC were suspended to a cell density of 1.25 x108/ml in MACS buffer [(0.5% bovine serum albumin, 2mM EDTA in phosphate buffered saline (PBS)] and 2.4 ml was dispensed into each tube.  To each tube, 300µl of mouse anti-human CD14 microbeads and tubes were placed at 4oC for 15 min before three-fold washing with 40 ml of ice-cold MACS buffer by centrifugation at 300 x g for 8 min.  Cells in each tube were suspended in 3 ml of MACS buffer and passed through an LS column mounted to a magnetic field.  The column was washed three times with 10 ml MACS buffer and bound cells were eluted by filling the column with 5 ml of MACS buffer forcing the cells down the column after removal from the magnetic field.  The purity of monocytes was confirmed by staining with goat anti-mouse IgG2a antibody conjugated to FITC and analysis using flow cytometry.  Typically, a purity of ≥ 97% was achieved for each sample.  For all subsequent assays unless otherwise stated, each well of a 6-well flat bottom plate (Costar, Corning, NY) was seeded with 5x106 monocytes and left overnight at 37oC in a humidified incubator containing 5%CO2 before infection with 2.5x107 bacteria (multiplicity of infection MOI 5:1).

extract_protocol: Cellular lysates were prepared in lysis buffer containing 20mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1 mM sodium fluoride, 1 mM sodium orthovanadate, 2.5 mM sodium pyrophosphate, protease inhibitor cocktail (Sigma-Aldrich) and 1% (v/v) Triton-X 100.

treatment_protocol: Bovine monocytes were rested overnight and then infected with the Mycoplasma bovis strain, Mb1 for 18 hours.

value: Bovine monocytes

tag: infection


title: control 25363_1_3

value: H295R tumor

value: male


title: J-7111491 (prim)


title: Monocytes alone BioRep3

source_name: Bovine monocytes


title: mitotane 25363_1_2


title: Mb1 Infected monocytes BioRep2


title: prostate_cancer_biopsy_sample_13


title: E-7111483 (prim)

value: E


title: prostate_cancer_biopsy_sample_5


title: 9-cisRA 25362_1_4


title: Mb1 Infected monocytes BioRep1


title: E-7111482 (met)


title: control 25362_1_3


title: combined 25363_1_1


title: C-7110391 (prim)

value: C


title: C-7111479 (met)

value: HRPBC


title: prostate_cancer_biopsy_sample_11


title: prostate_cancer_biopsy_sample_16


title: prostate_cancer_biopsy_sample_8


title: prostate_cancer_biopsy_sample_12


title: prostate_cancer_biopsy_sample_14


title: prostate_cancer_biopsy_sample_6


title: prostate_cancer_biopsy_sample_9


title: Monocytes alone Bio Rep1


title: prostate_cancer_biopsy_sample_10


title: combined 25362_1_2


title: prostate_cancer_biopsy_sample_7


title: prostate_cancer_biopsy_sample_4


title: A-7111475 (prim)

value: A


title: prostate_cancer_biopsy_sample_2


title: mitotane 25362_1_1


title: A-7111476 (met)

value: Metastasis


title: prostate_cancer_biopsy_sample_3


title: Monocytes alone BioRep2


title: SUM149_DAC

status: Public on Jun 06 2016

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: PO Box 15000

department: Pathology

institute: Dalhousie University

description: SUM149 DAC

hyb_protocol: standard Illumina protocol

scan_protocol: scanned according to Illumina protocols on iScan

data_processing:
Illumina GenomeStudio default settings
The non_normalized.txt contain unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: breast cancer cell line SUM149 decitabine-treated

label_protocol: standard Illumina protocol

growth_protocol: as described in Materials & Methods

extract_protocol: genomic DNA extracted with Invitrogen PureLink mini kit

treatment_protocol: for DAC (5-Aza-2'-deoxycytidine; decitabine) treatment, 1 uM DAC over 72 hours

tag: sample type

value: cell line

tag: cell line

value: breast cancer cell line

tag: subtype

value: basal-like

tag: treated with

value: 1 uM DAC over 72 hours


title: SUM1315_DAC

description: SUM1315 DAC

source_name: breast cancer cell line SUM1315 decitabine-treated

value: claudin-low


title: SUM159_NT

description: SUM159 NT

source_name: breast cancer cell line SUM159

value: none (NT)


title: MDA-MB-468_NT

source_name: breast cancer cell line MDA-MB-468


title: HCC70_NT

source_name: breast cancer cell line HCC70


title: prostate_cancer_biopsy_sample_1

tag: tissue


title: T47D_NT

source_name: breast cancer cell line T47D

value: luminal


title: SUM1315_NT

description: SUM1315 NT

source_name: breast cancer cell line SUM1315


title: SUM159_DAC

description: SUM159 DAC

source_name: breast cancer cell line SUM159 decitabine-treated


title: HCC1806_NT

description: HCC1806 NT

source_name: breast cancer cell line HCC1806


title: MDA-MB-453_NT

description: MDA-MB-453 NT

source_name: breast cancer cell line MDA-MB-453


title: MCF7_NT

source_name: breast cancer cell line MCF7


title: MCF10A_NT

source_name: normal breast cell line MCF10A

value: normal


title: MDA-MB-157

source_name: breast cancer cell line MDA-MB-157


title: HCC38_NT

source_name: breast cancer cell line HCC38


title: p3.2_patient

description: p3.2 patient

source_name: patient xenograft 3.2

value: patient xenograft

value: unknown


title: HCC1937_NT

description: HCC1937 NT

source_name: breast cancer cell line HCC1937


title: p45_patient

description: p45 patient

source_name: patient xenograft 45


title: MDA-MB-436_DAC

description: MDA-MB-436 DAC

source_name: breast cancer cell line MDA-MB-436 decitabine-treated


title: MDA-MB-436_NT

description: MDA-MB 436 NT

source_name: breast cancer cell line MDA-MB-436


title: Secondary antibody control anti-V5

city: München

first: Simone M.

last: Braendle

address: Marchioninistr. 15

institute: LMU München

description: secondary antibody control

hyb_protocol: see manufacturer's homepage

scan_protocol: Microarrays were scanned with the GenePix 4000B Scanner (Axon Instruments) at 635 nm wavelength using PMT700 and analyzed with the ProtoArray Prospector 5.2.1 program (LifeTechnologies).

data_processing: Signal intensities were compared to the mean signal intensity of the array and to the respective signal intensities produced by the isotype control (r8-18C5) and the secondary antibody control. Signals were considered positive if enriched five times compared to the mean array signal and three times compared to the isotype and secondary antibody control. Only duplicate signals were considered. In case of MS2-s5, only signals identified as "Hits" by the Prospector software were considered.

source_name: Secondary antibody control anti-V5

label_protocol: Not provided

value: Secondary antibody control anti-V5


title: Hs578Bst_NT

source_name: normal breast cell line Hs578Bst


title: Hs578T_DAC

description: Hs578T DAC

source_name: breast cancer cell line Hs578T decitabine-treated


title: SUM149_NT

description: SUM149 NT

source_name: breast cancer cell line SUM149


title: isotype control antibody 8-18C5

description: Isotype control with the humanized, recombinant 8-18C5 antibody

source_name: isotype control antibody 8-18C5

value: isotype control antibody 8-18C5


title: HCC1937_DAC

description: HCC1937 DAC

source_name: breast cancer cell line HCC1937 decitabine-treated


title: monoclonal antibody MS2-s5

description: Arrays were incubated with an OCB-derived monoclonal antibody obtained from CSF of a MS-patient.

source_name: OCB-derived monoclonal antibody from subject MS2

value: CSF

tag: patient

value: 24 years

value: Female

tag: diagnosis

value: MS


title: SKBR3_NT

source_name: breast cancer cell line SKBR3

tag: cell type


title: Hs578T_NT

description: Hs578T NT

source_name: breast cancer cell line Hs578T


title: HCC1599_NT

source_name: breast cancer cell line HCC1599


title: monoclonal antibody MS4

source_name: OCB-derived monoclonal antibody from subject MS4

value: 32 years

value: Male


title: monoclonal antibody MS1-s9

source_name: OCB-derived monoclonal antibody from subject MS1

value: 34 years


title: MDA-MB-231

source_name: breast cancer cell line MDA-MB-231

value: cell line

value: breast cancer cell line


title: monoclonal antibody MS1-s8


title: monoclonal antibody MS3-s1

source_name: OCB-derived monoclonal antibody from subject MS3


title: HCC1806_DAC

description: HCC1806 DAC

source_name: breast cancer cell line HCC1806 decitabine-treated

value: basal-like

value: 1 uM DAC over 72 hours


title: Peritoneal_macrophage_H8_at_0h_biological replicate_3

city: Edinburgh

first: Anna

middle: Eleonora

last: Karagianni

address: Easter Bush Campus

country: United Kingdom

institute: The Royal (Dick) School of Veterinary Studies and The Roslin Institute

description: Gene expression data from untreated peritoneal macrophages

hyb_protocol: Biotin labelled transcripts were prepared for hybridisation following the Nugen protocol for Gene Titan hybridisation (Affymetrix, Santa Clara, CA), using the Affymetrix Gene Titan Hybridization Wash and Stain Kit for WT Array Plates (PN 901622). The samples were hybridised to Equine Gene 1.1 and 1.0 ST Array Strips from Affymetrix, including 30,559 probe sets.

scan_protocol: The appropriate Hyb-Wash Scan protocol and the Gene Titan Hyb-Wash Stain Kit for the reagents (Affymetrix, Santa Clara, CA) was performed

data_processing: The data were analyzed with Partek Genomic Suite 6.6 and BioLayout Express3D softwares and  using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Equus caballus

source_name: Untreated peritoneal macrophages

label_protocol: Total RNA (50ng) was amplified by the Nugen Pico SL kit (Agilent, the Netherlands). Two and a half micrograms (2.5μg) of the cDNA produced was biotin labelled using the Nugen Encore labelling kit.

growth_protocol: Macrophages were isolated from the lungs and the peritoneal cavity from systemically healthy horses after euthanasia following  two separate protocols

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

treatment_protocol: Isolated cells from the bronchoalveolar and peritoneal lavage were seeded in plastic plates at 1x106 cells per mL in complete medium: RPMI-1640 medium supplemented with GlutaMAX™-I Supplement (Invitrogen Ltd, Paisley, UK), penicillin/streptomycin (Invitrogen Ltd, Paisley, UK) and 10% heat-inactivated horse serum (HS - Sigma Aldrich, cat no: H1138). Plates were incubated at 370C in 5% CO2 overnight. The following day, nonadherent cells were removed. New complete medium was added and adherent cells were stimulated with Lipopolysaccharide (100ng/mL) from Salmonella enterica serotype Minnesota Re 595 (L9764, Sigma-Aldrich, USA) and incubated for 6h.

tag: macrophage type

value: Peritoneal macrophage

tag: treatment

value: Untreated


title: Alveolar_macrophage_H3_at_6h_biological replicate_3

description: Gene expression data from Lipopolysaccharide alveolar macrophages

source_name: 6h Lipopolysaccharide treated alveolar macrophages

value: Alveolar macrophage

value: 6h Lipopolysaccharide treatment


title: [6411_28 / 5_125 cy5]-[8639_28 / 4_125 cy3]

city: Urbana

first: Mario

middle: Pietro Emilio

last: Vailati Riboni

state: IL

address: 1207 W Gregory Dr

department: Animal Science

country: USA

institute: University of Illinois at Urbana-Champaign

description: Sample were total RNA extracted from bovine (American Holstein) liver biopsy tissue

hyb_protocol: The labeled cRNA was fragmented and then hybridized to the microarray slide according to manufacturer’s protocol. Briefly, 825 ng of Cy3 and Cy5 labeled cRNA sample were combined, mixed with 11 μL of 10× Blocking Agent (Agilent Technologies Inc.), 2.2 μL of 25× Fragmentation Buffer (Agilent Technologies Inc.), and nuclease-free water (to a final volume of 55 μL); and then fragmented at 60°C for 30 s. The reaction was then stopped by adding 55 μL of 2× GEx Hybridization Buffer (Agilent Technologies Inc.), and the samples were loaded onto the slide. These were hybridized in a rotating hybridization oven (Agilent Technologies Inc.) at 65°C for 17 h.

scan_protocol: The slides were washed according to the manufacturer’s recommended procedures and scanned using a GenePix 4000B scanner (Axon Instruments Inc., Sunnyvale, CA) and GenePix Pro v.6.1 software. Resulting spots where features were substandard were flagged as bad and excluded from subsequent analysis.

