title: Seedlings_0.2% oxygen_60min

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

institute: University of Bayreuth

hyb_protocol: Hybridization was carried out as recommended by Affymetrix

scan_protocol: Scanning of microarray signals was carried out as recommended by Affymetrix

data_processing: Raw data (.cel-files) were normalized using the RMA algorithm.

organism: Arabidopsis thaliana

source_name: entire seedling

label_protocol: Biotinylated cRNA was prepared from cDNA samples

growth_protocol: Arabidopsis seedlings were grown for 14 days at 22°C under long day conditions (16h light) on vertically oriented agar plates supplemented with anorganic medium as described in Lauerer at al., (1993): Planta 190, 332–345.

extract_protocol: Total RNA was extracted from Arabidopsis seedlings using the FastRNA-Pro Green Kit with lysing matrix D (Q-Biogene, Heidelberg, Germany)

treatment_protocol: For hypoxia treatments, seedlings were flushed in plastic bags with 0.2% oxygen, 99.8% nitrogen for 30, 60, and 240 minutes.

tag: ecotype

tag: developmental stage

value: seedling 14 days after germination

value: 0.2% oxygen


title: fetal heart_cortisol_140d_ replicate 6

status: Public on Aug 07 2014

type: RNA

city: Gainesville

first: Maureen

last: Keller-Wood

state: FL

department: Pharmacodynamics

country: USA

institute: University of Florida

description: Gene expression at 140 days gestation in fetal heart septum following maternal cortisol infusion for 25 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.2 pmol Cy3/µg cRNA) was  fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the chip median and log transformed.

molecule: total RNA

organism: Ovis aries

source_name: fetal heart_cortisol_140d_ replicate 6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp Labeling 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: Continuous infusions of cortisol to the ewe were begun at approximately day 115 of gestation

extract_protocol: RNA was extracted with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen Rneasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols.Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer

treatment_protocol: Ewes were infused with 1mg/kg/day cortisol or vehicle from approximately day 120 to 130 of pregnancy (n=6/group) or from day 115 to term (n=7, cortisol; n=8 control). Fetal heart septum samples were then collected.

tag: tissue

value: fetal heart septum

tag: agent

value: cortisol

tag: time point

value: 140d gestation


title: zebrafish skeletal muscle TRAP 21 hpf

city: Bad Nauheim

first: Michael

middle: Patrick

last: Housley

state: Hessen

address: Ludwigstr. 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute

hyb_protocol: not provided

scan_protocol: Agilent Feature Extraction

data_processing: Agilent Feature Extraction Software used for background subtraction and linear LOWESS normalization

organism: Danio rerio

source_name: zebrafish larvae

label_protocol: NuGEN pico amp kit amplification

growth_protocol: 28°C, egg water supplemented with biotin

extract_protocol: Translating ribosome affinity purification followed by extraction with Trizol and column purification

treatment_protocol: time course during development 21, 24, 27, and 34 hours post fertilization (hpf)

tag: days post fertlization

value: larvae

source_name: zebrafish skeletal muscle TRAP

tag: hours post fertilization (hpf)


title: methylmercury-1/2-48h

city: Kyoto

first: Wataru

last: Fujibuchi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: 14P0100390-H03_1 48h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadArray in R

organism: Homo sapiens

source_name: KhES-3 cells

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

growth_protocol: Cultured on mTeSR1 with Matrigel™ for human ES cells

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

treatment_protocol: Cells are exposed to 1/2 lethal dose for 48 hours

tag: gender

value: male

tag: chemical category

value: neurotoxin

tag: treatment


title: Seedlings_0.2% oxygen_240min

label: biotin


title: zebrafish skeletal muscle TRAP 24 hpf


title: Seedlings_0.2% oxygen_30min


title: cyclopamine-1/2-48h

description: 14P0100390-H06_4 48h


title: valproic acid-1/2-48h

description: 14P0100390-H05_3 48h

value: valproic acid-1/2-48h


title: acrylamide-1/2-48h

description: 14P0100390-H04_2 48h


title: fetal heart_cortisol_140d_ replicate 5

source_name: fetal heart_cortisol_140d_ replicate 5


title: benzo a anthracene-1/2-48h

description: 14P0100390-H12_10 48h

value: genotoxin

value: benzo a anthracene-1/2-48h


title: control-48h

description: 14P0100390-H02_control 48h.

value: control


title: Seedlings_air_0min

value: air


title: Seedlings_air_240min


title: zebrafish skeletal muscle TRAP 27 hpf


title: fetal heart_cortisol_140d_ replicate 4

source_name: fetal heart_cortisol_140d_ replicate 4


title: zebrafish skeletal muscle TRAP 34 hpf


title: diethylstilbestrol-1/2-48h

description: 14P0100390-H10_8 48h


title: fetal heart_cortisol_140d_ replicate 1

source_name: fetal heart_cortisol_140d_ replicate 1


title: siFOXM1TOT24h

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: MCF-7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7 cells were maintained in MEM media with 5% Calf serum

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

treatment_protocol: MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3) or FOXM1 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 72 h of transfection, cells were treated with 0.1% control ethanol vehicle or 1 uM TOT for 24h

tag: source

value: Breast adenocarcinoma

tag: cell line

value: trans-hydroxy-tamoxifen TOT

tag: knockdown

value: FOXM siRNA


title: control-0h

description: 14P0100390-H01_control 0h


title: fetal heart_cortisol_130d_ replicate 6

description: Gene expression at 130 days gestation in fetal heart septum following maternal cortisol infusion for 10 days

source_name: fetal heart_cortisol_130d_ replicate 6

value: 130d gestation


title: 18 1500 ppm of hexanal was exposed in rats(T3 group)

status: Public on Aug 08 2014

city: Seoul

first: Yoon

last: Cho

address: hwarang-ro 14

country: South Korea

institute: KIST

description: miRNA expression after exposure to 1500ppm hexanal

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

organism: Rattus norvegicus

source_name: Lung, hexanal, 1500 ppm

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

growth_protocol: Fischer-344 rats of both sexes were obtained from at the age of 7-8 weeks from OrientBio, Inc(Korea). The animals were quarantined and acclimated for 5days before the start of experiment. The animals were housed in stainless-steel wire hanging cages(255W×465L×200H ㎜).The environment in the exposure chamber was maintained constant at a temperature of 22±3 ℃ and a relative humadity of 30-70%. All rats were given sterilized commercial pellet diet ( PMI Nutrition International, USA) and sterilized water.

extract_protocol: Total RNA, including miRNA, from lung tissue in rats extracted using Trizol following manufacturer's instructions.

treatment_protocol: Hexanal was inhaled for 5 weeks in Fischer-344 rats(approximately 7-8 weeks old). Atmospheres of hexanal aerosol were generated at target concentrations of 0(control), 600, 1000, 1500 mg/m3 in air. Rats were exposed to the target concentrations for 4h/day, 5days/week.

value: lung

value: 1500 ppm hexanal


title: siCtrlTOT24h rep1


title: fetal heart_cortisol_130d_ replicate 5

source_name: fetal heart_cortisol_130d_ replicate 5

value: fetal heart septum


title: siCtrlVeh24h rep2

value: ethanol


title: siFOXM1Veh24h rep1


title: fetal heart_cortisol_140d_ replicate 2

source_name: fetal heart_cortisol_140d_ replicate 2

value: cortisol

value: 140d gestation


title: siFOXM1Veh24h rep2


title: fetal heart_cortisol_140d_ replicate 3

source_name: fetal heart_cortisol_140d_ replicate 3


title: fetal heart_cortisol_130d_ replicate 4

source_name: fetal heart_cortisol_130d_ replicate 4


title: Primary human hepatic stellate cells, No treatment_24 h, replicate 2

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

description: Gene expression data from primary human hepatic stellate cells receiving no treatment for 24 h.

hyb_protocol: Following fragmentation, ~250 ng of single-stranded cRNA were hybridised on Affymetrix Human U133 Plus2 Expression Arrays (17 h, 45˚C, 60 rpm) in an Affymetrix 640 GeneChip® Hybridization Oven. GeneChips were washed and stained in an Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G GeneChip® Scanner.

data_processing: The data were processed and analysed using Matlab Bioinformatics and Statistical toolboxes. RMA was used as the normalisation method. In-house tools were used to remove batch effects and control for false discovery.

label: Biotin

source_name: Primary human hepatic stellate cells receiving no treatment for 24 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-5 ug total RNA (GeneChip(R) 3' IVT Plus Reagent Kit User Manual, Affymetrix).

growth_protocol: Primary human hepatic stellate cells suspended in complete hepatocyte cell culture medium (HM-5201) were seeded (120,000 cells/well) into 6-well culture plates and grown overnight at 37˚C, 10% CO2.

extract_protocol: Total RNA was extracted from cells using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following the manufacturer’s instructions.

treatment_protocol: Medium was removed and replaced for 24 h with medium containing 30 ug/ml nanoparticles, 30 ug/ml ZnSO4, or medium containing no treatment. Cells were incubated at 37˚C, 10% CO2 for 24 h.

tag: cell type

value: cultured primary human hepatic stellate cells

tag: treatment duration


title: fetal heart_cortisol_130d_ replicate 2

source_name: fetal heart_cortisol_130d_ replicate 2


title: Primary human hepatic stellate cells, Nanosun 30 ug/ml_24 h, replicate 2

description: Gene expression data from primary human hepatic stellate cells receiving treatment with 30 ug/mL Nanosun for 24 h.

source_name: Primary human hepatic stellate cells receiving treatment with 30ug/mL Nanosun for 24 h

value: Nanosun


title: Primary human hepatic stellate cells, Z-COTE 30ug/ml_24 h, replicate 2

description: Gene expression data from primary human hepatic stellate cells receiving treatment with 30 ug/mL Z-COTE for 24 h.

source_name: Primary human hepatic stellate cells receiving treatment with 30ug/mL Z-COTE for 24 h

value: Z-COTE


title: fetal heart_cortisol_130d_ replicate 3

source_name: fetal heart_cortisol_130d_ replicate 3


title: Primary human hepatic stellate cells, Z-COTE HP1 30 ug/ml_24 h, replicate 2

description: Gene expression data from primary human hepatic stellate cells receiving treatment with 30 ug/mL Z-COTE HP1 for 24 h.

source_name: Primary human hepatic stellate cells receiving treatment with 30ug/mL Z-COTE HP1 for 24 h

value: Z-COTE HP1


title: siCtrlTOT24h rep2


title: Primary human hepatic stellate cells, ZnSO4 30ug/ml_24 h, replicate 2

description: Gene expression data from primary human hepatic stellate cells receiving treatment with 30 ug/mL ZnSO4 for 24 h.

source_name: Primary human hepatic stellate cells receiving treatment with 30ug/mL ZnSO4 for 24 h


title: Primary human hepatic stellate cells, Z-COTE MAX 30 ug/ml_24 h, replicate 2

description: Gene expression data from primary human hepatic stellate cells receiving treatment with 30 ug/mL Z-COTE MAX for 24 h.

