title: SHN113

city: Montreal

first: Sabah

last: Hussain

state: Quebec

address: Roo L305, 687 Pine ave west

department: Medicine

country: Canada

institute: McGill University

description: replicate 2

source_name: Human skeletal myoblasts

growth_protocol: Cells were cultured in SkBM medium supplemented with 15% FBS.

extract_protocol: RNA was extracted with RNA extraction kit (Sigma), 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 were infected with adenoviruses expressing GFP, Ang-1 or Ang-2. They were then allowed to recover for 48h in growth medium containing 15% FBS. FBS was then reduced to 5% and RNA was then extracted 12hrs later.

tag: cell type

value: myoblasts

value: Cells infected with Ad-Ang-2


title: cDNA array  TM-1/Hai7124 10 DPA fiber set1

status: Public on May 24 2012

type: RNA

city: Nanjing

first: Tianzhen

last: Zhang

state: Jiangsu

country: China

institute: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 10DPA

hyb_protocol: Cy3 and Cy5-labeled cDNA resolved in 80 µL hybridization solution (3×SSC, 0.2% SDS, 5 × Denhart’s, 25% formamide). DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Slides were hybridized at 42°C overnight and transferred to fresh containers with Wash Solution 1 (0.2% SDS, 2 × SSC) at 42°C for 5 min and then immersed in Wash Solution 2 (0.2 × SSC) at room temperature for 5 min.

scan_protocol: All microarrays were scanned with a LuxScan scanner using the LuxScan 3.0 software (Captalbio Corp).

data_processing: All microarrays were analyzed using the LuxScan 3.0  software (Captalbio Corp). We quantified signal intensities of individual spots from the 16-bit TIFF images using LuxScan 3.0  software (Captalbio Corp). The nonlinear global-intensity-based LOWESS program (Yang et al., 2002) was applied for normalization.

molecule: total RNA

organism: Gossypium hirsutum

source_name: 10 DPA cotton fiber

label_protocol: Total RNA was labeled with Cy3 and Cy5 during cDNA synthesis using Klenow enzyme.

growth_protocol: G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 plants were grown in the field (Nanjing, China) in 2006.

extract_protocol: Total RNA of cotton was extracted from 5 DPA ovules and 10 to 25 DPA fibers of TM-1 and Hai7124 using a modified hot-borate method.

treatment_protocol: Developing ovules of TM-1 and Hai7124 were excised from each boll at 5, 10, 15, 20 and 25 DPA, and fiber cells in 10-25 DPA ovules were carefully dissected from the ovules. All harvested plant materials were immediately frozen in liquid nitrogen and stored at –70°C.

tag: strain

tag: tissue type

value: fibers

tag: developmental stage

value: 10 days post anthesis (DPA)

organism: Gossypium barbadense

tag: cultivar


title: Saccharopolyspora Px RNA 28h B

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

country: Italy

institute: National Research Council

hyb_protocol: The labeled cDNAs were then hybridized for 16 h at 50°C on individual GeneChips. After hybridization, GeneChips were washed and stained with streptavidin-conjugated phycoerythrin by using the Fluidic Station FS450 (Affymetrix) following the FS450_0005 Protocol. Fluorescent images of the microarrays were acquired using a GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Chips were scanned through GeneArray Scanner 3000 7G (Affymetrix) at an emission wavelenght of 560nm.

data_processing: The quality of the raw data obtained from microarray hybridization was assessed considering the MAS5.0 (Microarray Suite/Software, Affymetrix) control parameters after a global scaling at a target intensity of 100. Quality and control parameters as well as box plots of raw intensities indicated the overall high quality of the data set and the absence of any outlying sample. Probe level data was converted to expression values using both the Robust Multi-array Average (RMA) procedure  and the MAS5.0 algorithms. In the former case, PM values (Perfect Match) were background-adjusted, normalized using invariant set normalization, and log transformed. In the latter case, intensity levels were normalized using the Global Scaling option to target value (i.e. TGT=100).  Genes characterized by a statistically significant modulation of the expression level during the growth time course (within-class temporal differential expression) were identified using the EDGE software package, which is based on the Optimal Discovery Procedure  and allows identifying genes that are differentially expressed between two or more different biological conditions  or to perform significance analysis on time course experiments

label: biotin

organism: Saccharopolyspora erythraea

source_name: erythromycin-overproducing strain S. erythraea Px

label_protocol: The protocol consists in cDNA synthesis by reverse transcription (starting with 10 µg RNA), followed by cDNA fragmentation with DNase I and labeling with Terminal Deoxynucleotidyl Transferase.