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 30 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

source_name: Liver Biopsy

label_protocol: The Agilent platform was chosen to conduct the microarray experiment, using the 44K Bovine (V2) gene expression microarray chip (Agilent Technologies Inc.), following the manufacturer’s protocols. Briefly, a total of 200 ng of RNA per sample were used to generate first-strand cDNA, which was reverse transcribed to cRNA using the low-input quick amp labeling kit (Agilent Technologies Inc). The resulting cRNA was labeled with either Cy3 or Cy5 fluorescent dye, purified using RNeasy mini spin columns (Qiagen), and subsequently eluted in 30 μL of DNase-RNase-free water. The NanoDrop ND-1000 (Thermo Fisher Scientific Inc., Waltham, MA) was used to confirm the manufacturer’s recommended criteria for yield and specific activity of at least 0.825 μg and ≥6.

growth_protocol: Grazing dairy cows were managed through the dry period, untill 30 days post partum

extract_protocol: Liver tissue (30-50 mg) was homogenized in a TissueLyser II (Qiagen GmbH) for 2 × 2 min bursts at 30 Htz. Total RNA and DNA were extracted using a Qiagen AllPrep DNA/RNA mini kit (Qiagen GmbH) as per manufacturer’s instructions and RNA was treated with DNase (Ambion DNA-free kit; Ambion Inc., Austin, TX). The RNA quantity, purity, and integrity were determined using a NanoDrop ND-1000 (NanoDrop Technologies Inc., Wilmington, DE) and the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Average RNA Integrity Number (RIN) for samples at -7, 7, and 28 d relative to parturition were 8.18 (± 0.39), 7.77 (± 0.43), and 8.17 (± 0.45), respectively. RNA samples were stored at -80 °C until analysis.

treatment_protocol: Approximately 200 days before calving, cows were allocated randomly to one of six treatment groups in a 2 x 3 factorial arrangement: two pre-calving BCS categories (4.0 and 5.0; based on a 10-point scale: BCS4 and BCS5, respectively) and three levels of energy intake during the three wk preceding calving (75, 100, and 125% of estimated requirements). Cows in the BCS4 and BCS5 groups were managed through late lactation to ensure target calving BCS was achieved at dry off. Cows were then maintained until three wk before expected calving date, at which point they were managed within their pre-allotted pre-calving energy intake treatments by offering different allowances of fresh pasture/cow per day.

value: Liver

tag: bcs

tag: feeding (%)

tag: sampling time (days from parturition)


title: [3298_28 / 5_75 cy3]-[656_28 / 5_125 cy5]


title: [210_28 / 5_75 cy3]-[2303_28 / 4_125 cy5]


title: HCC1187_DAC

description: HCC1187 DAC

source_name: breast cancer cell line HCC1187 decitabine-treated


title: Peritoneal_macrophage_H7_at_0h_biological replicate_2


title: [5544_28 / 5_75 cy5]-[649_28 / 5_125 cy3]


title: Alveolar_macrophage_H4_at_6h_biological replicate_4


title: Peritoneal_macrophage_H6_at_0h_biological replicate_1


title: [7259_28 / 5_125 cy3]-[8669_28 / 4_125 cy5]


title: [652_28 / 5_75 cy5]-[9277_28 / 4_125 cy3]


title: HCC1395_NT

source_name: breast cancer cell line  HCC1395

value: claudin-low

value: none (NT)


title: [9240_28 / 4_75 cy3]-[9276_28 / 4_125 cy5]


title: HCC1187_NT

description: HCC1187 NT

source_name: breast cancer cell line HCC1187


title: DU4475_NT

source_name: breast cancer cell line Du4475

value: other


title: HCC1143_NT

source_name: breast cancer cell line HCC1143


title: [9262_28 / 4_75 cy5]-[9272_28 / 4_125 cy3]


title: Alveolar_macrophage_H1_at_6h_biological replicate_1


title: BT549_NT

source_name: breast cancer cell line BT549


title: BT20_NT

source_name: breast cancer cell line BT20


title: Alveolar_macrophage_H5_at_0h_biological replicate_5

description: Gene expression data from untreated alveolar macrophages

source_name: Untreated alveolar macrophages


title: Alveolar_macrophage_H4_at_0h_biological replicate_4


title: [7658_28 / 4_75 cy5]-[7671_28 / 5_75 cy3]


title: Alveolar_macrophage_H2_at_6h_biological replicate_2


title: Alveolar_macrophage_H5_at_6h_biological replicate_5


title: Alveolar_macrophage_H3_at_0h_biological replicate_3


title: Normal Control 6

city: Chicago

first: Dong

last: Xu

address: 2430 N. Halsted St.

institute: Ann & Robert H. Lurie Children's Hospital of Chicago Research Center

description: raw data files 1_ is Hy3 0_ is Hy5

hyb_protocol: Labeled samples were hybridized on the miRCURY LNA™ microRNA Array (6'th GEN) using Tecan hybridization stations.  The hybridization and washing steps are fully automated for excellent reproducibility.

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image analysis is then performed to quantify the signals on the array.

data_processing:
Before proceeding with data normalization a technical quality assessment is performed based on results from spike in controls, flagging of spots, background intensity levels and signal intensity distribution. The data obtained is normalized using methods applicable to the performed experiment. Following normalization of the quantified signals (background corrected) using the global Lowess regression algorithm, an unsupervised as well as supervised data analysis was performed
normalized data (normalized using relevant method). Data is separated in three sheets as outlined below: G: log2transformed normalized median intensity values (Hy3) M: log2transformed median ratios. This sheet is only included for Lowess normalized data. R: log2transformed normalized median intensity values (Hy5)
ThresholdFilteredData– includes the log2transformed normalized intensity values (Hy3) from the full dataset (in norm.xlsx) that are detected above background.  Data that are below the set threshold were omitted.

label: Hy3 and Hy5

source_name: Skeletal muscle

label_protocol: The total RNA from each sample was subjected RNA quality control in order to assess the integrity of the RNA.  Total RNA  from each sample was labeled with both Hy3 and Hy5 using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™.

extract_protocol: Skeletal muscle biopsy tissue from children with JDM and healthy controls was snap frozen and stored in liquide nitrogen. Total RNA was extracted from snap-freezing muscle tissue using the miRCURY RNA isolation kit from Exiqon according to the manufacturer’s protocol.

tag: race

value: White

tag: gender

tag: age at sample (y)

tag: disease state

value: normal control

value: skeletal muscle


title: Normal Control 5

description: raw data files 1_ is Hy3 0_ is Hy5

value: Male


title: Light-induced mycelia vs dark-grown mycelia Replicate 3

city: Murcia

first: Victoriano

last: Garre

state: Murcia

address: Facultad de Biología. Campus de Espinardo

department: Genetics and Microbiology

institute: University of Murcia

hyb_protocol: Microarrays where hybridized and washed according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

organism: Mucor circinelloides

source_name: R7BD C

label_protocol: Two-color Microarray-Based Gene Expression (Low input Quick-amp Labelling kit, Agilent)

growth_protocol: 250,000 spores per 9-cm petri dish were inoculated on solid YNB medium (pH 4.5) with a cellophane sheet and incubated for 18 days in the dark at 26ºC.

extract_protocol: Mycelia were ground to a fine powder using mortar and pestle in the presence of liquid nitrogen. Total RNA was isolation from 50-100 mg of ground mycelium using RNeasy RNA isolation kit (Qiagen) following supplier’s protocol

treatment_protocol: 20 min with with light (4.8 W m-2)

tag: strain

value: leuA mutant, wild-type for ligh responses

tag: condition

value: dark-grown mycelia

source_name: R7BL C

value: ligh-induced mycelia


title: Light-induced mycelia vs dark-grown mycelia Replicate 2

source_name: R7BL B

source_name: R7BO B


title: [5950_28 / 4_75 cy3]-[7258_28 / 5_125 cy5]


title: [3940_28 / 4_75 cy5]-[8616_28 / 5_125 cy3]


title: Alveolar_macrophage_H2_at_0h_biological replicate_2


title: inguinal fat_DIO_rep1

city: Nanjing

first: Jianghuan

last: Zou

state: Jiangsu

address: Xuefu Road 12

department: MARC

country: China

institute: Nanjing University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4858A-028005) for 17 hours at 65°C and 10 rpm in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent). The wash buffers contained 0.005% Triton X-102.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100617) to obtain background subtracted and spatially detrended green Processed Signal intensities.Normalized signal intensity (log2 transformed and quantile normalized) calculated from the green processed signal after Feature Extraction using the GeneSpring software version 11.0 (Agilent)

source_name: inguinal fat, DIO, replicate 1

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

growth_protocol: Adult male C57BL/6J mice were kept under 12 hr light/12 hr dark in specific pathogen-free room for 1 week to adapt to the housing condition. They were fed regular diet (6%, Xietong Organism) or high fat diet (60% fat, Research Diets) with free access to water and food. All animal experiments were approved by the Institutional Animal Care and Use Committees at MARC.

extract_protocol: RNA was extracted from inguinal fat using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 2-months-old male C57BL/6J mice were divided into diet-induced-obesity group (DIO) and control group (CTR). DIO mice were fed high fat diet (HFD, 60% energy from fat) ad lib for 1 month and then subjected to calorie restriction (CR) until they reached the equal body weight as chow diet-fed even-aged CTR mice, which took about three weeks. Both groups then were fed HFD ad lib, namely weight regain period (WR). At end of WR, inguinal fat of both groups were isolated for this microarray.

tag: tissuse

value: inguinal fat

value: male

tag: age


title: inguinal fat_DIO_CR_WR_rep1

source_name: inguinal fat, DIO, CR, WR, replicate 1


title: [6007_28 / 5_75 cy5]-[7202_28 / 4_75 cy3]

tag: tissue


title: inguinal fat_DIO_CR_WR_rep3

source_name: inguinal fat, DIO, CR, WR, replicate 3


title: inguinal fat_DIO_CR_WR_rep2

source_name: inguinal fat, DIO, CR, WR, replicate 2


title: Light-induced mycelia vs dark-grown mycelia Replicate 1

source_name: R7BL A

source_name: R7BO A


title: [9263_28 / 5_125 cy3]-[9658_7 / 5_125 cy5]

source_name: Liver Biopsy


title: inguinal fat_DIO_rep2

source_name: inguinal fat, DIO, replicate 2


title: Alveolar_macrophage_H1_at_0h_biological replicate_1


title: Normal Control 4

description: raw data files 1_ is Hy3 0_ is Hy5


title: Normal Control 2

description: raw data files 1_ is Hy3 0_ is Hy5

value: Female


title: Normal Control 3

description: raw data files 1_ is Hy3 0_ is Hy5


title: BT474_NT

source_name: breast cancer cell line BT474

tag: sample type

value: cell line

tag: cell line

value: breast cancer cell line

tag: subtype

tag: treated with


title: [7230_28 / 5_75 cy3]-[7602_7 / 5_75 cy5]


title: prostate_cancer_biopsy_sample_17

source_name: FFPE prostate cancer

tag: gs

tag: psa

tag: t-category

value: prostate biopsy


title: monoclonal antibody MS1-s2

source_name: OCB-derived monoclonal antibody from subject MS1

value: CSF

tag: patient

value: 34 years

tag: Sex

tag: diagnosis

value: MS


title: Normal Control 1

description: raw data files 1_ is Hy3 0_ is Hy5

tag: race

tag: gender

tag: age at sample (y)


title: JDM 17

description: raw data files 1_ is Hy3 0_ is Hy5

tag: disease state

value: Juvenile Dermatomyositis (JDM)


title: BMDM_GPS2KO_rep2

city: Huddinge

first: Eckardt

last: Treuter

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

description: Unstimulated Macrophage GPS2 KO BMDM

hyb_protocol: The hybridization was performed in Karolinska Institute, BEA core facility (http://www.bea.ki.se/) on the affymetrix gene ST 1.1 chip.