source_name: Primary human hepatic stellate cells receiving treatment with 30ug/mL Z-COTE MAX for 24 h

value: Z-COTE MAX


title: Primary human hepatic stellate cells, Nanosun 30 ug/ml_24 h, replicate 1


title: fetal heart_cortisol_130d_ replicate 1

source_name: fetal heart_cortisol_130d_ replicate 1


title: GBM Patient, #1

city: San Diego

first: Clark

middle: C

last: Chen

state: CA

address: 3855 Health Sciences Drive, Room 5345, Bay 5M

department: Neurosurgery

institute: UC San Diego

hyb_protocol: Following manufaturers protocols for HG-U133_PLUS_2 platform

scan_protocol: unknown

data_processing: Microarray data were GC Robust Multiarray Average normalized using R and the bioconductor.org package gcrma using a gene-level probeset, in order to allow pathway signature analysis.

source_name: Glioblastoma tissue sample

label_protocol: unknown

extract_protocol: Tumors were collected as fresh-frozen specimen

treatment_protocol: Patients were newly diagnosed and yet to undergo treatment for GBM.

tag: tissue type

value: Glioblastoma tumor

tag: grade

value: IV


title: siCtrlVeh24h rep1

source_name: MCF-7 cells

value: Breast adenocarcinoma

value: control


title: Primary human hepatic stellate cells, Z-COTE 30ug/ml_24 h, replicate 1


title: fetal heart_control_140d_ replicate 8

description: Gene expression at 140 days gestation in fetal heart septum

source_name: fetal heart_control_140d_ replicate 8


title: Primary human hepatic stellate cells, ZnSO4 30ug/ml_24 h, replicate 1


title: Primary human hepatic stellate cells, Z-COTE MAX 30 ug/ml_24 h, replicate 1


title: Primary human hepatic stellate cells, No treatment_24 h, replicate 1


title: fetal heart_control_140d_ replicate 6

source_name: fetal heart_control_140d_ replicate 6


title: fetal heart_control_140d_ replicate 5

source_name: fetal heart_control_140d_ replicate 5


title: SK-OV-3+BMP2+DM_biological rep1

first: Jin

last: Peng

address: 54 Shogoin Kawaharacho, Sakyo-ku

department: Department of Gynecology and Obstetrics

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from SK-OV-3 cell line cultured with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM)

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

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

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

source_name: SK-OV-3 cultured with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM)_biological rep1

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

growth_protocol: SK-OV-3 cells were incubated in 12 separate culture dishes, 3 dishes with PBS, 3 dishes with recombinant BMP2 (rBMP2) (100 ng/ml), 3 dishes with DM (5 μM) and 3 dishes with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM) in the culture medium for 24 hours prior to the analysis.


title: Ductal cells, Fbw7 KO, YFP, tamoxifen

city: London

first: Rocio

last: Sancho

state: London

address: 44 Lincoln's inn fileds

department: Mammalian Genetics

country: United Kingdom

institute: London Research Institute - CRUK

hyb_protocol: Following labelling samples were hybridized for 18 hr at 45C on Affymetrix Mouse Gene 1.0 ST GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 running GCOS software.

data_processing: Raw data were summarised at the core gene level using the “rma” (Robust Multichip Average) function from the Bioconductor package “oligo”, with default RMA background correction and quantile normalisation settings.

organism: Mus musculus

source_name: Pooled mouse KO pancreatic ductal cells, 7 days after tamoxifen injection (n=6 mice)

label_protocol: After fragmentation, labelling was performed using the NuGEN FL-Ovation cDNA Biotin module v2.

growth_protocol: Mice were maintained in CRUK animal facility following the standard regulations. All mice used were >6 weeks old.

extract_protocol: RNA from 30000 FACS sorted cells was extracted using RNAeasy-micro-kit (Qiagen) following the manufacturers instructions. The RNA (18ng) was amplified using the NuGEN WT-Ovation Pico RNA amplification System and converted using NuGEN WT-Ovation Exon Module.

treatment_protocol: When applicable mice were Intraperitoneally injected with tamoxifen for 5 consecutive days and the samples were collected 7 days after last tamoxifen injection

value: pooled ductal cells

tag: genotype

value: Fbw7 F/F; Ck19-CreERT; R26-LSL-YFP;

tag: cell label

value: YFP

value: tamoxifen

tag: genetic background


title: fetal heart_control_140d_ replicate 4

source_name: fetal heart_control_140d_ replicate 4

tag: tissue

value: fetal heart septum

tag: agent

tag: time point:


title: Ductal cells, Fbw7 WT, YFP, tamoxifen

source_name: Pooled mouse WT pancreatic ductal cells, 7 days after tamoxifen injection (n=6 mice)

value: Fbw7 +/+; Ck19-CreERT; R26-LSL-YFP;


title: Beta cells, Fbw7 WT, GFP, untreated

source_name: Pooled mouse WT pancreatic beta cells (n=3 mice)

value: pooled pancreatic beta cells

value: Fbw7 +/+; MIP-GFP;

value: GFP

value: untreated


title: SK-OV-3+DM_biological rep3

description: Gene expression data from SK-OV-3 cell line cultured with DM (5 μM)

source_name: SK-OV-3 cultured with DM (5 μM)_biological rep3


title: SK-OV-3+BMP2+DM_biological rep3

source_name: SK-OV-3 cultured with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM)_biological rep3


title: PBMC CMV biological repeat 2

city: Silver Spring

first: Haitao

last: Hu

state: MD

address: 503 Robert Grant Ave

department: US Military HIV Research Program

institute: Walter Reed Army Institute of Research

description: Gene expression data for Antigen-specific CD4 T cells sorted from Antigen-stimulated PBMC

hyb_protocol: The labeled cRNA were hybridized to Human Gene 2.0 ST Gene-Chips (Affymetrix) according to the manufacture’s instructions; The arrays were then washed and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A GeneChip 3000 7G scanner (Affymetrix) was used to collect fluorescence signal.

data_processing: Data were analyzed using the R computing environment version 2.12.2. The data were normalized using RMA.  The Affymetrix console has an integrated pipeline which generates RMA normalized data with some irrelevant rows filtered out.

source_name: PBMC donor 048 from WRAIR RV229-CMV stimulation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Human primary PBMC cells were maintained and grown in complete RPMI media supplemented with normal human serum

extract_protocol: Total RNA were extracted from the sorted cells using RNAesy plus mini kit (Qiagen)

treatment_protocol: Cells were CFSE-labeled and then stimulated with human Ad5 and CMV antigens (peptide pools) for 6 hours, followed by sorting of Ag-specific CD4 T cells from PBMC by FACS Aria based on CFSE-low

tag: individual

value: healthy donor 048

value: blood

value: PBMC

value: stimulated with CMV antigens

tag: cell type (total rna source)

value: antigen-specific CD4 T cells


title: SK-OV-3+BMP2+DM_biological rep2

source_name: SK-OV-3 cultured with recombinant BMP2 (rBMP2) (100 ng/ml) plus DM (5 μM)_biological rep2


title: fetal heart_control_140d_ replicate 2

source_name: fetal heart_control_140d_ replicate 2

tag: time point

value: 140d gestation


title: PBMC Ad5 biological repeat 3

source_name: PBMC donor 060 from WRAIR RV229-Ad5 stimulation

value: healthy donor 060

value: stimulated with Ad5 antigens


title: PBMC CMV biological repeat 3

source_name: PBMC donor 060 from WRAIR RV229-CMV stimulation


title: PBMC Ad5 biological repeat 2

source_name: PBMC donor 048 from WRAIR RV229-Ad5 stimulation


title: fetal heart_control_140d_ replicate 3

source_name: fetal heart_control_140d_ replicate 3

value: control


title: SK-OV-3+DM_biological rep1

source_name: SK-OV-3 cultured with DM (5 μM)_biological rep1


title: SUB32 Patient, rhinovirus-exposed

city: Tucson

first: Vincent

last: Gardeux

state: AZ

address: 1657 East Helen Street, PO Box 210240

department: Medicine

institute: University of Arizona

hyb_protocol: Hybridization were performed following Affymetrix protocols

scan_protocol: standard Affymetrix protocol

data_processing: The raw data were normalized according to the Robust Multiple-array Average (RMA) normalization. The normalization was applied on each patient data independently (2 paired samples at a time, to avoid bias in the single-patient experiments) using Affymetrix Power Tools (APT).

source_name: PBMC_ex vivo rhinovirus-infected

label_protocol: Labeling of cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: The live PBMCs had been isolated from blood samples collected from four human subjects under a protocol approved by The University of Arizona Internal Review Board. Whole blood was obtained from donors and placed in heparin tubes that were centrifuged according to standard protocols to obtain PBMCs, then each aliquoted in two paired samples. Each sample of the pair was subsequently exposed to and incubated with either (i) Human Rhinovirus serotype 16 obtained from the American Type Culture Collection (RV; ATCC® VR-283; ex vivo infected sample), or to (ii) sterile medium (control ex vivo non-infected sample) and incubated at 35°C. This protocol resulted in 4 ex vivo infected + 4 ex vivo controls = 8 paired samples. RNA was extracted from these samples, amplified, tagged and hybridized on Affymetrix Human Gene 1.0 ST microarrays according to standard operating procedures.

tag: subject id

value: SUB32 Patient

value: Peripheral blood mononuclear cells (PBMCs)

tag: exposed to

value: Human Rhinovirus serotype 16


title: SK-OV-3+DM_biological rep2

source_name: SK-OV-3 cultured with DM (5 μM)_biological rep2

tag: cell line


title: fetal heart_control_140d_ replicate 1

source_name: fetal heart_control_140d_ replicate 1

value: fetal heart septum


title: fetal heart_control_130d_ replicate 6

description: Gene expression at 130 days gestation in fetal heart septum

source_name: fetal heart_control_130d_ replicate 6

value: 130d gestation


title: PBMC CMV biological repeat 1

source_name: PBMC donor 026 from WRAIR RV229-CMV stimulation

value: healthy donor 026


title: SUB32 Patient, Control

source_name: PBMC_control ex vivo non-infected

value: sterile medium


title: SUB19 Patient, rhinovirus-exposed

value: SUB19 Patient


title: SK-OV-3+BMP2_biological rep2

description: Gene expression data from SK-OV-3 cell line cultured with recombinant BMP2 (rBMP2) (100 ng/ml)

source_name: SK-OV-3 cultured with recombinant BMP2 (rBMP2) (100 ng/ml)_biological rep2


title: SK-OV-3+BMP2_biological rep1

source_name: SK-OV-3 cultured with recombinant BMP2 (rBMP2) (100 ng/ml)_biological rep1


title: PBMC Ad5 biological repeat 1

source_name: PBMC donor 026 from WRAIR RV229-Ad5 stimulation


title: SUB19 Patient, Control


title: fetal heart_control_130d_ replicate 5

source_name: fetal heart_control_130d_ replicate 5


title: fetal heart_control_130d_ replicate 4

source_name: fetal heart_control_130d_ replicate 4


title: M8 Patient, rhinovirus-exposed

value: M8 Patient


title: SUB11 Patient, Control

value: SUB11 Patient


title: SK-OV-3_biological rep2

description: Gene expression data from SK-OV-3 cell line

source_name: SK-OV-3 cultured with PBS_biological rep2


title: SK-OV-3_biological rep3

source_name: SK-OV-3 cultured with PBS_biological rep3


title: BF638R in vivo Day 8 rep2

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

hyb_protocol: Hybridization was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

scan_protocol: Scanning was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142)

data_processing: Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using NimbleGen Systems DEVA 1.1 software as described on their web site.            Raw data (pair files) were subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185) using DEVA 1.1 software downloaded from Roche/NimbleGen as described on their web site (http://www.nimblegen.com/downloads/support/06271090001_DEVA_UserGuide_v1p2.pdf).