growth_protocol: For shake-flask experiments, spores in frozen aliquots were collected by centrifugation, re-suspended in medium 707 (for rehydration), and readily separated by vortexing. Individual aliquots (about 5 x 108 spores) were used to inoculate each 500 ml buffled Erlenmeyer flask containing 50 ml of the liquid media described above. Cultures were incubated at 30°C with shaking at 250 rpm. Bioreactor cultures were carried out by using Minifors mini-fermenters (Infors AG, Bottmingen, CH) that operated with a working volume of 1.5 l. Stirring was provided by Rushton-type impellors rotating at 250 rpm. Sterile air was supplied through a sparger. The bioreactors were equipped with pH electrode, pO2 electrode (polarographic), antifoam probe and Pt-100.

extract_protocol: For each time point, RNA was extracted from mycelium pellets deriving from 1-ml culture samples using the GeneElute™ total RNA Purification Kit (SIGMA), recovering it in 50 µl of Elution Solution. After extraction RNAs were quantified with a NanoDrop spectrophotometer (NanoDrop Technologies) and analyzed by capillary electrophoresis on a Agilent Bioanalyzer (Agilent). The RNA samples showing an RIN (RNA Integrity Number, a quality parameter calculated by the instrument software) value higher than 7 were processed for microarray hybridization,

tag: time


title: SHN109

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Homo sapiens

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

tag: treatment

value: Cells infected with Ad-Ang-1


title: Saccharopolyspora Px RNA 28h A

value: erythromycin-overproducing strain S. erythraea Px


title: cDNA array  TM-1/Hai7124 5 DPA ovule set3(dye-swap)

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 ovules at 5 DPA

source_name: 5 DPA cotton ovule

value: ovule

value: 5 days post anthesis (DPA)


title: SHN111

description: replicate 3


title: cDNA array  TM-1/Hai7124 5 DPA ovule set1


title: Saccharopolyspora Px RNA 36h A


title: SHN108

description: replicate 1


title: Saccharopolyspora Px RNA 72h B


title: SHN107

description: replicate 3

value: Cells infected with Ad-GFP


title: cDNA array  TM-1/Hai7124 5 DPA ovule set2


title: SHN112

description: replicate 1


title: SHN106

description: replicate 2


title: URMITE_homo sapiens_44K_HMEC_251485043182_1_1_HF_8H

city: Marseille

first: Gilles

last: Audoly

address: 27, bd J. Moulin

country: France

institute: URMITE

description: Rickettsia felis-infected (HMEC) human epithelial cells

hyb_protocol: hybridization on Whole Human genome 4x44K (Agilent) as recommended by the manufacturer

scan_protocol: Arrays were scanned with DNA Microarray Scanner (Agilent) and data were extracted using Feature Extractor (Agilent).

data_processing: The raw data, from the Agilent feature extraction software, were preprocessed with background subtraction and quantile normalization. This pretreatment was performed by using a bioconductor limma package, called Agi4x44PreProcess

source_name: without treatment

label_protocol: The RNA were labelled using the Quick Amp Labeling Kit one color (Agilent)

growth_protocol: Cells were grown at 37°C and atmosphere containing 5% of carbon dioxide in the MCDB-131 medium (Invitrogen, Paisley, UK) containing 10% of FCS (PAA Laboratories, 4061, Pasching, Germany) and 1 µg/ml of hydrocortisone (Sigma-Aldrich, 89552, Steinheim, Germany) as a growth factor

extract_protocol: The cells were harvested and subjected to RNA extraction using RNeasy mini kit (Qiagen). DNA contamination was removing using Turbo DNA free kit (Ambion).

treatment_protocol: chloramphenicol at the final concentration of 50µg/ml was added in both experimented (R.felis-infected) and control Petri dishes with cells for 8 hours


title: URMITE_homo sapiens_44K_HMEC_251485041073_1_1_HF_8H

value: Rickettsia felis-infected (HMEC) human epithelial cells


title: URMITE_homo sapiens_44K_HMEC_251485041073_1_3_HF_8H


title: SHN105

description: replicate 1


title: Melanoma culture M080201

city: Zürich

first: Daniel

middle: Simon

last: Widmer

address: Gloriastrasse 31

department: Dermatology

country: Switzerland

institute: University Hospital Zürich

hyb_protocol: Hybridisation was done with a GeneChip Hybridisation oven 640

scan_protocol: Washing and scanning was done on the GeneChip Fluidics Station 450, the scanner we used was the Affymetrix GeneChip scanner 7G

data_processing: The data was analyzed with GeneSpring GX11.0

source_name: primary ssm in situ. lower leg

label_protocol: The biotin-labelled RNA was hybridized to Affymetrix HG-U133 plus 2.0 oligonucleotide microarrays

growth_protocol: RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum, 5 mM glutamine, 1 mM sodium pyruvate, 5% CO2.