scan_protocol: The scanning was performed in Karolinska Institute, BEA core facility (http://www.bea.ki.se/).

data_processing:
CEL files were background subtracted, quantile normalized and summarized (Core level via median polish) using the RMA function (Robust Multichip Average) from the Oligo package in R/Bioconductor. Annotation via the getNetAffx function and pd.mogene.1.1.st.v1.
probe group file: pd.mogene.1.1.st.v1
meta-probeset file: pd.mogene.1.1.st.v1

source_name: Bone marrow derived macrophage

label_protocol: The labelling was performed in Karolinska Institute, BEA core facility (http://www.bea.ki.se/).

growth_protocol: The WT or GPS2 MKO mice were sacrificed at around 12-16 weeks age. The tibia and femur were isolated and washed in DPBS (without Ca2+). The bone marrow cells were collected by flushing the bone marrow with DPBS using a syringe.The cells were than filtered through 70 μm cell strainer and centrifuged at 1200 rpm for 10 minutes. The cells were then differentiated in DMEM containing 10% heat  inactivated FBS, 1% penicillin/streptomycin and 30% L929 conditional medium. The medium was changed every three days and the differentiation continues for 7 days.

extract_protocol: RNA was extracted using a QIAGEN RNA extraction kit according to the manufecture instructions.

treatment_protocol: The cells were not treated.

tag: genotype/variation


title: BMDM_GPS2KO_rep3

description: Unstimulated Macrophage GPS2 KO BMDM


title: JDM 18

description: raw data files 1_ is Hy3 0_ is Hy5

source_name: Skeletal muscle

value: Hispanic


title: JDM 16

description: raw data files 1_ is Hy3 0_ is Hy5

value: White


title: BMDM_WT_rep2

description: Unstimulated wild type BMDM

value: wild type


title: [5544_7 / 5_75 cy3]-[649_7 / 5_125 cy5]

value: Liver

tag: bcs

tag: feeding (%)

tag: sampling time (days from parturition)


title: [652_7 / 5_75 cy3]-[9277_7 / 4_125 cy5]

tag: tissue


title: BMDM_GPS2KO_rep1

description: Unstimulated Macrophage GPS2 KO BMDM

value: Male


title: JDM 15

description: raw data files 1_ is Hy3 0_ is Hy5

value: skeletal muscle


title: [210_7 / 5_75 cy5]-[2303_7 / 4_125 cy3]


title: [3298_7 / 5_75 cy5]-[656_7 / 5_125 cy3]


title: JDM 14

description: raw data files 1_ is Hy3 0_ is Hy5


title: JDM 13

description: raw data files 1_ is Hy3 0_ is Hy5


title: [7259_7 / 5_125 cy5]-[8669_7 / 4_125 cy3]


title: [6411_7 / 5_125 cy3]-[8639_7 / 4_125 cy5]


title: inguinal fat_DIO_rep3

source_name: inguinal fat, DIO, replicate 3

tag: strain

tag: tissuse

tag: age


title: Cyp1b1/Cyp1a1-null, BP-treated, 12 hour, bone marrow replicate 1

city: Madison

first: Colin

last: Jefcoate

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: UW-Madison

description:
9 samples pooled
DKO BP 12h 86

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17 hours, 65 degrees celcius, Surehyb chamber

scan_protocol: Slides are scanned on an Agilent DNA Microarray Scanner, model G2505B

data_processing: EDGE3 software (Mol. Pharm. Vol. 67, No. 4, 2005) was used to perform a limma analysis of the data.

label_protocol: Total RNA was amplified and labeled according to manufacturers' instructions. Agilent Two-color Microarray-based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Mice were housed in a AAALAC accreditated facility with 12hr light cycle and temperature control, food and water ad libitum.

extract_protocol: Total RNA was isolated using a Qiagen RNA easy isolation kit as described by the manufacturer.

treatment_protocol: Female mice (6 weeks old) were treated with the olive oil, benzo(a)pyrene (BP), 7,12-dimethylbenz(a)anthracene (DMBA) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) via intra-peritoneal injection (50 mg/kg). Mice were euthanized and bone marrow collected 6h or 12h post-treatment, as indicated.

value: 6 weeks

tag: agent

value: BP

tag: time

value: 12 hours

value: bone marrow

source_name: Pooled wild type C57BL/6j oil-treated bone marrow

value: Wild type

value: oil


title: Cyp1b1/Cyp1a1-null, oil-treated control, bone marrow replicate 1

description:
9 samples pooled
DKO Control 85

value: Female

value: control


title: BMDM_WT_rep3

description: Unstimulated wild type BMDM


title: JDM 12

description: raw data files 1_ is Hy3 0_ is Hy5


title: Cyp1b1/Cyp1a1-null, BP-treated, 12 hour, bone marrow replicate 2

description:
9 samples pooled
DKO BP 12h 87


title: Cyp1a1-null, BP-treated,  12 hour, bone marrow replicate 3

description:
9 samples pooled
1a1-ko BP 12h 97


title: JDM 11

description: raw data files 1_ is Hy3 0_ is Hy5


title: Cyp1a1-null, BP-treated,  12 hour, bone marrow replicate 2

description:
9 samples pooled
1a1-ko BP 12h 27


title: JDM 10

description: raw data files 1_ is Hy3 0_ is Hy5


title: BMDM_WT_rep1

description: Unstimulated wild type BMDM


title: JDM 9

description: raw data files 1_ is Hy3 0_ is Hy5


title: JDM 8

description: raw data files 1_ is Hy3 0_ is Hy5


title: [8209_7 / 4_125 cy3]-[8620_28 / 4_125 cy5]


title: [9240_7 / 4_75 cy5]-[9276_7 / 4_125 cy3]


title: [3940_7 / 4_75 cy3]-[8616_7 / 5_125 cy5]


title: [6007_7 / 5_75 cy3]-[7202_7 / 4_75 cy5]


title: [9262_7 / 4_75 cy3]-[9272_7 / 4_125 cy5]


title: [7658_7 / 4_75 cy3]-[7671_7 / 5_75 cy5]


title: [5950_7 / 4_75 cy5]-[7258_7 / 5_125 cy3]


title: Cyp1a1-null, BP-treated,  12 hour, bone marrow replicate 1

description:
9 samples pooled
1a1-ko BP 12h 26


title: Cyp1b1-null, DMBA-treated, 12 hour , bone marrow replicate 2

description:
9 samples pooled
1b1-ko DMBA 12h 71

value: DMBA


title: Cyp1a1-null, oil-treated control, bone marrow replicate 3

description:
9 samples pooled
1a1-ko Control 96


title: JDM 6

description: raw data files 1_ is Hy3 0_ is Hy5


title: JDM 5

description: raw data files 1_ is Hy3 0_ is Hy5


title: JDM 7

description: raw data files 1_ is Hy3 0_ is Hy5


title: Cyp1a1-null, oil-treated control, bone marrow replicate 2

description:
9 samples pooled
1a1-ko Control 95


title: Cyp1b1-null, DMBA-treated, 12 hour , bone marrow replicate 1

description:
9 samples pooled
1b1-ko DMBA 12h 70


title: JDM 4

description: raw data files 1_ is Hy3 0_ is Hy5


title: [203_7 / 4_75 cy3]-[3250_28 / 4_75 cy5]


title: Cyp1a1-null, oil-treated control, bone marrow replicate 1

description:
9 samples pooled
1a1-ko Control 94


title: JDM 3

description: raw data files 1_ is Hy3 0_ is Hy5

value: Asian


title: Cyp1b1-null, oil treated control, bone marrow replicate 1

description:
9 samples pooled
1b1-ko Control 72


title: [9263_-7 / 5_125 cy3]-[9658_28 / 5_125 cy5]


title: [7230_-7 / 5_75 cy3]-[7602_28 / 5_75 cy5]


title: JDM 2

description: raw data files 1_ is Hy3 0_ is Hy5

value: Juvenile Dermatomyositis (JDM)


title: Cyp1b1-null, oil treated control, bone marrow replicate 2

description:
9 samples pooled
1b1-ko Control 73


title: JDM 1

description: raw data files 1_ is Hy3 0_ is Hy5

value: Hispanic


title: [7230_7 / 5_75 cy3]-[7602_-7 / 5_75 cy5]


title: Wild type C57BL/6j, TCDD-treated, 12 hour, bone marrow replicate 3

description:
9 samples pooled
WT TCDD 12h 77

value: TCDD


title: Wild type C57BL/6j, TCDD-treated, 12 hour, bone marrow replicate 2

description:
9 samples pooled
WT TCDD 12h 76


title: Wild type C57BL/6j, TCDD-treated, 12 hour, bone marrow replicate 1

description:
9 samples pooled
WT TCDD 12h 75


title: [3298_-7 / 5_75 cy3]-[656_-7 / 5_125 cy5]


title: Wild type C57BL/6j, DMBA-treated, 12 hour, bone marrow replicate 3

description:
9 samples pooled
WT DMBA 12h 6


title: [9263_7 / 5_125 cy3]-[9658_-7 / 5_125 cy5]


title: Wild type C57BL/6j, DMBA-treated, 12 hour, bone marrow replicate 1

description:
9 samples pooled
WT DMBA 12h 4


title: Wild type C57BL/6j, DMBA-treated, 12 hour, bone marrow replicate 2

description:
9 samples pooled
WT DMBA 12h 5


title: Wild type C57BL/6j, oil-treated control, bone marrow replicate 3

description:
9 samples pooled
WT Control 3


title: Wild type C57BL/6j, BP-treated, 6 hour, bone marrow replicate 2

description:
9 samples pooled
WT BP 6h 62

value: 6 hours


title: Wild type C57BL/6j, BP-treated, 6 hour, bone marrow replicate 1

description:
9 samples pooled
WT BP 6h 61


title: [6411_-7 / 5_125 cy5]-[8639_-7 / 4_125 cy3]

value: Liver


title: [210_-7 / 5_75 cy3]-[2303_-7 / 4_125 cy5]


title: Wild type C57BL/6j, oil-treated control, bone marrow replicate 2

description:
9 samples pooled
WT Control 2


title: [8209_-7 / 4_125 cy3]-[8620_7 / 4_125 cy5]


title: Rumenpapillae_high-concentrate_rep4

first: ruiyang

last: zhang

state: jiangsu

address: tongwei road weigang no. 1

department: College of Animal Science and Technology

institute: nanjing agricultural university

hyb_protocol: Purify the labeled/amplified RNA.Prepare the 10X Blocking Agent.Prepare hybridization samples.Prepare the hybridization assembly.Place assembled slide chamber in rotisserie in a hybridization oven set to  65°C.Hybridize at 65°C for 17 hours.Add Triton X-102 to Gene Expression wash buffers.Prewarm Gene Expression Wash Buffer 2.Always use clean equipment when doing the hybridization and wash steps.Arrays were incubated at 65C for 17h in Agilent microarray hybridization chambers and subsequently washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) and Stabilization and Drying Solution (Agilent Technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US) with default settings

data_processing: the 75th percentile signal value to normalize Agilent one-color microarray signals for inter-array comparisons.the data were processed refer to the Agilent G2567AA Feature Extraction Software  Reference Guide.

source_name: Rumen papillae, high-concentrate,cow 2

label_protocol: Add 10 to 200 ng of total RNA to a 1.5-mL microcentrifuge tube in a final  volume of 1.5 µL.Add 2 µL of diluted Spike Mix to each tube. Prepare and add T7 Promoter Primer.Prewarm the 5X first strand buffer at 80°C for 3 to 4 minutes to ensure  adequate resuspensions of the buffer components.Prepare and add cDNA Master Mix.Prepare and add Transcription Master Mix.