organism: Bacteroides fragilis 638R

source_name: Samples of in vivo tissue cage grown cells Day8

label_protocol: Labeling was performed by at the FSU NimbleGen Microarray Facility, using standard protocols as described previously (Sund et al., 2008, Mol. Microbiol. 67:129-142).

growth_protocol: For in vitro samples: Overnight cultures of Bacteroides fragilis 638R were diluted into defined media contain either 0.5% glucose or 2% mucin glycans, and grown to mid-logarithmic phase at A550 of 0.5 complex media ( Rocha et al. 1996, J. Bacteriol. 178:6895). For in vivo samples, BF638R cells were grown in a tissue cage in rats and sampled on days 1,4, and 8 post-inoculation as described by Lobo et al. 2013, MicrobiologyOpen 2:326.

extract_protocol: Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.

tag: treatment

value: in vivo tissue cage grown cells

tag: time

tag: sample type


title: SUB11 Patient, rhinovirus-exposed

tag: cell type


title: BF638R in vivo Day 8 rep1

value: Samples of in vivo tissue cage grown cells Day8


title: BF638R in vivo Day 4 rep2

source_name: Samples of in vivo tissue cage grown cells Day4


title: M8 Patient, Control


title: fetal heart_control_130d_ replicate 2

source_name: fetal heart_control_130d_ replicate 2


title: BF638R in vivo Day 4 rep1

value: Samples of in vivo tissue cage grown cells Day4


title: fetal heart_control_130d_ replicate 3

source_name: fetal heart_control_130d_ replicate 3


title: SK-OV-3+BMP2_biological rep3

source_name: SK-OV-3 cultured with recombinant BMP2 (rBMP2) (100 ng/ml)_biological rep3


title: SK-OV-3_biological rep1

source_name: SK-OV-3 cultured with PBS_biological rep1


title: fetal heart_control_130d_ replicate 1

source_name: fetal heart_control_130d_ replicate 1


title: fetal lung_aldosterone_twin, replicate4

description:
aldo_4
Gene expression after 48h in aldosterone-treated fetal lung.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.5 pmol Cy3/ug cRNA) was fragmented and hybridized to Agilent-019921 Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112) background detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the chip median and log transformed.

source_name: fetal lung, aldosterone

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 450 ng RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 5 days after surgery, infusions were started.

extract_protocol: RNA was extracted with Trizol (Ambion, Carlsbad, CA), and purified through Qiagen RNeasy+ kits (QIAGEN, Valencia, CA) according to manufacturers' protocols. Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer.

treatment_protocol: 1 fetus of twins was infused with 0.2 mg aldosterone over 2 days and its twin was control. Lung samples were then collected.

value: fetal lung

value: aldosterone


title: fetal lung_control_twin, replicate4

description:
con_4
Gene expression after 48h in con fetal lung.

source_name: fetal lung, control


title: BF638R in vivo Day 1 rep2

source_name: Samples of in vivo tissue cage grown cells Day1


title: Lung cancer Basaloid44

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

hyb_protocol: 20 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 array.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray scanner

data_processing: The data was normalized by Robust Multi-Array average (RMA) algorithm (Genespring software; Agilente)

source_name: Lung Tumour

value: Lung Tumour

tag: age at surgery

tag: gender

value: M

tag: histology

value: BAS

tag: pt stage

tag: pn stage

tag: pm stage

tag: follow-up time (months)

tag: status

value: DEAD

tag: disease free survival in months

tag: relapse (event=1; no event=0)


title: Lung cancer Large Cell Neuroendocrine60

tag: tissue

value: LCNE

value: MX

value: ALIVE


title: fetal lung_aldosterone_twin, replicate3

description:
aldo_3
Gene expression after 48h in aldosterone-treated fetal lung.


title: fetal lung_control_twin, replicate3

description:
con_3
Gene expression after 48h in con fetal lung.

value: control


title: fetal lung_control_twin, replicate2

description:
con_2
Gene expression after 48h in con fetal lung.


title: BF638R in vivo Day 1 rep1

value: Samples of in vivo tissue cage grown cells Day1


title: Mut2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: ARR2PB-Cre;ROSA(N1IC) model, prostate sample 2

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.

label: Alexa Fluor 647

source_name: prostate from PB-NICD model

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

growth_protocol: Data were generated using mice of C57Bl/6 background. The ARR2PB-Cre transgenic mice were from Dr. Fen Wang at the Institute of Bioscience and Technology, Texas A&M Health Science Center (Jin et al., 2003, PMID:12949940). The Gt(ROSA)26Sortm1(Notch1)Dam/J (ICNf/f), and B6(Cg)-Gt(ROSA)26Sortm4(Ikbkb)Rsky/J mice were purchased from the Jackson Laboratory (Bar Harbor, ME).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

tag: strain

tag: genotype/variation

value: :ARR2PB-Cre;ROSA(N1IC) model (a.k.a. PB-NICD) that expresses the Notch1 intracellular domain (NICD or N1IC) in the prostate and develops prostatic intraepithelial neoplasia (PIN lesions).

label: Alexa Fluor 555

source_name: mouse, universal reference RNA

tag: reference

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: BF638R DM-mucin media rep2

source_name: grown in vitro to mid-log phase in defined media with mucin glycans

tag: treatment


title: Lung Squamous Cell Carcinoma66

value: SQC


title: Primary human hepatic stellate cells, Z-COTE HP1 30 ug/ml_24 h, replicate 1

source_name: Primary human hepatic stellate cells receiving treatment with 30ug/mL Z-COTE HP1 for 24 h

value: cultured primary human hepatic stellate cells

value: Z-COTE HP1

tag: treatment duration


title: Lung cancer Large Cell Neuroendocrine58


title: Lung cancer Large Cell Neuroendocrine59


title: BF638R DM-mucin media rep1

value: grown in vitro to mid-log phase in defined media with mucin glycans

tag: sample type


title: Mut1

description: ARR2PB-Cre;ROSA(N1IC) model, prostate sample 1


title: BF638R DM-glucose media rep3

source_name: grown in vitro to mid-log phase in defined media with glucose


title: WT4

description: wild-type model, sample 4

source_name: prostate from wild-type model

value: :control ROSA(N1IC) mice (NICD wild-type)


title: BF638R DM-glucose media rep2

value: grown in vitro to mid-log phase in defined media with glucose


title: Lung Squamous Cell Carcinoma65

value: Lung Tumour

tag: age at surgery


title: Lung cancer Carcinoid24

tag: gender

value: F

value: CARCI


title: Lung Squamous Cell Carcinoma64

value: M

tag: histology

value: DEAD


title: BF638R DM-glucose media rep1


title: Lung cancer Large Cell Neuroendocrine57

value: LCNE

tag: pt stage


title: fetal lung_aldosterone_twin, replicate1

description:
aldo_1
Gene expression after 48h in aldosterone-treated fetal lung.

value: fetal lung

value: aldosterone


title: fetal lung_aldosterone_twin, replicate2

description:
aldo_2
Gene expression after 48h in aldosterone-treated fetal lung.


title: Mut3

description: ARR2PB-Cre;ROSA(N1IC) model, prostate sample 3


title: Lung cancer Large Cell Neuroendocrine56

tag: pn stage


title: Mnase_Ctrl_3

status: Public on Aug 06 2014

type: genomic

city: Tsuruoka

first: Douglas

middle: Brian

last: Murray

state: Yamagata

address: Nipponkoku 403-1, Daihouji

institute: Institute for Advanced Biosciences

hyb_protocol: Followed the user guide (NimbleGen Arrays User’s Guide: ChIP-chip Arrays, version 6.2)

scan_protocol: Scanned on an Agilent Microarray Scanner (G2565BA, Agilent, Japan) https://www.chem.agilent.com/Library/usermanuals/Public/G2566-90017.pdf

data_processing: raw values on each channel were normalized by the least variant set (var < 0.1; Calza S, Valentini D, Pawitan Y (2008) Normalization of oligonucleotide arrays based on the least-variant set of genes. BMC Bioinformatics 9:140), then log ratio was calculated and the MNase control average was substracted. Processed_data file contains the following values: log2(MNase digest/genomic)-log2(avg(Mnase control)/avg(genomic)).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: ~1ug of sample was labeled according to the labeling kit instructions (NimbleGen Dual-Color Labeling Kit, Roche, Japan, catalog number: 06370270001).

extract_protocol: Samples (1 mL) were fixed in formaldehyde (1% v/v) and placed on a rotator (5 rpm, room temperature, 12 min), then neutralized with 0.1 volume of 2M glycine and placed again on a rotator (5 rpm, room temperature, 12 min). Samples were then centrifuged (5200g, room temperature, 1 min) and the supernatant was discarded. The pellets were stored at -80°C.   Cross-linked samples were thawed on ice, washed twice in 1 mL TBS and pelleted at 12000 g, 4°C, 2 min. Pellets were resuspended in 500 μL of Zymolyase digestion solution (50 mM Tris-HCl pH 7.4, 0.07% 2-Mercaptoethanol, 1000 U/mL of Zymolyase 100T) and incubated on a rotator (5 rpm, room temperature, 1 h). MNase (microccocal nuclease) digestion mix containing Igepal (0.1%), spermidine (200 μM), NaCl (50 mM), MgCl2 (5 mM) and CaCl2 (1mM) were added to the tubes to the final concentrations that are shown in parentheses. MNase (150 U) and RNase A (5 μL) were then added, and samples were incubated (37°C; 30 min). The NaCl, MgCl2, CaCl2 & MNase were omitted if genomic DNA was required. To stop the digestion, tubes were transferred to an ice bath then EDTA and SDS were added to a final concentration of 0.01 M and 0.05%, respectively.   Each sample was then centrifuged (12000 g, 4°C, 10 min), the supernatant was transferred, and 10 μL Proteinase K was added (20 μg in 100 μL of nuclease free water; Roche, Japan). After an overnight incubation (65°C, ~10h) the reaction mixture was transferred to 550 μL phenol:chloroform:isoamyl alcohol 25:24:1 in phase-lock tubes (MaXtract Low Density, Quiagen, Japan), and centrifuged (12000 g, room temperature, 5 min). The aqueous phase was transferred to a new tube in which ethanol (2 v/v), glycogen (0.04 v/v) and 5 M NaCl (0.04 v/v) were added. After centrifugation (12000 g, room temperature, 30 min), the supernatant was discarded and pellet was washed twice with 1 mL 80% ethanol. The pellet was then resuspended in 100 μL water and purified using QIAquick PCR purification kit (Qiagen) according to the manufacturer's instructions. The final samples were eluted in 100 μL nuclease-free water and stored at 4°C. MNase control samples were prepared by mixing 20 μL of purified genomic DNA sample with 480 μL with 50 mM Tris-HCl pH 7.4, and MNase digestion mix was added as above. After the addition of MNase (3 U), samples were incubated (37°C; 10 min), digestion was stopped and samples were purified as before.

tag: time-point (min)

tag: dissolved oxygen (%)


title: Mnase_Ctrl_1


title: Lung cancer ADK88

value: ADC

tag: pm stage

tag: follow-up time (months)

tag: status

value: ALIVE


title: WT2

description: wild-type model, sample 2

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: DNA_occupancy_TP32


title: DNA_occupancy_TP33


title: DNA_occupancy_TP31


title: CD304 Monocyte derived macrophage_Unstimulated

first: Tony

last: Segal

address: 5 University Street

institute: UCL

hyb_protocol: Labelled cRNA was hybridised to Illumina Human-WG6 v3.0 Expression BeadChips (Illumina) for 16 h at 58°C

scan_protocol: Scanned using the Beadarray reader

data_processing: Image data was processed using Genome Studio software. The Sample data were trimmed to include only the genes that were expressed consistently in our monocyte derived macrophages. Only probes that were detected at p < 0.01 in at least 50% of the samples were retained for analysis.

label_protocol: standard Illumina protocol

growth_protocol: Peripheral venous blood samples were collected into heparin (5 U/ml). Mononuclear cells were isolated by differential centrifugation (900 g, 30 mins, 20°C) over Lymphoprep® (Axis-Shield, Oslo, Norway) and washed twice with sterile phosphate-buffered saline (PBS) (GIBCO, Paisley, UK) at 300 g (5 mins, 20°C). Cells were resuspended in 10 ml RPMI (Invitrogen, Paisley, UK) supplemented with 100 U/ml of penicillin (GIBCO) and 100 mg/ml streptomycin (GIBCO) and 20 mM Hepes buffer (Sigma-Aldridge, Poole, UK) (RPMI), and plated at a density of approximately 5×106 cells/ml in 8cm2 NunclonTM Surface tissue culture dishes (Nunc, Roskilde, Denmark). After an initial culture period of 2 h at 37°C, 5% CO2, the non-adherent cells were discarded and 10 ml of fresh RPMI supplemented with 10% foetal bovine serum (FBS) (Sigma) (10% FBS/RPMI) added to each tissue culture dish. Cells were then cultured for 5 days at 37°C, 5% CO2, with the addition of a further 10 ml fresh 10% FBS/RPMI after 24 h. Adherent cells were scraped on day 5 and re-plated at 105/well for cytokine analysis and 106/well for RNA extraction in X-Vivo-15 medium (Cambrex, Walkersville, MD, USA).

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen)

treatment_protocol: cells are untreated

tag: disease

value: Crohn's Disease

tag: stimulation

value: Unstimulated

tag: batch


title: DNA_occupancy_TP30


title: Mnase_Ctrl_2


title: HC201 Monocyte derived macrophage_Unstimulated

value: Healthy Control


title: DNA_occupancy_TP28


title: WT1

description: wild-type model, sample 1

tag: strain

tag: genotype/variation

tag: reference


title: HC310 Monocyte derived macrophage_Unstimulated


title: HC300 Monocyte derived macrophage_Unstimulated


title: CD433 Monocyte derived macrophage_Unstimulated


title: CD276 Monocyte derived macrophage_Unstimulated


title: fetal heart_control_140d_ replicate 7

description: Gene expression at 140 days gestation in fetal heart septum

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.2 pmol Cy3/µg cRNA) was  fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112)  background detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data were normalized to the chip median and log transformed.

source_name: fetal heart_control_140d_ replicate 7

tag: tissue

value: fetal heart septum

tag: agent

value: control

tag: time point

value: 140d gestation


title: HC279 Monocyte derived macrophage_Unstimulated

tag: gender


title: CD306 Monocyte derived macrophage_Unstimulated


title: DNA_occupancy_TP27


title: DNA_occupancy_TP26


title: HC280 Monocyte derived macrophage_Unstimulated


title: CD438 Monocyte derived macrophage_Unstimulated


title: CD414 Monocyte derived macrophage_Unstimulated


title: HC250 Monocyte derived macrophage_Unstimulated


title: WT3

description: wild-type model, sample 3

value: :control ROSA(N1IC) mice (NICD wild-type)


title: DNA_occupancy_TP22


title: DNA_occupancy_TP21


title: DNA_occupancy_TP23


title: DNA_occupancy_TP20


title: CD418 Monocyte derived macrophage_Unstimulated


title: CD434 Monocyte derived macrophage_Unstimulated

value: F


title: MNEP_SEEDLING_REP2

city: Tallahassee

first: Daniel

last: Vera

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

hyb_protocol: Per manufacturer instructions for NimbleGen dual-color Arrays

data_processing: Generation of probe-level log2 ratios (Cy3/Cy5) was performed with NimbleScan 2.6 (Roche). Probe-level log2 (Cy3/Cy5) ratios were quantile-normalized using the R statistical computing software.

organism: Zea mays

source_name: nucleosomal DNA from seedling nuclei

label_protocol: Per manufacturer instructions for NimbleGen dual-color Labeling kit

extract_protocol: Ten grams of seedling tissue, or 1g of immature ear tissue, were ground under liquid nitrogen with a mortar and pestle and crosslinked by stirring for 10 minutes in 10 mL ice-cold nuclear isolation buffer with 1% formaldehyde. Fixation was stopped with 125 mM Glycine for 5 minutes. Tissue was pelleted at 2,000 x g for 10 min at 4ºC in a swinging-bucket centrifuge, then the tissue pellet was resuspended in 25 mL nucleus isolation buffer with 1% hexylene glycol and 1% Triton X-100. After 5 minutes of gentle rotary shaking, nuclear suspensions were filtered through 2 layers of miracloth (Calbiochem) and nuclei were pelleted at 2,000 x g for 10 min at 4ºC.  Nuclei were washed once with 10 mL nuclear isolation buffer, and resuspended in 10 mL MNase digestion buffer (50 mM Tris-HCl pH 7.5, 320 mM sucrose, 4 mM MgCl2, 1 mM CaCl2). Nuclei were sequentially filtered through 150, 100, 50 and 30 µm CellTric® filters (Partec), pelleted at 2,000 x g for 10 min at 4ºC, resuspended in 1 ml of MNase Digestion Buffer, flash frozen in liquid nitrogen, and stored at -80C until use. 100 uL nuclei were digested with MNase at 37 C for 5 minutes and stopped with 20 mM EGTA. 100 uL diH20 was added to each sample and nuclei were decrosslinked with 1% SDS and 100 ug/mL Proteinase K overnight at 65 ºC. DNA was phenol-chloroform extracted, ethanol precipitated, and resuspended in diH20. Digested DNA were treated with 40 ug/mL RNase A and run in a 1% agarose gel. 100-200-bp DNA fragments were excised and gel extracted with the Qiaex II gel extraction kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Mnase digestion

tag: cultviar

value: seedling

tag: mnase concentration

value: 2 U/mL MNase

tag: buffer

value: MNEP (15mm Tris HCl pH 7.5, 300Mm Sucrose, 5mM MgCl2, 60Mm KCl, 15Mm NaCl, 0.1Mm PMSF, 0.1Mm EGTA, 0.5Mm DTT, 1% Triton-X10)

tag: fraction

value: nucleosomal DNA

source_name: bare genomic DNA from seedling nuclei

value: bare genomic DNA


title: DNA_occupancy_TP24

tag: time-point (min)

tag: dissolved oxygen (%)


title: MNEP_SEEDLING_REP1

scan_protocol: Per manufacturer instructions for NimbleGen dual-color Arrays


title: DNA_occupancy_TP25


title: DNA_occupancy_TP19


title: CD371 Monocyte derived macrophage_Unstimulated


title: MNEP_EARSHOOT_REP2

source_name: nucleosomal DNA from earshoot nuclei

value: immature ear

source_name: bare genomic DNA from earshoot nuclei


title: DNA_occupancy_TP18


title: MNEP_EARSHOOT_REP1

value: 2 U/mL Mnase


title: tlo1-HA ChIP replicate 1

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

description: Co-hybridization of genomic DNA from C. dubliniensis whole cell extracts and anti-HA ChIP DNA immuoprecipitated from a Tlo1-HA tagged strain

hyb_protocol: Competitive hybridization was carried out on a whole genome C. dubliniensis oligonucleotide microarray consisting of 175,758 unique 60mer probes, spaced at 20 bp intervals (Agilent Technologies). Array hybridization and washing were carried out using standard Agilent Technologies CGH hybridization buffers and washes.

scan_protocol: Scanning of the array was carried out on an Agilent G2565B rotating multi-slide hyb-scanner (Agilent Technologies) using a 5 µm resolution and PMT settings at 100% for both channels (Green/Red). The scan area was set to 61 X 21.6 mm. The raw images were processed using Agilent Feature Extraction software suite v 10.5.1.1. and feature extraction was automatically carried out using the ‘CGH automatic’ programme to align and normalize fluorescent probe spots on the array.

data_processing: Data were read into the Bioconductor package Ringo and pre-processed with the “nimblegen” method. This was followed by merging of replicates and smoothing with a window half size of 500 bp. ChIP-enriched regions were calculated with an enrichment threshold based firstly on a 0.8 percentile, followed by a more stringent 0.9 percentile which was used for the analysis presented here. Genes were assigned to an enrichment region if they overlapped up to 500 bp away from the gene boundaries. The resulting list of candidates was filtered for a Ringo peak score >= 3.886. For visualisation of the data a JBrowse instance was set up on http://bioinf.gen.tcd.ie/jbrowse1.6/cdub.html

organism: Candida dubliniensis

source_name: Candida dubliniensis strain tlo1-HA whole cell extract DNA

label_protocol: Microarray chip analysis (CGH Microarray) was carried out as described in the Agilent Yeast ChIP-on-chip analysis protocol handbook (Version 9.2, 2007).Experiments were performed with triplicate biological replicate samples. The IP samples were labelled with Cy5 and input samples (total lysate control) were labelled with Cy3. One sample was dye swapped.

growth_protocol: Candida cells were cultured in standard YEPD broth at 30˚C until they reached OD600nm 2.0