extract_protocol: Total RNA was isolated using TRIZOL Reagent according to manufacturer's instruction (Life Technologies, Carlsbad, CA, US). The RNA quantity and purity were determined by NanoDrop ND-1000 spectrophotometer at 260/280 nm. The integrity of total RNA was assessed with an Agilent Bioanalyzer 2100. The RNA Integrity Numbers (RINs) for the samples were obtained. All the RNA samples showed 7.6 or higher RIN values and 28S/18S > 1.5, indicating sufficient quality to be used for microarray.

tag: breed

value: Holstein cattle

value: female

tag: diet

value: high-concentrate diet (HC; 70% concentrate feed)

value: Rumen papillae


title: Wild type C57BL/6j, oil-treated control, bone marrow replicate 1

description:
9 samples pooled
WT Control 1

value: 6 weeks


title: [7259_-7 / 5_125 cy3]-[8669_-7 / 4_125 cy5]


title: [6007_-7 / 5_75 cy5]-[7202_-7 / 4_75 cy3]


title: Rumenpapillae_high-concentrate_rep2

source_name: Rumen papillae, high-concentrate,cow 4


title: Rumenpapillae_high-concentrate_rep3

source_name: Rumen papillae, high-concentrate,cow 1


title: [7658_-7 / 4_75 cy5]-[7671_-7 / 5_75 cy3]


title: [9262_-7 / 4_75 cy5]-[9272_-7 / 4_125 cy3]


title: [5950_-7 / 4_75 cy3]-[7258_-7 / 5_125 cy5]


title: Rumenpapillae_high-concentrate_rep1

source_name: Rumen papillae, high-concentrate,cow 3


title: [9240_-7 / 4_75 cy3]-[9276_-7 / 4_125 cy5]


title: Rumenpapillae_low-concentrate_rep3

source_name: Rumen papillae, low-concentrate,cow 3

value: low-concentrate diet (LC; 40% concentrate feed)


title: [203_28 / 4_75 cy3]-[3250_-7 / 4_75 cy5]


title: [3940_-7 / 4_75 cy5]-[8616_-7 / 5_125 cy3]


title: [8209_28 / 4_125 cy3]-[8620_-7 / 4_125 cy5]


title: [203_-7 / 4_75 cy3]-[3250_7 / 4_75 cy5]


title: Rumenpapillae_low-concentrate_rep4

source_name: Rumen papillae, low-concentrate,cow 4


title: Rumenpapillae_low-concentrate_rep2

source_name: Rumen papillae, low-concentrate,cow 2


title: 11_Air_24

status: Public on Jun 05 2016

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

hyb_protocol: Labeled cRNA (500 ng) was then hybridized to HumanHT-12 V4 BeadChipTM  arrays (Illumina, San Diego, CA, USA) containing 47,231 transcripts (targeting approximate 31,000 annotated genes) at 55°C overnight following staining with 1 lg/mL streptavidin-Cy3 (Amersham Biosciences, Piscataway, NJ, USA) for visualization. Washing of the arrays was performed using Illumina high-stringency wash buffer for 30min at 55°C.

scan_protocol: Scanning was done according to standard Illumina protocols.

data_processing: Probe intensity and detection data were obtained using Illumina BeadStudio software using quantile normalization with background correction and imputation of missing probes, data were mean centered per chip prior to analysis. Background corrected, non-normalized intensity data are also provided. Quality standards for hybridization, labeling, staining, background signal, and basal level of housekeeping gene expression for each chip were verified.

source_name: Primary coronary artery endothelial cells

label_protocol: An aliquot of 440 ng total RNA of each sample as input material. In vitro transcription of cDNA to cRNA was performed overnight using biotin-11-deoxyuridine triphosphate (biotin-11-dUTP) to label the cRNA product. The cRNA yields were quantified with a spectrophotometer

growth_protocol: Primary human coronary artery endothelial cells (hCAECs) were obtained from a commercial supplier (Lonza). hCAECs were utilized at passage 5 for this experiment. hCAECs were plated on 48-well plates, grown to confluence, and serum-starved overnight.

extract_protocol: Cells were washed with PBS, lysed, and immediately cell lysates from duplicate samples were pooled and collected for RNA purification. Total RNA was isolated from pooled samples using RNeasy Mini Prep Kits (Qiagen).

treatment_protocol: Plasma was added at a 10% dilution with media and hCAECs were so incubated for 24h prior to washing with phosphate-buffered saline and isolation of hCAEC RNA. Two wells of treated hCAECs were pooled for each subject to isolate sufficient RNA.

tag: subject#

tag: air condition

value: Filtered Air

tag: time (hours)

tag: cell type


title: 11_Air_2

value: Primary coronary artery endothelial cells


title: 11_Air_0


title: 2_Air_0


title: 11_DE_2

value: Diesel Engine Exhaust


title: 2_Air_2


title: Rumenpapillae_low-concentrate_rep1

source_name: Rumen papillae, low-concentrate,cow 1

tag: gender


title: 11_DE_0


title: [652_-7 / 5_75 cy5]-[9277_-7 / 4_125 cy3]

source_name: Liver Biopsy


title: 2_DE_2


title: 2_Air_24


title: 3_Air_2


title: 3_Air_0


title: 2_DE_24


title: 2_DE_0


title: 11_DE_24


title: 3_DE_2


title: 4_Air_0


title: 3_Air_24


title: 4_DE_0


title: 3_DE_0


title: 4_DE_2


title: 4_Air_24


title: 4_DE_24


title: 5_Air_0


title: 4_Air_2


title: 5_DE_24


title: 5_DE_2


title: 6_DE_0


title: 6_Air_24


title: 5_Air_24


title: 6_DE_24


title: 6_Air_0


title: 3_DE_24


title: 7_Air_2


title: 7_DE_0


title: 7_DE_24


title: 6_Air_2


title: 7_Air_24


title: 7_Air_0


title: 7_DE_2


title: 9_Air_2


title: 5_Air_2


title: 9_Air_0


title: 5_DE_0


title: 9_DE_0


title: 6_DE_2


title: 9_Air_24


title: 9_DE_2


title: [5544_-7 / 5_75 cy5]-[649_-7 / 5_125 cy3]


title: 9_DE_24


title: PC3_siRNA2_rep1

city: Tampere

first: Antti

last: Ylipää

address: Korkeakoulunkatu 1

country: Finland

institute: Tampere University of Technology

hyb_protocol: Labeled cRNA was fragmented in 25X fragmentation buffer, in presence of 10X blocking agent and hybridization mix was subsequently prepared by adding the recommended volume of 2X GEx hybridization Buffer HI-RPM. Samples were hybridized at 65 degrees for 17 hrs, enclosed into SureHyb hybridization chambers and then washed in wash buffer 1 and 2 sequentially.

scan_protocol: Slides were scanned using Agilent G2565AA scanner and images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Data were quantile normalized using Matlab (R2012b) and log2 ratios were computed taking into account the dye swap.

source_name: PC-3 prostate cancer cell line transfected with siRNA2 targeting TPCAT-10-36067

label_protocol: 50 ng of total RNA were primed using T7 Promoter Primer Mix, then reverse transcribed to cDNA using AffinityScript and cRNA was subsequently obtained using T7 RNA Polymerase, according to the Agilent two-color labeling reaction protocol. The cRNA was then purified using Qiagen's RNeasy mini spin columns, according to the manufacturer's instuctions.

growth_protocol: Prostate cancer cell lines were grown in recommended medium at 37 degrees to 90% confluence and subsequently transferred onto 24-well plate to obtain a 30-50% confluence value.

extract_protocol: Total RNA was extracted from cells using TRI Reagent according to the manufacturer's instructions.

treatment_protocol: Cells in 24-well plate were divided into three groups of 6 replicates each: we had three different siRNAs all targeting TPCAT-10-36067. Arrays were made for only siRNAs 2 and 3. Interferin was used as transfection reagent according to the manufacturer's instructions.

tag: cell line

value: prostate cancer cells

tag: sirna

value: siRNA2 targeting TPCAT-10-36067

source_name: PC-3 prostate cancer cell line, non-transfected


title: PC3_siRNA3_rep1

source_name: PC-3 prostate cancer cell line transfected with siRNA3 targeting TPCAT-10-36067

value: siRNA3 targeting TPCAT-10-36067


title: meyer-00114: ovary_TCGA-61-2102

status: Public on Jun 04 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: ovary

tag: Sex

value: FEMALE

tag: diseasestaging

value: IIIC

tag: cancersite

value: OVARY

tag: clinicaldiagnosis

value: Serous Cystadenocarcinoma

tag: individual

tag: tumorgrading

tag: external id


title: meyer-00114: ovary_TCGA-61-2098

scan_protocol: See mage-tab files linked to series entry for additional details

tag: age

tag: tissue


title: meyer-00114: ovary_TCGA-61-2097

data_processing: See mage-tab files linked to series entry for additional details

value: IIC


title: meyer-00114: ovary_TCGA-61-2110

label_protocol: See mage-tab files linked to series entry for additional details

value: NOT SPECIFIED


title: meyer-00114: ovary_TCGA-61-2104

extract_protocol: See mage-tab files linked to series entry for additional details