extract_protocol: Pellets that were stored at 4 °C were resuspended in 3 ml of pre-spheroplasting buffer (200 mM Tris pH 9.5, 10 mM Dithiothreitol [DTT], prepared immediately prior to use). The resulting pellet was washed with 5 ml spheroplasting buffer (1.2 M sorbitol, 20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [HEPES] pH 7.4), followed by centrifugation as before. Supernatants were discarded and pellets re-suspended in 5ml spheroplasting buffer. Zymolyase 100T (AMS Biotechnology, Abingdon, UK) was added to each suspension to a final concentration of 0.4 mg/ml from a pre-prepared 10 mg/ml stock solution (prepared in 1.2 M Sorbitol).  4-(2-Aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF) was added to each suspension to a final concentration of 0.5 mM from a pre-prepared 100 mM stock solution. Progress of spheroplasting was checked in 45 minute intervals by preparing a wet mount of 10 μl of the suspension and viewing on a light microscope. Number of spheroplasts was represented as a percentage of 100 randomly counted cells.At this point, 5 ml of pre-chilled post-spheroplasting buffer (1.2 M Sorbitol, 1mM MgCl2, 20 mM 1,4-Piperazinediethanesulfonic acid [PIPES] pH 6.8) was added followed by centrifugation at 2,000 x g for 5 min at 4°C. While keeping all samples stored in ice, the supernatant was removed and the pellet washed with 5 ml of pre-chilled PBS with the addition of 0.5 mM AEBSF. Samples were centrifuged as before and the supernatant discarded. Cell pellets were washed with 5 ml of pre-chilled Buffer 1 (0.25 % v/v Triton X-100, 10 mM ethylenediaminetetraaceticacid [EDTA] pH 8.0, 0.5 mM ethylene glycol tetra-acetic acid [EGTA], 10 mM HEPES pH 6.5) with the addition of 0.5 mM AEBSF. Samples were then centrifuged at 2,000 x g for 5 min at 4°C and the supernatants discarded. Cell pellets were washed with 5 ml of pre-chilled Buffer 2 (200 mM NaCl, 1mM EDTA pH 8.0, 0.5 mM EGTA, 10 mM HEPES pH 6.5) with the addition of 0.5 mM AEBSF. Samples were centrifuged at 2,000 x g for 5 min at 4°C and the supernatants discarded.  Cell pellets (kept at 4°C) were re-suspended in 1.5 ml pre-chilled Extraction Buffer (140 mM NaCl, 1mM EDTA, 1% v/v Triton X-100, 0.1% w/v Deoxycholate [DOC], 50 mM HEPES pH 7.5). Pepstatin A (solution in methanol) was added to a final concentration of 10 ug/ml. E64 (solution in water) was added to a final concentration of 10 μM. 1.5 μl of 500X Benzamidine hydrochloride hydrate and 2 μg/ml A-protinin.  Samples were then sonicated using a modified sonication probe (Branson Ultrasonics, Danbury, CT, USA) for 25 s at 100 % duty, power setting 2.75 followed by 120 s rest period on ice. The sonication step was carried out a total of 8 times. The resulting solution was transferred to a 2 ml microcentrifuge tube (Eppendorf) and was then centrifuged at 16,000 x g for 5 min at 4 °C. The supernatant was transferred to a new 2 ml microcentrifuge tube (Eppendorf) and was subjected to an additional sonication step of 16,000 x g for 15 min at 4 °C. The supernatant  (lysate) was transferred to a new 2 ml microcentrifuge tube (Eppendorf). 120 μl of this solution was transferred to a new 1.5 ml microcentrifuge tube (Eppendorf), labeled as ‘input’ and stored at – 20 °C.  The remaining lysate was split into fractions of 600 μl in separate 2 ml microcentrifuge tubes (Eppendorf). To two of these, 900 μl of ice-cold IP dilution buffer (167 mM Tris-HCl, 167 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100) was added. To one tube, any remaining lysate was frozen at - 20 °C. To one tube, Anti-HA 12CA5 antibody (Roche Diagnostics, UK) was added at a final concentration of 4 μg/ml. This tube was marked as ‘IP.’ Nothing was added to the other tube labeled ‘no-Ab’ (no antibody control) and both were incubated overnight at 4 °C on a rotating wheel (Thermo Fisher Scientific).    To immunoprecipitate the chromatin, 70 μl of Protein A sepharose-agarose bead slurry (Santa Cruz Biotech, California, USA) was added to both tubes and tubes were mixed on rotating wheel (Thermo Fisher Scientific) at 4 °C for 4 h. Tubes were then centrifuged at 16,000 x g for 2 min and supernatant was discarded taking care not to disturb the sepharose-agarose beads. 1 ml of ice-cold Extraction Buffer was added to each tube and briefly mixed by hand, followed by centrifugation at 16,000 x g for 2 min. Supernatant was discarded and 1 ml of ice-cold Extraction Buffer was added to each tube followed by mixing on a rotating wheel (Thermo Fisher Scientific) at 4 °C for 5 min. Tubes were centrifuged at 16, 000 x g for 2 min and supernatant was discarded.   1 ml of ice-cold High-Salt Extraction buffer (500 mM NaCl, 1 mM EDTA, 1 % (v/v) Triton X-100, 0.1% (w/v) Sodium Deoxycholate and 50 mM HEPES, pH 7.5] was added to each tube, and briefly mixed by hand, followed by centrifugation at 16,000 x g for 2 min. Supernatant was discarded and 1 ml of ice-cold High-Salt Extraction buffer was added to each tube followed by mixing on a rotating wheel (Thermo Fisher Scientific) at 4 °C for 5 min. Tubes were centrifuged at 16,000 x g for 2 min and supernatant was discarded.   1 ml of ice-cold LiCl Wash Buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM NP-40, 0.5% (w/v) Sodium Deoxycholate and 1 mM EDTA) was added to each tube, and briefly mixed by hand, followed by centrifugation at 16,000 x g for 2 min. Supernatant was discarded and 1 ml of ice-cold LiCl wash buffer was added to each tube followed by mixing on a rotating wheel (Thermo Fisher Scientific) at 4 °C for 5 min. Tubes were centrifuged at 16, 000 x g for 2 min and supernatant was discarded.   1 ml of ice-cold TE was added to each tube, and briefly mixed by hand, followed by centrifugation at 16,000 x g for 2 min. Supernatant was discarded and 1 ml of ice-cold TE was added to each tube followed by mixing on a rotating wheel (Thermo Fisher Scientific) at 4 °C for 5 min. Tubes were centrifuged at 16, 000 x g for 2 min and supernatant was discarded.     To elute the sample, 150 μl of EB1 (50 mM Tris-HCl pH 8.0 10 mM EDTA, 1 % (w/v) SDS)  was added to each tube of beads. The mixtures were incubated at 65 °C in a circulating water bath (Clifton, UK) for 15 min. Tubes were centrifuged at 16,000 x g for 5 min and the supernatants were transferred to two new 1.5 ml microcentrifuge tubes (Eppendorf). 210 μl of EB2 (10 mM Tris pH 8.0, 1 mM EDTA, 0.67% w/v sodium dodecyl sulphate) was added to the bead mixtures to elute any remaining protein-DNA molecules. The tubes were incubated at 65 °C in a circulating water bath (Clifton, UK) for 5 min and centrifuged at 16,000 x g for 5 min and the supernatants were added to the tubes containing EB1 (i.e. supernatants for each reaction were pooled – keeping ‘IP’ and ‘No Ab control’ reactions distinct).  At this point, the total lysate control was thawed on ice and diluted 1:4 with Elution Buffer.    The three fractions (IP, No Ab control and input) were incubated at 65 °C in a circulating water bath (Clifton, UK) for 18 h to reverse cross-links.  Samples were diluted with TE to bring final concentration of SDS to 0.5 % (w/v). RNaseA was added to each tube to a concentration of 50 μg/ml and tubes were incubated at 37 °C in a circulating water bath (Clifton, UK) for 1 h. Proteinase K was added to each tube to a final concentration of 500 μg/ml and tubes were incubated at 37 °C in a circulating water bath (Clifton, UK) for 2 h. LiCl was added to each tube to a final concentration of 0.4 M and 600 μl of Phenol-Chloroform-Isoamyl Alcohol (24:24:1; pH 8.0) was added to both tubes. Tubes were mixed by vortexing for 1 min and centrifuged at 16,000 x g for 5 min. The aqueous layer was transferred to a new 1.5 ml microcentrifuge tube (Eppendorf) for each of the reactions. 600 μl of chloroform was added to each reaction and mixed vigorously by vortexing for 1 min. Mixtures were centrifuged at 16,000 x g for 5 min and the aqueous layers were transferred to a new 1.5 ml microcentrifuge

treatment_protocol: Cultures were centrifuged and the cell pellets washed in PBS. Washed pellets were re-suspended in 20 ml of 10 mM diemethyl adipimidate (DMA) -PBS in the polystyrene tubes and incubated at room temperature for 45 min with mixing on a Unimax mixing tray (Heidolph, Germany).  Samples were then centrifuged as before and the supernatants disposed of. Cells were washed in 10 ml PBS and centrifuged once again. Supernatants were disposed of and cell pellets were re-suspended in 36 ml PBS. 1 ml of 37% formaldehyde was added to each sample and then each sample (about 40 ml) was transferred to 100 ml Erlenmyer narrow-neck flasks (Fisher Scientific) and incubated at 30 °C with shaking at 200 r.p.m. in an orbital incubator (Gallenkamp) for exactly 30 min.  2 ml of sterile 5M glycine was added to each flask to quench crosslinking reactions and samples were left to incubate for a further 10 min. Sample were then transferred to 50 ml polystyrene tubes (Greiner Bio-One) and centrifuged as before with the supernatants being disposed of. At this point, pellets were stored on ice at 4 °C for up to 48 h prior to additional processing.

value: HA-tagged Tlo1p

tag: chip antibody

source_name: Candida dubliniensis strains tlo1-HA anti-HA ChIP


title: tlo1-HA ChIP replicate 2

value: Anti-HA 12CA5 antibody (Roche Diagnostics, UK)


title: BFA_SEEDLING_REP2

value: APEL (20mM Tris HCl pH 7.8, 250mM sucrose, 5mM MgCl2, 5mM KCl, 40% glycerol, 0.25% Triton X-100 0.1% BME)


title: CD379 Monocyte derived macrophage_Unstimulated

value: M

tag: disease

value: Crohn's Disease

value: Unstimulated


title: tlo1-HA ChIP replicate 3


title: HC249 Monocyte derived macrophage_Unstimulated

value: Healthy Control

tag: stimulation


title: CD242 Monocyte derived macrophage_Unstimulated

tag: batch


title: BFA_EARSHOOT_REP2


title: BFA_SEEDLING_REP1


title: DNA_occupancy_TP17


title: DNA_occupancy_TP16


title: BFA_EARSHOOT_REP1


title: HC247 Monocyte derived macrophage_Unstimulated


title: APEL_SEEDLING_REP1


title: APEL_EARSHOOT_REP1


title: DNA_occupancy_TP14


title: APEL_EARSHOOT_REP2


title: CD325 Monocyte derived macrophage_Unstimulated


title: CD34 Monocyte derived macrophage_Unstimulated


title: DNA_occupancy_TP15


title: fetal lung_control_twin, replicate1

first: Maureen

last: Keller-Wood

institute: University of Florida

description:
con_1
Gene expression after 48h in con fetal lung.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

value: fetal lung

tag: treatment

value: control


title: HC183 Monocyte derived macrophage_Unstimulated


title: EARSHOOT_MODERATE_REP2

source_name: nucleosomal DNA from moderately-digested earshoot nuclei

treatment_protocol: moderte Mnase digestion

value: 30 U/mL Mnase

value: BFA (15mM PIPES-NaOH pH 6.8, 0.32mM sorbitol, 80mM KCl 20mM, NaCl 0.5mM, EGTA 2.0mM, EDTA 1mM, DTT 0.15mM spermine, 0.05mM spermidine)