title: meyer-00114: ovary_TCGA-61-2111

value: IV


title: meyer-00114: ovary_TCGA-61-2109


title: meyer-00114: ovary_TCGA-61-2094


title: meyer-00114: ovary_TCGA-61-2113


title: PC3_siRNA2_rep2


title: meyer-00114: ovary_TCGA-61-2092


title: meyer-00114: ovary_TCGA-61-2088


title: meyer-00114: ovary_TCGA-61-2087

value: IC


title: meyer-00114: ovary_TCGA-61-2018


title: PC3_siRNA3_rep2


title: meyer-00114: ovary_TCGA-61-2017


title: meyer-00114: ovary_TCGA-61-2095


title: meyer-00114: ovary_TCGA-61-2096


title: meyer-00114: ovary_TCGA-61-2012


title: meyer-00114: ovary_TCGA-61-2009


title: meyer-00114: ovary_TCGA-61-2003


title: meyer-00114: ovary_TCGA-61-1914


title: meyer-00114: ovary_TCGA-61-1919


title: meyer-00114: ovary_TCGA-61-2000


title: meyer-00114: ovary_TCGA-61-1917

value: IIIB


title: meyer-00114: ovary_TCGA-61-1918


title: meyer-00114: ovary_TCGA-61-1995


title: meyer-00114: ovary_TCGA-61-2002


title: meyer-00114: ovary_TCGA-61-1915


title: meyer-00114: ovary_TCGA-61-1998


title: meyer-00114: ovary_TCGA-61-1913


title: meyer-00114: ovary_TCGA-61-2016


title: meyer-00114: ovary_TCGA-61-1907


title: meyer-00114: ovary_TCGA-61-1906


title: meyer-00114: ovary_TCGA-61-1910


title: meyer-00114: ovary_TCGA-61-2008


title: meyer-00114: ovary_TCGA-61-1911

value: IIA


title: meyer-00114: ovary_TCGA-61-1901


title: meyer-00114: ovary_TCGA-61-1900


title: meyer-00114: ovary_TCGA-61-1903

value: IB


title: meyer-00114: ovary_TCGA-61-1743


title: meyer-00114: ovary_TCGA-61-1738


title: meyer-00114: ovary_TCGA-61-1730


title: meyer-00114: ovary_TCGA-61-1741


title: meyer-00114: ovary_TCGA-61-1736


title: meyer-00114: ovary_TCGA-61-1904


title: meyer-00114: ovary_TCGA-61-1734


title: meyer-00114: ovary_TCGA-61-1740


title: meyer-00114: ovary_TCGA-61-1733


title: meyer-00114: ovary_TCGA-61-1737


title: meyer-00114: ovary_TCGA-61-1728


title: meyer-00114: ovary_TCGA-61-1727


title: meyer-00114: ovary_TCGA-61-1895


title: meyer-00114: ovary_TCGA-61-1724


title: meyer-00114: ovary_TCGA-61-1722


title: meyer-00114: ovary_TCGA-61-1899


title: meyer-00114: ovary_TCGA-61-1725


title: meyer-00114: ovary_TCGA-61-2101


title: meyer-00114: ovary_TCGA-59-2363

value: IIIA


title: meyer-00114: ovary_TCGA-59-2355


title: meyer-00114: ovary_TCGA-61-1721


title: meyer-00114: ovary_TCGA-59-2352


title: meyer-00114: ovary_TCGA-59-2354


title: meyer-00114: ovary_TCGA-57-1993


title: meyer-00114: ovary_TCGA-57-1994


title: meyer-00114: ovary_TCGA-59-2349

value: IA


title: meyer-00114: ovary_TCGA-57-1586


title: meyer-00114: ovary_TCGA-57-1585


title: meyer-00114: ovary_TCGA-57-1992


title: meyer-00114: ovary_TCGA-57-1583


title: meyer-00114: ovary_TCGA-57-1582


title: meyer-00114: ovary_TCGA-57-1584


title: meyer-00114: ovary_TCGA-36-1581


title: meyer-00114: ovary_TCGA-59-2351


title: meyer-00114: ovary_TCGA-59-2350


title: meyer-00114: ovary_TCGA-36-1580


title: meyer-00114: ovary_TCGA-59-2348


title: meyer-00114: ovary_TCGA-36-1577


title: meyer-00114: ovary_TCGA-36-1576


title: meyer-00114: ovary_TCGA-36-1578


title: meyer-00114: ovary_TCGA-36-1575


title: meyer-00114: ovary_TCGA-36-1574


title: meyer-00114: ovary_TCGA-36-1571


title: meyer-00114: ovary_TCGA-36-1570


title: meyer-00114: ovary_TCGA-36-1568


title: meyer-00114: ovary_TCGA-36-1569


title: meyer-00114: ovary_TCGA-31-1959


title: meyer-00114: ovary_TCGA-31-1953


title: meyer-00114: ovary_TCGA-31-1950


title: meyer-00114: ovary_TCGA-31-1951


title: meyer-00114: ovary_TCGA-31-1956


title: meyer-00114: ovary_TCGA-31-1944


title: meyer-00114: ovary_TCGA-31-1946


title: meyer-00114: ovary_TCGA-30-1892


title: meyer-00114: ovary_TCGA-30-1891


title: meyer-00114: ovary_TCGA-30-1887


title: meyer-00114: ovary_TCGA-30-1867

value: GX


title: meyer-00114: ovary_TCGA-30-1880


title: meyer-00114: ovary_TCGA-30-1862


title: meyer-00114: ovary_TCGA-30-1861


title: meyer-00114: ovary_TCGA-30-1866


title: meyer-00114: ovary_TCGA-30-1860


title: meyer-00114: ovary_TCGA-30-1859


title: meyer-00114: ovary_TCGA-30-1856


title: meyer-00114: ovary_TCGA-30-1855


title: meyer-00114: ovary_TCGA-30-1857


title: meyer-00114: ovary_TCGA-30-1718


title: meyer-00114: ovary_TCGA-30-1714


title: meyer-00114: ovary_TCGA-29-1784


title: meyer-00114: ovary_TCGA-30-1853


title: meyer-00114: ovary_TCGA-29-2427


title: meyer-00114: ovary_TCGA-29-2414


title: meyer-00114: ovary_TCGA-29-1778


title: meyer-00114: ovary_TCGA-29-1781


title: Biomaterial: Blood [CH94]

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Hybridization of the Cytoscan HD microarray was carried out in the Hybridization Oven 645 while subsequent washing and staining were performed using the Fluidics Station 450.

scan_protocol: The array was scanned with the Scanner 3000 7G

data_processing: The array image was acquired using Chromosome Analysis Suite (ChAS) Software | Affymetrix. Both quality control step and copy number analysis were performed using the Chromosome Analysis Suite Software (ChAS version 2.0; Affymetrix): (1) the raw data file (.CEL) was normalized using the default options; (2) an unpaired analysis was performed using as baseline 270 HapMap samples in order to obtain Copy numbers value from .CEL files while the amplified and/or deleted regions were detected using a standard Hidden Markov Model (HMM) method. To prevent the detection of false positive CNVs arising due to inherent microarray “noise”, only alterations that involved at least 25 consecutive probes and that were more than 25 kb in length were considered in the analysis of gains and losses in our study.

source_name: family member_PAIS

label_protocol: The CytoScan HD assay was performed starting with 250 ng DNA. Briefly, total genomic DNA was digested with a restriction enzyme (NspI), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer. After digestion with DNase I, the PCR products were labeled with a biotinylated nucleotide analogue, using terminal deoxynucleotidyl transferase and hybridized to the microarray, according to the manufacturer's instructions.

extract_protocol: Genomic DNA samples were extracted from whole blood specimens of the patient and his relatives using QIAamp DNA Blood Maxi Kit (Qiagen). Genomic DNA was extracted from secondary RSC  of the index case using QIAamp DNA mini Kit (Qiagen). DNA quantity and quality was measured by reading the whole absorption spectrum (220–750 nm) with NanoDrop and calculating DNA concentration and absorbance ratio at both 260/280 and 230/260 nm. Each sample was then quantified with the Qubit fluorometer using the Quant-iT dsDNA  HS Assay ccording to the manufacturer’s instructions. The quality of each DNA sample was assessed through the gel-electrophotometry.

tag: subject

value: Cousin; CH94

tag: subject condition/phenotype

value: PAIS

value: peripheral blood


title: meyer-00114: ovary_TCGA-29-1777

value: FEMALE


title: meyer-00114: ovary_TCGA-29-1783

value: IIIC


title: meyer-00114: ovary_TCGA-29-1775

value: OVARY


title: meyer-00114: ovary_TCGA-29-1774

value: Serous Cystadenocarcinoma


title: meyer-00114: ovary_TCGA-29-1770


title: meyer-00114: ovary_TCGA-29-1785


title: meyer-00114: ovary_TCGA-29-1769


title: meyer-00114: ovary_TCGA-29-1771


title: meyer-00114: ovary_TCGA-29-1763

value: IIC


title: Biomaterial: Blood [BT53I]

source_name: proband_PAIS and RSC

value: Proband

value: PAIS and RSC


title: meyer-00114: ovary_TCGA-29-1766

value: PERITONEUM (OVARY)


title: Biomaterial: Blood [CH92]

source_name: family member_unaffected

value: Father; CH92

value: Unaffected


title: Biomaterial: Secondary Recto Sigmoid Cancer [BT56]

value: Secondary Recto Sigmoid Cancer


title: meyer-00114: ovary_TCGA-29-1768

value: IV


title: meyer-00114: ovary_TCGA-29-1761


title: meyer-00114: ovary_TCGA-29-1776


title: meyer-00114: ovary_TCGA-29-1711


title: meyer-00114: ovary_TCGA-29-1710


title: meyer-00114: ovary_TCGA-29-1762


title: meyer-00114: ovary_TCGA-29-1707


title: meyer-00114: ovary_TCGA-29-1705


title: meyer-00114: ovary_TCGA-29-1699


title: meyer-00114: ovary_TCGA-29-1703


title: Biomaterial: Blood [CH91]

value: Ount; CH91


title: meyer-00114: ovary_TCGA-29-1697


title: meyer-00114: ovary_TCGA-29-1764


title: meyer-00114: ovary_TCGA-29-1695


title: meyer-00114: ovary_TCGA-29-1694

value: GX


title: Biomaterial: Blood [CH90]