title: DNA_occupancy_TP13


title: EARSHOOT_MODERATE_REP3


title: APEL_SEEDLING_REP2

value: seedling


title: EARSHOOT_MODERATE_REP1


title: DNA_occupancy_TP11


title: EARSHOOT_LIGHT_REP3

source_name: nucleosomal DNA from lightly-digested earshoot nuclei

treatment_protocol: light Mnase digestion


title: HC242 Monocyte derived macrophage_Unstimulated

value: F


title: DNA_occupancy_TP12


title: CD76 Monocyte derived macrophage_Unstimulated


title: EARSHOOT_LIGHT_REP2

value: nucleosomal DNA


title: DNA_occupancy_TP10


title: CD274 Monocyte derived macrophage_Unstimulated


title: EARSHOOT_MODERATE_REP4

value: bare genomic DNA


title: EARSHOOT_HEAVY_REP4

source_name: nucleosomal DNA from heavily-digested earshoot nuclei

treatment_protocol: heavy Mnase digestion

value: immature ear

value: 300 U/mL Mnase


title: EARSHOOT_LIGHT_REP1

value: 2 U/mL Mnase


title: EARSHOOT_HEAVY_REP3


title: DNA_occupancy_TP9


title: EARSHOOT_LIGHT_REP4


title: HC241 Monocyte derived macrophage_Unstimulated


title: CD400 Monocyte derived macrophage_Unstimulated


title: DNA_occupancy_TP7


title: DNA_occupancy_TP8


title: HC243 Monocyte derived macrophage_Unstimulated


title: ROOT_LIGHT

source_name: nucleosomal DNA from lightly-digested seedling root nuclei

extract_protocol: Ten grams of seedling tissue, or 1g of immature ear tissue, were ground under liquid nitrogen with a mortar and pestle and crosslinked by stirring for 10 minutes in 10 mL ice-cold BFA (15mM PIPES-NaOH pH 6.8, 0.32mM sorbitol, 80mM KCl 20mM, NaCl 0.5mM, EGTA 2.0mM, EDTA 1mM, DTT 0.15mM spermine, 0.05mM spermidine) with 1% formaldehyde. Fixation was stopped with 125 mM Glycine for 5 minutes. Tissue was pelleted at 2,000 x g for 10 min at 4ºC in a swinging-bucket centrifuge, then the tissue pellet was resuspended in 25 mL nucleus isolation buffer with 1% hexylene glycol and 1% Triton X-100. After 5 minutes of gentle rotary shaking, nuclear suspensions were filtered through 2 layers of miracloth (Calbiochem) and nuclei were pelleted at 2,000 x g for 10 min at 4ºC.  Nuclei were washed once with 10 mL BFA, and resuspended in 10 mL MNase digestion buffer (50 mM Tris-HCl pH 7.5, 320 mM sucrose, 4 mM MgCl2, 1 mM CaCl2). Nuclei were sequentially filtered through 150, 100, 50 and 30 µm CellTric® filters (Partec), pelleted at 2,000 x g for 10 min at 4ºC, resuspended in 1 ml of MNase Digestion Buffer, flash frozen in liquid nitrogen, and stored at -80C until use. 100 uL nuclei were digested with MNase at 37 C for 5 minutes and stopped with 20 mM EGTA. 100 uL diH20 was added to each sample and nuclei were decrosslinked with 1% SDS and 100 ug/mL Proteinase K overnight at 65 ºC. DNA was phenol-chloroform extracted, ethanol precipitated, and resuspended in diH20. Digested DNA were treated with 40 ug/mL RNase A and run in a 1% agarose gel. 100-200-bp DNA fragments were excised and gel extracted with the Qiaex II gel extraction kit (Qiagen) following the manufacturer’s instructions.

value: seedling root

source_name: bare genomic DNA from seedling root nuclei


title: EARSHOOT_HEAVY_REP2


title: EARSHOOT_HEAVY_REP1


title: SHOOT_HEAVY

source_name: nucleosomal DNA from heavily-digested seedling shoot nuclei

value: seedling shoot

source_name: bare genomic DNA from seedling shoot nuclei


title: SHOOT_LIGHT

source_name: nucleosomal DNA from lightly-digested seedling shoot nuclei


title: ROOT_HEAVY

source_name: nucleosomal DNA from heavily-digested seedling root nuclei


title: EARSHOOT_MODERATE_REP2

treatment_protocol: moderate Mnase digestion


title: CD122 Monocyte derived macrophage_Unstimulated


title: HC232 Monocyte derived macrophage_Unstimulated

value: M


title: HC231 Monocyte derived macrophage_Unstimulated


title: EARSHOOT_LIGHT_REP2


title: EARSHOOT_LIGHT_REP1


title: HC225 Monocyte derived macrophage_Unstimulated


title: DNA_occupancy_TP5


title: CD397 Monocyte derived macrophage_Unstimulated

value: Crohn's Disease


title: CD329 Monocyte derived macrophage_Unstimulated

value: Unstimulated


title: CD392 Monocyte derived macrophage_Unstimulated


title: HC226 Monocyte derived macrophage_Unstimulated

value: Healthy Control


title: DNA_occupancy_TP6


title: EARSHOOT_HEAVY_REP2


title: EARSHOOT_HEAVY_REP1


title: EARSHOOT_MODERATE_REP1


title: DNA_occupancy_TP4


title: DNA_occupancy_TP1


title: DNA_occupancy_TP3


title: DNA_occupancy_TP2


title: HC128 Monocyte derived macrophage_Unstimulated


title: CD178 Monocyte derived macrophage_Unstimulated


title: HC237 Monocyte derived macrophage_Unstimulated


title: CD267 Monocyte derived macrophage_Unstimulated


title: HC204 Monocyte derived macrophage_Unstimulated


title: HC224 Monocyte derived macrophage_Unstimulated


title: HC202 Monocyte derived macrophage_Unstimulated


title: CD401 Monocyte derived macrophage_Unstimulated


title: Cd7i

city: Otsu

first: Takahisa

last: Nakayama

state: Shiga

address: Seta Tsukinowa-cho

department: Pathology 1

institute: Shiga University of Medical Science

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Human CGH Microarray 8x60K  (Agilent, GPL10152) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 10.7.3.1. Linear normalization method with default parameters (protocol CGH_107_Sep09 and Grid: 021924_D_F_20100501 and protocol CGH_107_Sep09 and Grid: 021924_D_F_20111015)  was used in signal intensity extraction procedure.

source_name: Invasive part of invasive gastric cancer

label_protocol:
250ng DNA was labelled using the Genomic DNA ULS Labeling Kit coupling method (Agilent – 5190-0419).
250ng DNA was labelled using the SureTag DNA Labeling Kit coupling method (Agilent – 5190-3400).

growth_protocol: Gastric archival materials from ESD and operative resection were selected to this study. Formalin-fixed paraffin embedded tissues (FFPE) of a total 59  epithelial non-invasive and invasive neoplasms from 38 patients from 2009 to 2013

extract_protocol: GenomeDNA was extracted with phenol-chloroform-isoamylalcohol extraction method and further treated using the Maxtract high density extraction column(QIAGEN).Eluted DNA was assessed for purity using the Nanodrop-1000 and double stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer's instructions. GenomeDNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) Kit(SIGMA). For each WGA 100 ng of starting material was used. The amplified DNA product was purified using the GeneElute PCR Clean-Up Kit(SIGMA).

treatment_protocol: Tumour samples were obtained from 5-micro-thick tissue sections using a laser microdissection system (LMD6000, Leica Microsystems, Wetzlar, Germany). Each tumour samples were dissected from at least > 6mm2 area, in which neoplastic cells were accounted for 90% of total cell count. These cells were then digested in 200mg/ml proteinase K solution for 70±2 hours at 370C

value: FFPE tissue from operative resection

tag: labeling method

value: Genomic DNA ULS Labeling Kit

tag: vienna catagory

source_name: corresponding non-neoplastic sample

value: FFPE tissue from oparative resection


title: Cd7m

description: protocol CGH_107_Sep09 and Grid: 021924_D_F_20111015

source_name: Intramucosal part of invasive gastric cancer

tag: tissue


title: Cd9m


title: HC199 Monocyte derived macrophage_Unstimulated


title: Cm1

source_name: Intramucosal gastric cancer


title: Cm3


title: Cd9i


title: Cm4


title: Cd8i

description: protocol CGH_107_Sep09 and Grid: 021924_D_F_20100501


title: Cd8m


title: Cd6i


title: Cm2


title: Cm5


title: Cm7


title: Cd6m


title: Cm8


title: Cd5m


title: Cm6


title: Cd5i


title: D14 iPS

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the Affymetrix Power Tools (APT) Software Package. Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).

source_name: human iPS cells

label_protocol: biotin

extract_protocol: RNeasy kit (Quiagen)

treatment_protocol: CD34+ HSC from cord blood were cultured with StemSpan Medium (StemCell Technologies, Vancouver, Canada) supplemented with 100 ng/ml SCF, 50 ng/ml FLT-3 ligand, 20 ng/ml TPO and 10 ng/ml hyper-IL-6 and infected with Puro-eGFP vector (Supporting Information Fig. S1A). iPS cells were obtained from human fibroblasts by transduction with Oct4, Sox2, Klf4 and c-myc in retrovirus or Sendai virus vectors (Supplemental Materials and Methods). iPS hybrids were produced from iPS cells and HSC by polyethylene glycol (PEG) fusion and cells were seeded onto Matrigel coated culture dishes. Puromycin selection (4 μg/ml, Sigma-Aldrich, USA) was applied 48 hours later and hybrid colonies were picked one week later and cultured on mouse embryonic fibroblasts (MEF) feeder. The same procedure was used to produce ES hybrids from human H9 ES cells.

tag: cell type

value: iPS cells

tag: differentiation days


title: Cd4m


title: HC227 Monocyte derived macrophage_Unstimulated

tag: gender


title: HSC

source_name: hematopoietic stem cells from umbilical cord blood


title: HC228 Monocyte derived macrophage_Unstimulated


title: CD362 Monocyte derived macrophage_Unstimulated


title: Cd4i


title: Cd1m


title: Cd3i


title: Cd2i


title: CD378 Monocyte derived macrophage_Unstimulated


title: D2 iPS


title: HC203 Monocyte derived macrophage_Unstimulated


title: D7 iPS


title: Cd1i


title: HC196 Monocyte derived macrophage_Unstimulated


title: D0 iPS


title: Cd16i


title: HC86 Monocyte derived macrophage_Unstimulated


title: Cd16m


title: D4 Hybrid

source_name: pluripotent iPS/somatic cell hybrids

value: pluripotent iPS/somatic cell hybrids


title: Cd3m


title: Cd14m


title: Cd15m


title: D14 Hybrid


title: Cd13m


title: D7 Hybrid


title: D2 Hybrid


title: Cd15i


title: CD394 Monocyte derived macrophage_Unstimulated


title: CD368 Monocyte derived macrophage_Unstimulated


title: Cd14i


title: Cd13i


title: CD352 Monocyte derived macrophage_Unstimulated

value: F


title: Cd12i


title: Cd11i


title: T47D-2

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit, P/N 900720

scan_protocol: gene chip scanner 3000 7G

data_processing: apt-probeset-summarize -a rma -c HuGene-1_0-st-v1.r4.clf -p HuGene-1_0-st-v1.r4.pgf  -m HuGene-1_0-st-v1.r4.mps --annotation-file HuGene-1_0-st-v1.na31.hg19.transcript.csv