value: Mother; CH90


title: meyer-00114: ovary_TCGA-29-1696


title: meyer-00114: ovary_TCGA-29-1693


title: meyer-00114: ovary_TCGA-29-1691


title: meyer-00114: ovary_TCGA-29-1690


title: meyer-00114: ovary_TCGA-29-1688


title: meyer-00114: ovary_TCGA-25-2404


title: meyer-00114: ovary_TCGA-25-2409


title: meyer-00114: ovary_TCGA-25-2401


title: meyer-00114: ovary_TCGA-25-2408


title: meyer-00114: ovary_TCGA-29-1702


title: meyer-00114: ovary_TCGA-29-1698


title: meyer-00114: ovary_TCGA-25-2396


title: meyer-00114: ovary_TCGA-25-2400


title: meyer-00114: ovary_TCGA-25-2397


title: meyer-00114: ovary_TCGA-25-2399


title: meyer-00114: ovary_TCGA-29-1701


title: meyer-00114: ovary_TCGA-25-2398


title: meyer-00114: ovary_TCGA-25-2392


title: meyer-00114: ovary_TCGA-25-2393


title: meyer-00114: ovary_TCGA-25-2391


title: meyer-00114: ovary_TCGA-25-1871


title: meyer-00114: ovary_TCGA-25-1870


title: meyer-00114: ovary_TCGA-25-1633


title: meyer-00114: ovary_TCGA-25-1634


title: meyer-00114: ovary_TCGA-25-1635


title: meyer-00114: ovary_TCGA-25-2042


title: meyer-00114: ovary_TCGA-25-1630


title: meyer-00114: ovary_TCGA-25-1628


title: meyer-00114: ovary_TCGA-25-1632


title: meyer-00114: ovary_TCGA-25-1631


title: meyer-00114: ovary_TCGA-25-1627


title: meyer-00114: ovary_TCGA-25-1626


title: meyer-00114: ovary_TCGA-25-1623


title: meyer-00114: ovary_TCGA-25-1625


title: meyer-00114: ovary_TCGA-25-1329


title: meyer-00114: ovary_TCGA-25-1322


title: meyer-00114: ovary_TCGA-25-1328


title: meyer-00114: ovary_TCGA-25-1323


title: meyer-00114: ovary_TCGA-25-1326


title: meyer-00114: ovary_TCGA-25-1324


title: meyer-00114: ovary_TCGA-25-1877


title: meyer-00114: ovary_TCGA-25-1318


title: meyer-00114: ovary_TCGA-25-1321


title: meyer-00114: ovary_TCGA-25-1320


title: meyer-00114: ovary_TCGA-25-1319


title: meyer-00114: ovary_TCGA-25-1314


title: meyer-00114: ovary_TCGA-25-1315


title: meyer-00114: ovary_TCGA-25-1317


title: meyer-00114: ovary_TCGA-25-1316


title: meyer-00114: ovary_TCGA-25-1878


title: meyer-00114: ovary_TCGA-29-2428


title: meyer-00114: ovary_TCGA-29-2425


title: meyer-00114: ovary_TCGA-25-1313


title: meyer-00114: ovary_TCGA-24-2298


title: meyer-00114: ovary_TCGA-25-1312


title: meyer-00114: ovary_TCGA-24-2295


title: meyer-00114: ovary_TCGA-24-2297


title: meyer-00114: ovary_TCGA-24-2293

value: NOT SPECIFIED


title: meyer-00114: ovary_TCGA-24-2290


title: meyer-00114: ovary_TCGA-25-1325


title: meyer-00114: ovary_TCGA-24-2289


title: meyer-00114: ovary_TCGA-24-2288


title: meyer-00114: ovary_TCGA-24-2271


title: meyer-00114: ovary_TCGA-24-2280


title: meyer-00114: ovary_TCGA-24-2267

value: IIB


title: meyer-00114: ovary_TCGA-24-2254

value: FEMALE


title: meyer-00114: ovary_TCGA-24-2260

value: IIIB


title: meyer-00114: ovary_TCGA-24-2038

value: IIIA

value: OVARY

value: GB


title: meyer-00114: ovary_TCGA-24-2036


title: meyer-00114: ovary_TCGA-24-2261

value: IIIC

value: Serous Cystadenocarcinoma


title: meyer-00114: ovary_TCGA-24-2262


title: meyer-00114: ovary_TCGA-24-2035


title: meyer-00114: ovary_TCGA-24-2030


title: meyer-00114: ovary_TCGA-24-2033


title: meyer-00114: ovary_TCGA-24-2027


title: meyer-00114: ovary_TCGA-24-2024


title: meyer-00114: ovary_TCGA-24-2023


title: meyer-00114: ovary_TCGA-24-2019


title: meyer-00114: ovary_TCGA-24-2020


title: meyer-00114: ovary_TCGA-24-2029


title: meyer-00114: ovary_TCGA-24-1930


title: meyer-00114: ovary_TCGA-24-2026


title: meyer-00114: ovary_TCGA-24-1928


title: meyer-00114: ovary_TCGA-24-2281

value: IIA


title: meyer-00114: ovary_TCGA-24-1920


title: meyer-00114: ovary_TCGA-24-1923


title: meyer-00114: ovary_TCGA-24-1850


title: meyer-00114: ovary_TCGA-24-1846


title: meyer-00114: ovary_TCGA-24-1849


title: meyer-00114: ovary_TCGA-24-1847


title: meyer-00114: ovary_TCGA-24-1845


title: meyer-00114: ovary_TCGA-24-1843


title: meyer-00114: ovary_TCGA-24-1844


title: meyer-00114: ovary_TCGA-24-1616


title: meyer-00114: ovary_TCGA-24-1614


title: meyer-00114: ovary_TCGA-24-1604


title: meyer-00114: ovary_TCGA-24-1567


title: meyer-00114: ovary_TCGA-24-1603


title: meyer-00114: ovary_TCGA-24-1564


title: meyer-00114: ovary_TCGA-24-1563


title: meyer-00114: ovary_TCGA-24-1565


title: meyer-00114: ovary_TCGA-24-1562


title: meyer-00114: ovary_TCGA-24-1558


title: meyer-00114: ovary_TCGA-24-1924


title: meyer-00114: ovary_TCGA-24-1553


title: meyer-00114: ovary_TCGA-24-1555


title: meyer-00114: ovary_TCGA-24-1560


title: meyer-00114: ovary_TCGA-24-1557


title: meyer-00114: ovary_TCGA-24-1551


title: meyer-00114: ovary_TCGA-24-1549


title: meyer-00114: ovary_TCGA-24-1545


title: meyer-00114: ovary_TCGA-24-1546


title: meyer-00114: ovary_TCGA-24-1544


title: meyer-00114: ovary_TCGA-24-1474


title: meyer-00114: ovary_TCGA-24-1548


title: meyer-00114: ovary_TCGA-24-1842


title: meyer-00114: ovary_TCGA-24-1471


title: meyer-00114: ovary_TCGA-24-1469


title: meyer-00114: ovary_TCGA-24-1470


title: meyer-00114: ovary_TCGA-24-1467


title: meyer-00114: ovary_TCGA-24-1463


title: meyer-00114: ovary_TCGA-24-1464


title: meyer-00114: ovary_TCGA-24-1435


title: meyer-00114: ovary_TCGA-24-1466


title: meyer-00114: ovary_TCGA-24-1436


title: meyer-00114: ovary_TCGA-24-1434


title: meyer-00114: ovary_TCGA-24-1552


title: meyer-00114: ovary_TCGA-24-1556


title: meyer-00114: ovary_TCGA-24-1431


title: meyer-00114: ovary_TCGA-24-1430


title: meyer-00114: ovary_TCGA-24-1428


title: meyer-00114: ovary_TCGA-24-1424


title: meyer-00114: ovary_TCGA-24-1423


title: meyer-00114: ovary_TCGA-24-1550


title: meyer-00114: ovary_TCGA-24-1426


title: meyer-00114: ovary_TCGA-24-1425


title: meyer-00114: ovary_TCGA-24-1427


title: meyer-00114: ovary_TCGA-24-1419


title: meyer-00114: ovary_TCGA-24-1418


title: meyer-00114: ovary_TCGA-24-1105


title: meyer-00114: ovary_TCGA-24-1416


title: meyer-00114: ovary_TCGA-24-1104


title: meyer-00114: ovary_TCGA-24-1417


title: meyer-00114: ovary_TCGA-24-1413


title: meyer-00114: ovary_TCGA-24-0982


title: meyer-00114: ovary_TCGA-24-1103


title: meyer-00114: ovary_TCGA-24-0980


title: meyer-00114: ovary_TCGA-24-0979


title: meyer-00114: ovary_TCGA-24-0975


title: meyer-00114: ovary_TCGA-24-0968


title: meyer-00114: ovary_TCGA-24-0970


title: meyer-00114: ovary_TCGA-23-2081


title: meyer-00114: ovary_TCGA-24-0966


title: meyer-00114: ovary_TCGA-24-1422


title: meyer-00114: ovary_TCGA-23-2079


title: meyer-00114: ovary_TCGA-23-2077


title: meyer-00114: ovary_TCGA-23-2072


title: meyer-00114: ovary_TCGA-23-1123


title: meyer-00114: ovary_TCGA-23-1122


title: meyer-00114: ovary_TCGA-23-1809

value: IIC


title: meyer-00114: ovary_TCGA-23-2078


title: meyer-00114: ovary_TCGA-23-1119


title: meyer-00114: ovary_TCGA-23-1121


title: meyer-00114: ovary_TCGA-23-1120


title: meyer-00114: ovary_TCGA-24-0981


title: meyer-00114: ovary_TCGA-23-1113


title: meyer-00114: ovary_TCGA-23-1116


title: meyer-00114: ovary_TCGA-23-1117


title: meyer-00114: ovary_TCGA-23-1111


title: meyer-00114: ovary_TCGA-23-1107


title: meyer-00114: ovary_TCGA-23-1031


title: meyer-00114: ovary_TCGA-23-1114


title: meyer-00114: ovary_TCGA-23-1109


title: meyer-00114: ovary_TCGA-23-2084


title: meyer-00114: ovary_TCGA-23-1030


title: meyer-00114: ovary_TCGA-23-1124


title: meyer-00114: ovary_TCGA-23-1029


title: meyer-00114: ovary_TCGA-23-1027


title: meyer-00114: ovary_TCGA-23-1026


title: meyer-00114: ovary_TCGA-23-1028


title: meyer-00114: ovary_TCGA-23-1024


title: meyer-00114: ovary_TCGA-23-1021


title: meyer-00114: ovary_TCGA-23-1118


title: meyer-00114: ovary_TCGA-23-1023


title: meyer-00114: ovary_TCGA-20-1684


title: meyer-00114: ovary_TCGA-20-1686


title: meyer-00114: ovary_TCGA-20-1685


title: meyer-00114: ovary_TCGA-20-0996


title: meyer-00114: ovary_TCGA-20-0991


title: meyer-00114: ovary_TCGA-23-1110


title: meyer-00114: ovary_TCGA-20-1682


title: meyer-00114: ovary_TCGA-13-2060


title: meyer-00114: ovary_TCGA-20-0990


title: meyer-00114: ovary_TCGA-20-0987


title: meyer-00114: ovary_TCGA-23-1032


title: meyer-00114: ovary_TCGA-13-1512


title: meyer-00114: ovary_TCGA-13-1511


title: meyer-00114: ovary_TCGA-13-1507


title: meyer-00114: ovary_TCGA-13-1506


title: meyer-00114: ovary_TCGA-13-1505


title: meyer-00114: ovary_TCGA-13-1501


title: meyer-00114: ovary_TCGA-13-1499


title: meyer-00114: ovary_TCGA-13-1504


title: meyer-00114: ovary_TCGA-23-1022


title: meyer-00114: ovary_TCGA-13-1498


title: meyer-00114: ovary_TCGA-13-1500


title: meyer-00114: ovary_TCGA-13-1497


title: meyer-00114: ovary_TCGA-20-1687


title: meyer-00114: ovary_TCGA-20-1683


title: meyer-00114: ovary_TCGA-13-1491


title: meyer-00114: ovary_TCGA-13-1494


title: meyer-00114: ovary_TCGA-13-1492


title: meyer-00114: ovary_TCGA-13-1496


title: meyer-00114: ovary_TCGA-13-1489


title: meyer-00114: ovary_TCGA-13-1488


title: meyer-00114: ovary_TCGA-13-1495


title: meyer-00114: ovary_TCGA-13-1487


title: meyer-00114: ovary_TCGA-13-1484


title: meyer-00114: ovary_TCGA-13-1485


title: meyer-00114: ovary_TCGA-13-1483


title: meyer-00114: ovary_TCGA-13-1510


title: meyer-00114: ovary_TCGA-13-1479


title: meyer-00114: ovary_TCGA-13-1481


title: meyer-00114: ovary_TCGA-13-1509


title: meyer-00114: ovary_TCGA-13-1412


title: meyer-00114: ovary_TCGA-13-1410


title: meyer-00114: ovary_TCGA-13-1411


title: meyer-00114: ovary_TCGA-13-1409


title: meyer-00114: ovary_TCGA-13-1407


title: meyer-00114: ovary_TCGA-13-1408


title: meyer-00114: ovary_TCGA-13-0923


title: meyer-00114: ovary_TCGA-13-1404


title: meyer-00114: ovary_TCGA-13-0921


title: meyer-00114: ovary_TCGA-13-1403


title: meyer-00114: ovary_TCGA-13-0924


title: meyer-00114: ovary_TCGA-13-1482


title: meyer-00114: ovary_TCGA-13-0919


title: meyer-00114: ovary_TCGA-13-0920


title: meyer-00114: ovary_TCGA-13-0911


title: meyer-00114: ovary_TCGA-13-1477


title: meyer-00114: ovary_TCGA-13-0912


title: meyer-00114: ovary_TCGA-13-0913


title: meyer-00114: ovary_TCGA-13-0916


title: meyer-00114: ovary_TCGA-13-0908


title: meyer-00114: ovary_TCGA-13-1405


title: meyer-00114: ovary_TCGA-13-0905


title: meyer-00114: ovary_TCGA-13-0906


title: meyer-00114: ovary_TCGA-13-0900


title: meyer-00114: ovary_TCGA-13-0901


title: meyer-00114: ovary_TCGA-13-0910


title: meyer-00114: ovary_TCGA-13-0899


title: meyer-00114: ovary_TCGA-13-0897


title: meyer-00114: ovary_TCGA-13-0904


title: meyer-00114: ovary_TCGA-13-0894


title: meyer-00114: ovary_TCGA-13-0903


title: meyer-00114: ovary_TCGA-13-0891


title: meyer-00114: ovary_TCGA-13-0889


title: meyer-00114: ovary_TCGA-13-0886


title: meyer-00114: ovary_TCGA-13-0887


title: meyer-00114: ovary_TCGA-13-0884


title: meyer-00114: ovary_TCGA-13-0890


title: meyer-00114: ovary_TCGA-13-0885


title: meyer-00114: ovary_TCGA-13-0883


title: meyer-00114: ovary_TCGA-13-0893


title: meyer-00114: ovary_TCGA-13-0805


title: meyer-00114: ovary_TCGA-13-0799


title: meyer-00114: ovary_TCGA-13-0800


title: meyer-00114: ovary_TCGA-13-0807


title: meyer-00114: ovary_TCGA-13-0797


title: meyer-00114: ovary_TCGA-13-0802


title: meyer-00114: ovary_TCGA-13-0803


title: meyer-00114: ovary_TCGA-13-0801


title: meyer-00114: ovary_TCGA-13-0804


title: meyer-00114: ovary_TCGA-13-0795


title: meyer-00114: ovary_TCGA-13-0791


title: meyer-00114: ovary_TCGA-13-0768


title: meyer-00114: ovary_TCGA-13-0794


title: meyer-00114: ovary_TCGA-13-0793


title: meyer-00114: ovary_TCGA-13-0764


title: meyer-00114: ovary_TCGA-13-0765


title: meyer-00114: ovary_TCGA-13-0761


title: meyer-00114: ovary_TCGA-13-0762


title: meyer-00114: ovary_TCGA-13-0760


title: meyer-00114: ovary_TCGA-13-0888


title: meyer-00114: ovary_TCGA-13-0757


title: meyer-00114: ovary_TCGA-13-0727


title: meyer-00114: ovary_TCGA-13-0755


title: meyer-00114: ovary_TCGA-13-0730


title: meyer-00114: ovary_TCGA-13-0751


title: meyer-00114: ovary_TCGA-13-0792


title: meyer-00114: ovary_TCGA-13-0725


title: meyer-00114: ovary_TCGA-13-0726


title: meyer-00114: ovary_TCGA-13-0724


title: meyer-00114: ovary_TCGA-13-0720


title: meyer-00114: ovary_TCGA-13-0723


title: meyer-00114: ovary_TCGA-10-0938


title: meyer-00114: ovary_TCGA-13-0714


title: meyer-00114: ovary_TCGA-13-0717


title: meyer-00114: ovary_TCGA-13-0766


title: meyer-00114: ovary_TCGA-10-0937


title: meyer-00114: ovary_TCGA-10-0936


title: meyer-00114: ovary_TCGA-10-0935


title: meyer-00114: ovary_TCGA-13-0758


title: meyer-00114: ovary_TCGA-10-0933


title: meyer-00114: ovary_TCGA-10-0931


title: meyer-00114: ovary_TCGA-10-0934


title: meyer-00114: ovary_TCGA-10-0930


title: meyer-00114: ovary_TCGA-10-0927


title: meyer-00114: ovary_TCGA-10-0928


title: meyer-00114: ovary_TCGA-10-0925


title: meyer-00114: ovary_TCGA-09-2056


title: meyer-00114: ovary_TCGA-09-2053


title: meyer-00114: ovary_TCGA-09-2051


title: meyer-00114: ovary_TCGA-09-2055

value: IC


title: meyer-00114: ovary_TCGA-09-2049


title: meyer-00114: ovary_TCGA-09-2050


title: meyer-00114: ovary_TCGA-09-2048


title: 3-si-con

city: Suwon

first: jeehoon

last: lee

state: Gyoungido

address: San5, Woncheondong

department: Pharmacology

country: South Korea

institute: Ajou university, School of Medicine

description: control siRNA

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

organism: Rattus norvegicus

source_name: Gene expression data from control siRNA transfected astrocytes

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Primary astrocytes were prepared by trypsinization. To deplete microglia and meningeal cells, astrocytes were incubated with serum-free MEM for 2 days before use

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

treatment_protocol: Astrocytes transfect with control siRNA or SHP siRNA and treated with IFN-γ in the presence or absence of GW for 3 h

tag: strain

value: Sprague-Dawley

value: 1 day-old

value: cerebral cortex

value: astrocytes


title: 3-IFN-γ -siSHP-GW

description: SHP siRNA, IFN-γ, GW

source_name: Gene expression data from IFN-γ- and GW-treated astrocytes that were SHP siRNA transfected


title: 2-IFN-γ -siSHP-GW

description: SHP siRNA, IFN-γ, GW


title: meyer-00114: ovary_TCGA-09-2045

value: IV


title: meyer-00114: ovary_TCGA-09-2044


title: 3-IFN-γ -siC

description: control siRNA, IFN-γ

source_name: Gene expression data from IFN-γ-treated astrocytes that were control siRNA transfected


title: 2-IFN-γ -siC-GW

description: control siRNA, IFN-γ, GW

source_name: Gene expression data from IFN-γ- and GW-treated astrocytes that were control siRNA transfected


title: 2-IFN-γ -siC

description: control siRNA, IFN-γ


title: 3-IFN-γ -siC-GW

description: control siRNA, IFN-γ, GW


title: 2-si-con

description: control siRNA


title: 1-si-con

description: control siRNA


title: 1-IFN-γ -siSHP-GW

description: SHP siRNA, IFN-γ, GW


title: meyer-00114: ovary_TCGA-09-1674


title: meyer-00114: ovary_TCGA-09-1675


title: meyer-00114: ovary_TCGA-09-2043


title: 1-IFN-γ -siC-GW

description: control siRNA, IFN-γ, GW


title: meyer-00114: ovary_TCGA-09-2054


title: meyer-00114: ovary_TCGA-09-1673


title: meyer-00114: ovary_TCGA-10-0926


title: meyer-00114: ovary_TCGA-09-1669


title: 1-IFN-γ -siC

description: control siRNA, IFN-γ


title: meyer-00114: ovary_TCGA-09-1667


title: meyer-00114: ovary_TCGA-09-1666


title: meyer-00114: ovary_TCGA-09-1668


title: meyer-00114: ovary_TCGA-09-1665


title: meyer-00114: ovary_TCGA-09-1664


title: meyer-00114: ovary_TCGA-09-1662


title: meyer-00114: ovary_TCGA-09-1661


title: meyer-00114: ovary_TCGA-09-1659


title: meyer-00114: ovary_TCGA-09-0369


title: meyer-00114: ovary_TCGA-09-0367


title: meyer-00114: ovary_TCGA-09-1670


title: meyer-00114: ovary_TCGA-09-0366


title: meyer-00114: ovary_TCGA-09-0365


title: meyer-00114: ovary_TCGA-09-0364


title: meyer-00114: Cell_TCGA-07-0249

value: NOT SPECIFIED

value: Cell


title: U87-PIR8041_1

city: New Haven

first: Yong

last: Zhu

state: Connecticut

address: 60 College St

institute: Yale School of Public Health

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were processed in Illumina GenomeStudio (v. 2011.1) with average normalization

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit at the Yale Center for Genome Analysis

growth_protocol: U87 cells were maintained in EMEM w/ 10% FBS and 1% P/S prior to treatment

extract_protocol: Total RNA was isolated 24h post-transfection by the miRNeasy Mini Kit, QIAGEN

treatment_protocol: Cells were transfected w/ a synthetic piR-8041 mimic or NC oligo (miScript Inhibitor Negative Control, QIAGEN) with RNAiMax per the manufacturer's protocol to final oligo concentration of 25nM

tag: transfected with

tag: time point

value: 24h post transfection


title: meyer-00114: ovary_TCGA-04-1655

value: FEMALE

value: IIIB


title: U87-PIR8041_2


title: U87-NC_2

value: NC


title: U87-NC-2

data_processing: Data were processed in Illumina GenomeStudio (v.2011.1) with average normalization.

treatment_protocol: Cells were transfected w/ a synthetic piR-598 mimic or NC oligo (miScript Inhibitor Negative Control, QIAGEN) with RNAiMax per the manufacturer's protocol to final oligo concentration of 25nM

value: NC oligo


title: U87-PIR598-2

value: a synthetic piR-598 mimic


title: meyer-00114: ovary_TCGA-04-1654

value: IIIC

value: OVARY

value: Serous Cystadenocarcinoma


title: U87-NC_1


title: meyer-00114: ovary_TCGA-04-1652


title: HCC827_Esh9-1_Rep1

city: Maywood

first: Takeshi

last: Shimamura

address: 2160 S. 1st Ave LUHS Cancer  Center Rm205

department: Molecular Pharmacology and Therapeutics

institute: Loyola University Chicago

description: HCC827 Cells transduced with lentivirus coding for shRNA targeting EGFR

hyb_protocol: The fragmented cRNA ws added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution was then removed. The chips were transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured. These measures provide the basis of subsequent biostatistical analysis. The data was transferred to a file-system from which it can be downloaded via a password-protected URL.

data_processing: Normalized and analyzed using GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/), selecting RMA method

source_name: NSCLC cells

label_protocol: At DFCI Microarray core, RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis was then carried out. The double-stranded cDNA was used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates. The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles. The cRNA was quantified spectrophotometrically and purity of the cRNA was also assessed by spectrophometric measurements. Those cRNA's that fall outside of an acceptable range was not routinely carried forward in the analysis. The purified cRNA was fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Cells were grown in RPMI supplemented with 5% FBS and antibiotics (HCC827 and ERC4). Exponentially growing cells were harvested with RNAeasy Plus Mini kit (Qiagen). Cells were grown in RPMI supplemented with 5% FBS, antibiotics, and 5ug/ml puromycin (HCC827NT and HCC827Esh9). Exponentially growing cells were harvested with RNAeasy Plus Mini kit (Qiagen).

extract_protocol: RNA was isolated using RNAeasy Plus Mini kit (Qiagen)

tag: resistance

value: EGFR TKI resistant

tag: cell type


title: meyer-00114: ovary_TCGA-04-1651


title: HCC827_Esh9-1_Rep2

tag: cell line

value: HCC827 Cells transduced with lentivirus coding for shRNA targeting EGFR


title: U87-PIR598-1


title: U87-NC-1


title: meyer-00114: ovary_TCGA-04-1649

tag: Sex


title: HCC827_Esh9-1_Rep3


title: HCC827NT_Rep1

description: HCC827 Cells transduced with lentivirus coding for non-target shRNA (control)


title: meyer-00114: ovary_TCGA-04-1646

tag: diseasestaging


title: HCC827NT_Rep3

value: HCC827 Cells transduced with lentivirus coding for non-target shRNA (control)


title: ERC4_Rep2

description: erlotinib resistant

value: erlotinib resistant


title: ERC4_Rep3

description: erlotinib resistant


title: meyer-00114: ovary_TCGA-04-1638

tag: cancersite


title: meyer-00114: ovary_TCGA-04-1542

tag: clinicaldiagnosis


title: ERC4_Rep1

description: erlotinib resistant


title: meyer-00114: ovary_TCGA-04-1536

tag: individual


title: meyer-00114: ovary_TCGA-04-1525

tag: tumorgrading


title: meyer-00114: ovary_TCGA-04-1519

tag: external id


title: HCC827NT_Rep2


title: meyer-00114: ovary_TCGA-04-1530

tag: age


title: meyer-00114: ovary_TCGA-04-1517

tag: tissue


title: meyer-00114: ovary_TCGA-04-1514

value: IIIA


title: HCC827_Rep1

description: Parental Cells

value: Parental Cells


title: HCC827_Rep3

description: Parental Cells


title: Liver NC ZT12 FT 0714F-02_ZT12 NC13 LIVER

city: Irvine

first: Yu

last: Liu

state: California

address: UCI

department: Computer Science

institute: University of California, Irvine

description: RNA level of mouse tissue at certain ZT under certain fecal transplant condition, all labeled

hyb_protocol: Microarrays were erformed at the UCI Genomics High-throughput Facility, University of California, Irvine, as previously described(Eckel-Mahan et al., 2013).

data_processing:
PLIER, data compared to GSE52333
For microarray data, at each time point of interest, Bayesian regularized t-test (Baldi & Long, 2001; Kayala & Baldi, 2012) was performed between experimental group and control group (i.e. HFD vs CC, HF-R vs CC-R) and p values were calculated. Transcripts passing p value <0.05 were considered differential at that time point.

label: probe

source_name: Mouse cell extracted at labeled ZT

growth_protocol: Age-matched male C57BL/6J mice (Jackson Laboratory) were maintained on a 12 hr light/12 hr dark cycle with ad libitum access of food and water. Animals’ care and use was in accordance with guidelines of the Institutional Animal Care and Use Committee at the University of California, Irvine. Male C57BL/6J germ free mice were kindly provided by Dr. Sarkis Mazmanian (California Institute of Technology).

extract_protocol: RNA was extracted using TRIzol reagent (GIBCO BRL Life Technologies) and cleaned up with RNeasy spin column (Qiagen). Quality of purified RNAs was checked with an Agilent Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were fed a control chow (CC) (Harlan Laboratories, TD. 110870) or HFD (60% kcal fat, Research Diets, D12492) with ad libitum access to both diets. 2020X (Harlan Laboratories) was used as a CC for antibiotics treatment experiment. All diets used in this study were irradiated or autoclaved to avoid contamination from diets.

value: Liver

tag: diet (fecal donor)

value: Normal Chow

tag: zt


title: Liver NC ZT12 FT 0714F-02_ZT12 NC8 LIVER

scan_protocol: Microarrays were erformed at the UCI Genomics High-throughput Facility, University of California, Irvine, as previously described(Eckel-Mahan et al., 2013).


title: meyer-00114: ovary_TCGA-04-1365


title: meyer-00114: ovary_TCGA-04-1364


title: Liver KD ZT12 FT 0714F-02_ZT12 KD13 LIVER

label_protocol: Microarrays were erformed at the UCI Genomics High-throughput Facility, University of California, Irvine, as previously described(Eckel-Mahan et al., 2013).