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents, P/N 900652

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

tag: cell line

tag: acetylation level

value: Acetyl


title: D0 Hybrid


title: Cd11m


title: Cd10i


title: Cd10m


title: B8

source_name: Gastric adenoma

value: SureTag DNA Labeling Kit


title: T47D-1


title: B9

value: FFPE tissue from ESD


title: Cd2m


title: CD330 Monocyte derived macrophage_Unstimulated


title: HC186 Monocyte derived macrophage_Unstimulated


title: T47D-3


title: SkBr3-3

value: Hypo


title: CD128 Monocyte derived macrophage_Unstimulated


title: B7


title: HC15 Monocyte derived macrophage_Unstimulated


title: D4 iPS


title: CD388 Monocyte derived macrophage_Unstimulated


title: HC223 Monocyte derived macrophage_Unstimulated


title: CD56 Monocyte derived macrophage_Unstimulated


title: B4


title: MdaMB361-3


title: B5


title: B2


title: B3


title: A7


title: MdaMB361-2


title: CD387 Monocyte derived macrophage_Unstimulated


title: B12


title: B11


title: SkBr3-2


title: B1


title: HC167 Monocyte derived macrophage_Unstimulated


title: CD121 Monocyte derived macrophage_Unstimulated


title: SkBr3-1


title: CD319 Monocyte derived macrophage_Unstimulated


title: A6


title: MdaMB361-1


title: A4


title: Cd12m


title: MCF7-2


title: B10


title: MCF7-3


title: B6


title: MCF7-1


title: CD273 Monocyte derived macrophage_Unstimulated


title: CD374 Monocyte derived macrophage_Unstimulated


title: A2


title: HC119 Monocyte derived macrophage_Unstimulated


title: A5


title: A3


title: A1


title: 18 1500 ppm of hexanal was exposed in rats(T3 group)

first: Yoon

last: Cho

address: hwarang-ro 14

institute: KIST

description: Gene expression after exposure to 1500ppm hexanal

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Lung, hexanal, 1500 ppm

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

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

value: lung

value: male

value: 1500 ppm hexanal


title: 38 1500 ppm of hexanal was exposed in rats(T3 group)

value: female


title: BT474-2


title: 32 1000 ppm of hexanal was exposed in rats(T2 group)

description: Gene expression after exposure to 1000ppm hexanal

source_name: Lung, hexanal, 1000 ppm

value: 1000 ppm hexanal


title: 33 1000 ppm of hexanal was exposed in rats(T2 group)


title: 36 1500 ppm of hexanal was exposed in rats(T3 group)


title: 31 1000 ppm of hexanal was exposed in rats(T2 group)


title: 16 1500 ppm of hexanal was exposed in rats(T3 group)


title: CD367 Monocyte derived macrophage_Unstimulated

value: M

value: Crohn's Disease

value: Unstimulated


title: 37 1500 ppm of hexanal was exposed in rats(T3 group)


title: BT474-1


title: 11 1000 ppm of hexanal was exposed in rats(T2 group)


title: 12 1000 ppm of hexanal was exposed in rats(T2 group)


title: 13 1000 ppm of hexanal was exposed in rats(T2 group)


title: 28 600 ppm of hexanal was exposed in rats(T1 group)

description: Gene expression after exposure to 600ppm hexanal

source_name: Lung, hexanal, 600 ppm

value: 600 ppm hexanal


title: CD50 Monocyte derived macrophage_Unstimulated


title: HC165 Monocyte derived macrophage_Unstimulated

value: Healthy Control


title: 27 600 ppm of hexanal was exposed in rats(T1 group)


title: CD369 Monocyte derived macrophage_Unstimulated


title: CD377 Monocyte derived macrophage_Unstimulated


title: 8 600 ppm of hexanal was exposed in rats(T1 group)


title: 26 600 ppm of hexanal was exposed in rats(T1 group)


title: 7 600 ppm of hexanal was exposed in rats(T1 group)


title: 6 600 ppm of hexanal was exposed in rats(T1 group)


title: 23 filtered clean air was exposed in rats(control group)

description: Gene expression after exposure to filtered clean air

source_name: Lung, filtered clean air(control)

value: filtered clean air


title: 21 filtered clean air was exposed in rats(control group)


title: 2 filtered clean air was exposed in rats(control group)


title: 3 filtered clean air was exposed in rats(control group)


title: 17 1500 ppm of hexanal was exposed in rats(T3 group)


title: CD17 Monocyte derived macrophage_Unstimulated


title: MDM(PBMCcultureadherence)_day5_donor3

city: Iowa City

first: Joel

last: Graff

state: IA

address: 400 EMRB

department: Internal Medicine

institute: University of Iowa

description: MDMs(PBMC) 3

data_processing: SDS v2.3 and SDS RQ Manager v1.2 software (Applied Biosystems); the non_normalized.txt contains Non-normalized Ct values

label: FAM (TaqMan)

source_name: Monocyte-derived macrophages derived from unfractionated PBMC cultures and isolated on day 4 based on adherence and rested 1 day as pure MDM culture

label_protocol: cDNA was generated using the TaqMan Reverse Transcription Kit and Megaplex Primer Pool A v2.0.  Preamplification was performed using TaqMan PreAmp Master Mix and Megaplex PreAmp Primer Pool A v2.0.  Finally, TLDA cards were loaded with pre-amplified reactions and PCR was performed on a 7900HT Fast Real Time PCR System (Applied Biosystems).

growth_protocol: Monocytic cells were isolated from blood samples using two standard protocols.  Each method started with peripheral blood mononuclear cells (PBMCs) isolated using Ficoll-Paque Plus (GE Healthcare) density gradients.  In the first method, monocytes were isolated on the day of blood donation directly from PBMCs using CD14 MicroBeads (Miltenyi Biotec).  Monocyte samples were collected at the time of sorting to provide a reference/control sample.  The remaining purified monocytes were then cultured in tissue culture plates at 1e6 cells/ml in RP-10 supplemented with M-CSF (50 ng/ml).  The adherent cells were considered MDMs after 5 days of differentiation. The second method, selects MDMs from total PBMC cultures based on adherence.  Briefly, PBMCs were cultured in Petri dishes at a density of 5e6 cells/ml in RP-10 (RPMI 1640 (Gibco) with FBS (10% v/v; Gibco) and L-glutamine (2mM; Gibco)) supplemented with M-CSF (5ng/ml; eBioscience).  After 4 days of culture, Petri plates were washed extensively with HBSS lacking divalent cations (Gibco) to remove nonadherent cells.  The adherent MDMs were trypsinized and pelleted.  Upon resuspension at 1e6 cells/ml in RP-10 with M-CSF (5ng/ml), the MDMs were incubated one additional day.

extract_protocol: Total RNA purification using TRIzol Reagent

tag: donor id

value: donor 3

value: Monocyte-derived macrophages (MDM)

tag: purification method

value: Adherent cells from PBMC culture

tag: days in culture


title: MDM(PBMCcultureadherence)_day5_donor2

description: MDMs(PBMC) 2

value: donor 2


title: CD359 Monocyte derived macrophage_Unstimulated

value: F


title: CD385 Monocyte derived macrophage_Unstimulated


title: HC154 Monocyte derived macrophage_Unstimulated


title: laevis_ICD_38_2

city: Willimsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

department: Biology

institute: College of William and Mary

description: Upregulation of the Notch pathway during swimming tadpole stage

hyb_protocol: 500 ng of RNA from each sample was used as input.  The 3’ IVT Express kit was used to prepare the samples according to the manufacturer’s instructions with the exception that the in vitro transcription reaction was carried out for 16 hours rather than the 4 hours recommended by the manufacturer.

scan_protocol: Scanning was performed using a GeneChip Scanner 3000 7G according to manufacturer's protocols.

data_processing: Differentially expressed (DE) genes were determined using a two-sample linear design model with group-means parameterization with Bayes correction according to the method of Smyth.  This analysis was implemented with the limma packages in Bioconductor and reported with p-values adjusted for multiple tests using the Benjamini-Hochberg procedure. Normalized hybridization intensities are reported in the data table as log2 transformed values. Normalized values before log2 transformation were used for statistical testing.

organism: Xenopus laevis

source_name: Whole embryo, ICD-injected, stage 38

extract_protocol: Embryos were raised to stages 18, 28, and 38 for RNA collection. To obtain total RNA, 10 embryos from each stage and condition were homoginized in Tri Reagent and extracted with BCP according to the manufacturer's protocol. RNA from the aqueous phase was purified using the Qiagen RNeasy Mini kit.

treatment_protocol: Embryos were injected into one blastomere at the two cell stage with 1.5 ng of one of the following: capped RNA constructs synthesized in vitro; a DNA Binding mutant of suppressor of hairless (DBM), a construct that suppresses Notch signaling; the Intracelluar Domain (ICD), which activates the Notch signaling pathway; or Green Fluorescent Protein (GFP) as a tracer and control for the injection procedure.  The DBM and ICD constructs were kind gifts from Dr. Chris Kintner. Capped RNA was synthesized in vitro using mMessage Machine (Ambion) following the manufacturer’s protocol.

tag: Stage

tag: injected construct

value: ICD


title: CD386 Monocyte derived macrophage_Unstimulated

tag: disease


title: laevis_DBM_38_3

description: Downregulation of the Notch pathway during swimming tadpole stage

source_name: Whole embryo, DBM-injected, stage 38

label_protocol: 500 ng of RNA from each sample was used as input.  The 3’ IVT Express kit was used to prepare the samples according to the manufacturer’s instructions with the exception that the in vitro transcription reaction was carried out for 16 hours rather than the 4 hours recommended by the manufacturer.

value: DBM


title: BT474-3

value: Acetyl


title: laevis_ICD_38_3


title: MDM(PBMCcultureadherence)_day5_donor1

description: MDMs(PBMC) 1

value: donor 1


title: 22 filtered clean air was exposed in rats(control group)

city: Seoul

value: lung

value: female


title: HC136 Monocyte derived macrophage_Unstimulated

tag: stimulation


title: HC169 Monocyte derived macrophage_Unstimulated

value: M

tag: batch


title: laevis_GFP_38_3

description: No change to the Notch pathway (control) during swimming tadpole stage

source_name: Whole embryo, GFP-injected, stage 38

value: GFP


title: laevis_GFP_38_2


title: laevis_GFP_38_1


title: MDM(beadpurified)_day5_donor3

description: MDMs(CD14) 3

source_name: Monocyte-derived macrophages derived from CD14 Microbead purified monocytes cultured ex vivo for 5 days

value: CD14 Microbeads


title: 1 filtered clean air was exposed in rats(control group)

value: male

tag: treatment


title: Embryo male DKK1 rep 5

city: Gainesville

first: Anna

middle: Carolina

last: Denicol

state: FLORIDA

address: 28 NW 35th Terrace

department: Animal Sciences

hyb_protocol: Initial concentration of cDNA was 23 ng/ml in the hybridization cocktail. Array hybridization conditions were 45°C for 18 h accodring to manufacturer's instructions. Following hybridization, fluidics protocol FS 450-007 was used for array washing and staining.

scan_protocol: Arrays were scanned using the GeneChip scanner 3000 7G (Affymetrix).

data_processing: Data were processed using Affymetrix Expression Console software. Method for data pre-processing and normalization was RMA. Normalized data was analyzed by ANOVA using JMP Genomics software and the model included effects of treatment, sex and the interaction. Sequential goodness of fit test was the method used for multiple testing correction.

organism: Bos taurus

source_name: Male embryo_morula stage_DKK1 for 24 h

label_protocol: cDNA was labeled with biotin (starting cDNA concentration was 5 µg) using Nugen's Encore Biotin Module and following manufacturer's instructions.

growth_protocol: Embryos were cultured in vitro in 50 μl drops of SOF-BE1 medium under 5% O2, 5% CO2 and balance N2. Temperature was 38.5°C.

extract_protocol: RNA extraction was performed using Qiagen micro kit according to manufacturer's instructions.

treatment_protocol: Embryos were treated at day 5 of development (day 0 = insemination) with 5 μl of vehicle (DPBS/BSA 0.1%) or 100 ng/ml DKK1 human recombinant (final concentration).

value: embryo

value: morula stage

tag: treated with

value: DKK1 for 24 h


title: laevis_DBM_38_2


title: MDM(beadpurified)_day5_donor2

description: MDMs(CD14) 2

value: Monocyte-derived macrophages (MDM)


title: laevis_ICD_38_1


title: Embryo male control rep 5

source_name: Male embryo_morula stage_vehicle for 24 h

value: vehicle for 24 h


title: CD48 Monocyte derived macrophage_Unstimulated

value: Crohn's Disease

value: Unstimulated


title: MDM(beadpurified)_day5_donor1

description: MDMs(CD14) 1


title: laevis_DBM_38_1


title: Embryo female DKK1 rep 5

source_name: Female embryo_morula stage_DKK1 for 24 h


title: laevis_ICD_s28_3

description: Upregulation of the Notch pathway during tailbud formation

source_name: Whole embryo, ICD-injected, stage 28

value: ICD


title: CD22 Monocyte derived macrophage_Unstimulated

value: F


title: Embryo female control rep 5

source_name: Female embryo_morula stage_vehicle for 24 h


title: Monocyte_day0_donor3

description: Monocytes 3

source_name: CD14 Microbead-purified monocytes purified from human PBMC

value: donor 3

value: Monocytes


title: HC120 Monocyte derived macrophage_Unstimulated

value: Healthy Control


title: Monocyte_day0_donor2

description: Monocytes 2

value: donor 2


title: Monocyte_day0_donor1

description: Monocytes 1

value: donor 1


title: CD328 Monocyte derived macrophage_Unstimulated


title: laevis_ICD_s28_1


title: CD382 Monocyte derived macrophage_Unstimulated


title: CD141 Monocyte derived macrophage_Unstimulated

value: M


title: laevis_GFP_s28_3

description: No change to the Notch pathway (control) during tailbud formation

source_name: Whole embryo, GFP-injected, stage 28

value: GFP


title: laevis_ICD_s28_2


title: HC175 Monocyte derived macrophage_Unstimulated


title: Embryo female DKK1 rep 4

value: female


title: laevis_GFP_s28_1


title: laevis_GFP_s28_2


title: Embryo female control rep 4

value: embryo


title: Embryo male DKK1 rep 4

value: male

value: morula stage


title: CD389 Monocyte derived macrophage_Unstimulated


title: hMSC

type: SRA

first: Nicholas

middle: John

last: Dibb

address: Du Cane Road

department: Surgery and Cancer

institute: Imperial College London

description: MicroRNA sequencing results

library_source: transcriptomic

data_processing:
After trimming adaptor sequences a total of 253, 791 unfiltered reads were obtained and of these 25,724 were selected thatt were between 15 and 28 nucleotides in length.  These were copared to annotated mature miRNAs (miRBase v13.0 leading to the identification of 162 mature miRNAs.  The number of reads for each miRNA and related isomiRs are recorcded in the file hMSC
Genome_build: miRBase v13
Supplementary_files_format_and_content: hMSC.xis

source_name: Foetal mesenchymal stem cells

growth_protocol: Grown in DMEM + 10% FBS at 5% CO2

extract_protocol:
Total RNA prepared using Trizol
Libraries made according to Molnar A et al., 2007 Nature 447, 1126-29.  Briefly, Briefly, small RNAs were excised from a 15% 7M Urea PAGE and extracted with 0.3 M NaCl. RNAs were ligated to 5’ and 3’ adapters for PCR amplification using 454-forward (5'-GCC TCC CTC GCG CCA TCA GCA GCC ATG GGA ATT CCT CAC TAA-3') and 454-reverse  (5'-GCC TTG CCA GCC CGC TCA GAC AGT CCA TGG ATT G-3') primers. PCR products were separated on a 10% native PAGE and the amplified ligation products were excised and sequenced with 454 technology (454 sequencing platform)

treatment_protocol: Harvested at passage 5 to 6, no additional treatment

value: first trimester mesenchymal undifferentiated stem cells

tag: passage

value: 5 to 6

tag: molecule subtype

value: miRNA


title: Embryo male control rep 4

tag: tissue

value: vehicle for 24 h


title: Embryo female control rep 3


title: CD200 Monocyte derived macrophage_Unstimulated

value: Crohn's Disease

value: Unstimulated


title: laevis_DBM_s28_3

description: Downregulation of the notch pathway during tailbud formation

source_name: Whole embryo, DBM-injected, stage 28

value: DBM


title: Embryo female DKK1 rep 3

value: DKK1 for 24 h


title: laevis_DBM_s28_2


title: Embryo male DKK1 rep 3


title: laevis_DBM_s28_1


title: CD384 Monocyte derived macrophage_Unstimulated


title: HC125 Monocyte derived macrophage_Unstimulated

value: Healthy Control


title: CD278 Monocyte derived macrophage_Unstimulated


title: Embryo male control rep 3


title: laevis_GFP_s18_2

description: No change to the Notch pathway (control) during neurulation

source_name: Whole embryo, GFP-injected, stage 18


title: Embryo male DKK1 rep 2


title: CD381 Monocyte derived macrophage_Unstimulated


title: laevis_ICD_s18_2

description: Upregulation of the Notch pathway during neurulation

source_name: Whole embryo, ICD-injected, stage 18

value: ICD


title: laevis_GFP_s18_3


title: laevis_ICD_s18_3


title: Embryo female control rep 2


title: Embryo female DKK1 rep 2


title: CD316 Monocyte derived macrophage_Unstimulated


title: Embryo male control rep 2


title: CD383 Monocyte derived macrophage_Unstimulated


title: Embryo female DKK1 rep 1


title: HC160 Monocyte derived macrophage_Unstimulated

value: F


title: laevis_ICD_s18_1


title: CD232 Monocyte derived macrophage_Unstimulated

value: M


title: HC158 Monocyte derived macrophage_Unstimulated


title: Embryo female control rep 1


title: laevis_DBM_s18_3

description: Downregulation of the Notch pathway during neurulation

source_name: Whole embryo, DBM-injected, stage 18


title: laevis_DBM_s18_2


title: HC139 Monocyte derived macrophage_Unstimulated


title: Embryo male DKK1 rep 1


title: MIA_m

first: Jung Min

last: Kim

address: Gangnam-gu Teheran-ro 216

department: Department of Health Genomics

institute: NAR Center, Inc. & Genoplan, Inc.

description: monolayer culture condition in the MIA PaCa-2 cells

hyb_protocol: cRNAs were fragmented and then applied directly onto an assembled Agilent Human GE 4x44K v2 Microarray. The arrays were hybridized at 65°C for 17 h in an Agilent hybridization oven.

scan_protocol: The hybridized microarrays were washed as per the manufacturer’s protocol (Agilent Technology), and hybridization images were analyzed with an Agilent DNA Microarray Scanner.

data_processing: The mean fluorescence intensity for each spot was calculated, and the local background was subtracted using the Agilent Feature Extraction software package. All data normalization and the selection of up- and downregulated genes were performed using GeneSpring GX 7.3 (Agilent Technology).

source_name: MIA PaCa-2 cells

label_protocol: For control and test RNAs, the synthesis of fluorescent target cRNAs and hybridizations were performed using the Low RNA Input Linear Amplification Kit PLUS (Agilent Technology), according to the manufacturer’s instructions.

growth_protocol: MiaPaCa-2 pancreatic cancer cell was maintained in RPMI 1640 with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA from monolayered cells or spheroid at Day6 and Day13 was extracted using the TRIZOL reagent (Gibco BRL, Rockville, MD, USA), according to the manufacturer’s instructions. RNA was treated with RNase-free DNase I (Promega, Madison, WI, USA) to reduce DNA contamination.

treatment_protocol: Monolayer-cultured cells grown in 6 well plates were harvested at 100% confluency, while spheroids were collected on the designated day after plating.

tag: disease state

value: pancreatic cancer

value: MIA PaCa-2 cells

tag: culture condition

value: monolayer

tag: time

value: control


title: MIA_s_D6

description: spheroid culture condition (6-day) in the MIA PaCa-2 cells

tag: cell line

value: spheroid

value: day 6


title: laevis_DBM_s18_1


title: laevis_GFP_s18_1

value: GFP


title: MIA_s_D13

description: spheroid culture condition (13-day) in the MIA PaCa-2 cells

value: day 13


title: Embryo male control rep 1

tag: gender

value: male

value: embryo

value: morula stage

value: vehicle for 24 h


title: SIRT1 KO mouse liver, ZT 16, replicate 3

status: Public on Aug 05 2014

city: Irvine

first: Paolo

last: Sassone-Corsi

state: CALIFORNIA

address: Sprague Hall

institute: University of California, Irvine

description:
SIRT1 KO 16.6
Gene expression data from mouse liver at indicated ZT.

hyb_protocol: 3.3ug of the labeled, fragmented single-stranded cDNA was hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 2.0 ST array.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing:
The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).
The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: liver, SIRT1 KO, ZT 16

label_protocol: Labeling using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent was done to covalently link to biotin.

growth_protocol: Animals were housed in 12 hour Light/Dark conditions and harvested over the circadian cycle.

extract_protocol: Total RNA was prepared by Trizol extraction, and RNA was cleaned-up prior to array analysis with Qiagen RNeasy clean-up kit.

treatment_protocol: WT and SIRT6 liver-specific knockout mice, and WT and SIRT1 liver-specific knockout mice, were harvested every 4 hours over the circadian cycle and livers were flash frozen in liquid nitrogen after sacrifice.

tag: strain/background

tag: genotype/variation

value: SIRT1 KO

value: liver

tag: circadian cycle time point

value: ZT 16


title: SIRT1 KO mouse liver, ZT 16, replicate 1

description:
SIRT1 KO 16.4
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 20, replicate 1

description:
SIRT1 KO 20.4
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT1 KO, ZT 20

value: ZT 20


title: SIRT1 KO mouse liver, ZT 4, replicate 2

description:
SIRT1 KO 4.5
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT1 KO, ZT 4

value: ZT 4


title: SIRT1 KO mouse liver, ZT 20, replicate 2

description:
SIRT1 KO 20.5
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 8, replicate 2

description:
SIRT1 KO 8.5
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT1 KO, ZT 8

value: ZT 8


title: SIRT1 KO mouse liver, ZT 16, replicate 2

description:
SIRT1 KO 16.5
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 0, replicate 1

description:
SIRT1 KO 0.4
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT1 KO, ZT 0

value: ZT 0


title: SIRT1 KO mouse liver, ZT 12, replicate 2

description:
SIRT1 KO 12.5
Gene expression data from mouse liver at indicated ZT.

source_name: liver, SIRT1 KO, ZT 12

value: ZT 12


title: WT mouse liver, ZT 20, replicate 3 [SIRT1]

description:
WT SIRT1 20.3
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 20

value: WT


title: SIRT1 KO mouse liver, ZT 12, replicate 3

description:
SIRT1 KO 12.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 0, replicate 3

description:
SIRT1 KO 0.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 4, replicate 1

description:
SIRT1 KO 4.4
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 20, replicate 3

description:
SIRT1 KO 20.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 4, replicate 3

description:
SIRT1 KO 4.6
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 8, replicate 1

description:
SIRT1 KO 8.4
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 16, replicate 2 [SIRT1]

description:
WT SIRT1 16.2
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 16


title: SIRT1 KO mouse liver, ZT 12, replicate 1

description:
SIRT1 KO 12.4
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 20, replicate 2 [SIRT1]

description:
WT SIRT1 20.2
Gene expression data from mouse liver at indicated ZT.


title: SIRT1 KO mouse liver, ZT 0, replicate 2

description:
SIRT1 KO 0.5
Gene expression data from mouse liver at indicated ZT.


title: WT mouse liver, ZT 12, replicate 3 [SIRT1]

description:
WT SIRT1 12.3
Gene expression data from mouse liver at indicated ZT.

source_name: liver, WT, ZT 12


title: WT mouse liver, ZT 20, replicate 1 [SIRT1]

description:
WT SIRT1 20.1
Gene expression data from mouse liver at indicated ZT.