value: Ketogenic


title: meyer-00114: ovary_TCGA-04-1371

value: FEMALE


title: Liver NC ZT12 FT 0714F-02_ZT12 NC11 LIVER


title: meyer-00114: ovary_TCGA-04-1367


title: Liver NC ZT12 FT 0714F-02_ZT12 NC7 LIVER


title: Liver KD ZT12 FT 0714F-02_ZT12 KD12 LIVER


title: Liver KD ZT12 FT 0714F-02_ZT12 KD8 LIVER


title: Liver KD ZT12 FT 0714F-02_ZT12 KD10 LIVER


title: meyer-00114: ovary_TCGA-04-1362

value: IIC


title: Liver HF ZT12 FT 0714F-02_ZT12 HF13 LIVER

value: High Fat


title: Liver NC ZT0 FT 0714F-02_ZT0 NC6 LIVER


title: Liver HF ZT12 FT 0714F-02_ZT12 HF10 LIVER


title: Liver HF ZT12 FT 0714F-02_ZT12 HF9 LIVER


title: meyer-00114: ovary_TCGA-04-1361

value: IIIB


title: Liver NC ZT0 FT 0714F-02_ZT0 NC5 LIVER


title: HCC827_Rep2

description: Parental Cells


title: meyer-00114: ovary_TCGA-04-1360

value: IA


title: meyer-00114: ovary_TCGA-04-1357


title: meyer-00114: ovary_TCGA-04-1356


title: Liver NC ZT0 FT 0714F-02_ZT0 NC1 LIVER


title: Liver NC ZT0 FT 0714F-02_ZT0 NC4 LIVER


title: Liver KD ZT0 FT 0714F-02_ZT0 KD7 LIVER


title: Liver HF ZT12 FT 0714F-02_ZT12 HF7 LIVER


title: meyer-00114: ovary_TCGA-04-1349

value: IV


title: Liver KD ZT0 FT 0714F-02_ZT0 KD5 LIVER


title: Liver KD ZT0 FT 0714F-02_ZT0 KD3 LIVER


title: meyer-00114: ovary_TCGA-04-1348

value: OVARY


title: daf-16;pmk-1, vhp-1 RNAi (ad), replicate 1

city: Berkeley

first: Michael

last: Shapira

state: CA

address: 3060 Valley Life Sciences Bldg room 5163

department: Integrative Biology

institute: UC Berkeley

description: poly T cDNA

hyb_protocol: Hybridizations were done at 43C overnight (16-  > 20hrs) in formamide-based buffer using the Genisphere Array350 labeling system in   chambers humidified with 4X SSC buffer

scan_protocol: Scanned on a GenePix 4000B scanner, Images quantified using Genepix Pro 6

data_processing: Median intensity values were used, Signal to Noise (background checking) threshold of 2, LOWESS normalized, cross-file cutoff of 0.7 using MIDAS software

organism: Caenorhabditis elegans

source_name: daf-16;pmk-1 mutants fed vhp-1 RNAi during adulthood

label_protocol: Samples labeled using the Genisphere Array 350 labeling system

growth_protocol: Animals grown at 25oC

extract_protocol: Total RNA extracted using Trizol (Invitrogen)

treatment_protocol: Animals fed control  or vhp-1 RNAi during development (egg to L4) or adulthood (L4-D2)

tag: strain

tag: age at time of rnai

source_name: Mixed stage C.elegans fed E.coli strain OP50


title: daf-16;pmk-1, control RNAi (ad), replicate 2

description: poly T cDNA

source_name: daf-16;pmk-1 mutants fed control RNAi during adulthood


title: meyer-00114: ovary_TCGA-04-1347

value: Serous Cystadenocarcinoma


title: Liver HF ZT0 FT 0714F-02_ZT0 HF4 LIVER


title: Liver KD ZT0 FT 0714F-02_ZT0 KD1 LIVER


title: Liver HF ZT0 FT 0714F-02_ZT0 HF5 LIVER


title: daf-16;pmk-1, control RNAi (ad), replicate 1

description: poly T cDNA


title: Liver HF ZT0 FT 0714F-02_ZT0 HF3 LIVER


title: meyer-00114: ovary_TCGA-04-1351

value: IIIC


title: meyer-00114: ovary_TCGA-04-1346


title: meyer-00114: ovary_TCGA-04-1350


title: meyer-00114: ovary_TCGA-04-1343


title: daf-16;pmk-1, vhp-1 RNAi (dev), replicate 1

description: poly T cDNA

source_name: daf-16;pmk-1 mutants fed vhp-1 RNAi during development

value: egg


title: daf-16;pmk-1, vhp-1 RNAi (ad), replicate 2

description: poly T cDNA


title: meyer-00114: ovary_TCGA-04-1342


title: daf-16;pmk-1, vhp-1 RNAi (dev), replicate 2

description: poly T cDNA


title: daf-16;pmk-1, control RNAi (dev), replicate 2

description: poly T cDNA

source_name: daf-16;pmk-1 mutants fed control RNAi during development


title: HaWRKY10_rep3

city: Santa Fe

first: Karina

last: Ribichich

state: Santa Fe

address: Colectora Ruta Nac. Nº168 km. 0

country: Argentina

institute: IAL

description: overexpression replicate

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Helianthus annuus

source_name: Leaves from V3 stage sunflower

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

growth_protocol: Sunflower plants were grown in soil and in a controlled growth chamber under a long-day photoperiod (16-h light and 8-h dark at 25 °C) with an illumination of 130–150 µE m-2 s-1 and 40–65% relative humidity for 2–3 weeks

extract_protocol: Samples were immediately frozen in liquid nitrogen and conserved at -80°C until their processing. High quality total RNA was isolated from 100 mg of frozen material using the Trizol® method (Invitrogen, Argentina). The genomic DNA was eliminated after treatment with Dnase I using DNAse I® (Invitrogen, Argentina), according to manufacturer's instructions. RNA concentration was measured using an Implen nanophotometer (Implen GmbH, Munich, Germany). Purity of total RNA was determined by 260/280 and 260/230 nm ratios, the integrity was checked by electrophoresis in 1% agarose gel and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay.

treatment_protocol: Sunflower leaf discs were obtained from V3 sunflower plants as described in Manavella and Chan, Nature Protocols 2009 (doi:10.1038/nprot.2009.178)

tag: construct

value: pBI121_35S Promoter:HaWRKY10

tag: genotype/variation

value: HaWRKY10 overexpression

value: sunflower leave discs


title: Liver HF ZT0 FT 0714F-02_ZT0 HF2 LIVER


title: Gut NC ZT12 FT 0714F-02_ZT12 NC11 DI

value: Gut (DI)


title: meyer-00114: ovary_TCGA-04-1341

value: NOT SPECIFIED


title: Gut NC ZT12 FT 0714F-02_ZT12 NC12 DI

value: Normal Chow


title: meyer-00114: ovary_TCGA-04-1338


title: HaWRKY10_rep2

description: overexpression replicate


title: HaWRKY10_rep1

description: overexpression replicate


title: daf-16;pmk-1, control RNAi (dev), replicate 1

description: poly T cDNA


title: Gut NC ZT12 FT 0714F-02_ZT12 NC9 DI


title: Gut NC ZT12 FT 0714F-02_ZT12 NC10 DI


title: meyer-00114: ovary_TCGA-04-1337


title: pBI121_rep3

description: control replicate

value: pBI121_35S Promoter:GUS

value: control


title: meyer-00114: ovary_TCGA-09-1672

value: FEMALE


title: kgb-1, vhp-1 RNAi (ad), replicate 3

description: poly T cDNA

source_name: kgb-1 mutants fed vhp-1 RNAi during adulthood


title: kgb-1, vhp-1 RNAi (ad), replicate 2

description: poly T cDNA


title: meyer-00114: ovary_TCGA-04-1336

source_name: ovary


title: meyer-00114: ovary_TCGA-04-1335

value: IB


title: kgb-1, vhp-1 RNAi (ad), replicate 1

description: poly T cDNA


title: pBI121_rep2

description: control replicate


title: Gut KD ZT12 FT 0714F-02_ZT12 KD13 DI

value: Ketogenic


title: kgb-1, control RNAi (ad), replicate 4

description: poly T cDNA

source_name: kgb-1 mutants fed control RNAi during adulthood


title: Gut KD ZT12 FT 0714F-02_ZT12 KD8 DI


title: meyer-00114: ovary_TCGA-04-1332


title: Gut KD ZT12 FT 0714F-02_ZT12 KD12 DI


title: pBI121_rep1

description: control replicate


title: kgb-1, control RNAi (ad), replicate 3

description: poly T cDNA


title: Gut KD ZT12 FT 0714F-02_ZT12 KD10 DI


title: meyer-00114: ovary_TCGA-04-1331


title: meyer-00114: ovary_TCGA-01-0642


title: meyer-00114: ovary_TCGA-01-0637


title: kgb-1, control RNAi (ad), replicate 2

description: poly T cDNA


title: meyer-00114: ovary_TCGA-01-0639


title: Gut HF ZT12 FT 0714F-02_ZT12 HF9 DI

value: High Fat


title: kgb-1, control RNAi (ad), replicate 1

description: poly T cDNA


title: meyer-00114: ovary_TCGA-01-0638


title: kgb-1, vhp-1 RNAi (dev), replicate 3

description: poly T cDNA

source_name: kgb-1 mutants fed vhp-1 RNAi during development


title: meyer-00114: ovary_TCGA-01-0636


title: kgb-1, vhp-1 RNAi (dev), replicate 2

description: poly T cDNA


title: Gut HF ZT12 FT 0714F-02_ZT12 HF8 DI


title: meyer-00114: ovary_TCGA-01-0633


title: kgb-1, control RNAi (dev), replicate 3

description: poly T cDNA

source_name: kgb-1 mutants fed control RNAi during development


title: kgb-1, control RNAi (dev), replicate 2

description: poly T cDNA


title: Gut HF ZT12 FT 0714F-02_ZT12 HF12 DI


title: Gut NC ZT0 FT 0714F-02_ZT0 NC6 DI


title: Gut NC ZT0 FT 0714F-02_ZT0 NC3 DI


title: meyer-00114: ovary_TCGA-01-0631


title: Gut HF ZT12 FT 0714F-02_ZT12 HF10 DI


title: Gut NC ZT0 FT 0714F-02_ZT0 NC4 DI


title: meyer-00114: ovary_TCGA-04-1648


title: kgb-1, control RNAi (dev), replicate 1

description: poly T cDNA


title: meyer-00114: ovary_TCGA-01-0630


title: Gut NC ZT0 FT 0714F-02_ZT0 NC1 DI


title: N2, vhp-1 RNAi (ad), replicate 3

description: poly T cDNA

source_name: N2 fed vhp-1 RNAi during adulthood


title: meyer-00114: ovary_TCGA-01-0629


title: N2, vhp-1 RNAi (ad), replicate 2

description: poly T cDNA


title: Gut KD ZT0 FT 0714F-02_ZT0 KD5 DI


title: meyer-00114: ovary_TCGA-01-0628


title: kgb-1, vhp-1 RNAi (dev), replicate 1

description: poly T cDNA


title: Gut KD ZT0 FT 0714F-02_ZT0 KD4 DI


title: N2, control RNAi (ad), replicate 3

description: poly T cDNA

source_name: N2 fed control RNAi during adulthood


title: N2, control RNAi (ad), replicate 2

description: poly T cDNA


title: N2, vhp-1 RNAi (ad), replicate 1

description: poly T cDNA


title: N2, vhp-1 RNAi (dev), replicate 3

description: poly T cDNA

source_name: N2 fed vhp-1 RNAi during development


title: N2, control RNAi (ad), replicate 1

description: poly T cDNA


title: N2, vhp-1 RNAi (dev), replicate 1

description: poly T cDNA


title: N2, vhp-1 RNAi (dev), replicate 2

description: poly T cDNA


title: Gut HF ZT0 FT 0714F-02_ZT0 HF5 DI


title: Gut KD ZT0 FT 0714F-02_ZT0 KD1 DI


title: Gut HF ZT0 FT 0714F-02_ZT0 HF2 DI


title: Gut HF ZT0 FT 0714F-02_ZT0 HF4 DI


title: Gut KD ZT0 FT 0714F-02_ZT0 KD6 DI