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

tag: cell line

tag: braf

value: wt

tag: nras

tag: cell culture phenotype

value: invasive


title: Gene Expression of Rat Subcommisural Organ

city: Lyon

first: jacques

last: champier

address: rue Guillaume Paradin

department: neuroonology

hyb_protocol: Transcriptomic approach was performed on amplified RNA (aRNA) by the genomic platform facility ProfilXpert (Lyon, France) using oligonucleotide microarrays (CodeLink™ Rat Whole Genome Bioarray, General Electric Health Care). Biotin-labelled aRNA (10 ug) from rat tissue were fragmented using 5ug of fragmentation buffer then mixed with 240 ul of Amersham hybridization solution (GE Healthcare Europe GmbH, Saclay, France) and injected on CodeLink™ Rat Whole Genome Bioarray containing 36,736 rat oligonucleotide geneprobes (GE Healthcare Europe GmbH). The arrays were hybridized overnight at 37°C at 15g in an incubator, then washed in stringent TNT buffer at 46°C for 1 h before performing streptavidin-cy5 (GE Healthcare) detection step.

scan_protocol: The arrays were scanned using a Genepix 4000B scanner (Axon, Union City, CA, USA) and Genepix software, with a laser set at 635 nm, the laser power at 60% and the photomultiplier tube voltage at 60%.

data_processing: The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and a normalized hybridization signal for each spot on the array. CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array: spot with signal intensity below this threshold was referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution.

organism: Rattus norvegicus

source_name: normal rat

label_protocol: Total RNA (3 ng) was amplified and biotin-labelled by two round of in vitro transcription using a MessageAmp aRNA kit (Austin, Texas, USA) following the manufacturer’s protocol. Before amplification, spikes of different concentrations of synthetic mRNA were added to all samples and were used to determine the quality of all the process. aRNA yield was measured with a UV spectrophotometer and the quality verified on nanoships using Agilent 2100 Bioanalyzer.

extract_protocol: The isolated cells in 20 μl of lysis buffer were mixed with 50 μl of lysis buffer and homogenized and RNA extraction performed using a Qiagen RNeasy Micro® kit (Qiagen France SAS, Courtaboeuf, France) following the manufacturer’s instructions. The quality of the total RNA was evaluated on picochips using an Agilent 2100 bioanalyser (RNA 6000 Pico Lab Chip, Agilent Technologies, Massy, France).

treatment_protocol: LCM was performed on an Arcturus® PixCell II® machine. This technique uses a capsule (CapSure® LCM Caps) with a transparent thermosensitive film. Under microscopy, a low power infrared laser beam (980 nm) is used to cut around the edge of the regions of interest, resulting in the melting and adherence of the film to these regions. The optimal laser characteristics were 7.5 μm diameter, 45 mW strength, and 1.4 ms beam time. Cells were captured from the SCO, SFO, PG, and third ventricle ependyma. The ventricular wall cells captured were taken from a region at a distance from the SCO or SFO to avoid contamination and photographs were taken before and after sampling. Only the regions of interest remained on the film when the capsule was removed. The microdissected tissues were released from the film by centrifugation in 20 μl of lysis buffer solution (Qiagen®) and frozen at - 80°C.

value: Sprague-Dawley

tag: gender

value: male

value: adult

tag: tissue

value: Subcommisural Organ


title: Melanoma culture M080310

source_name: primary n.c. right cheek


title: ΔcrzA/scrA 30min Replicate 2

status: Public on May 23 2012

city: Ribeirao Preto

first: Wagner

middle: Rodrigo

last: de Souza

state: Sao Paulo

address: Av do Cafe

department: Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

description: Biological replicate 2 of 2. ΔcrzA/scrA- A. nidulans treated with calcium for 30 min

hyb_protocol: For the hybridization, 825 ng of each labeled cRNA was mixed with Agilent™ Fragmentation Mix and incubated at 60 °C for exactly 30 minutes to fragment RNA. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 100 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in an oven (Agilent G2545A Hybridization Oven) set to 65 °C for 17 hours. After, microarray slides were washed according to Agilent’s instruction

scan_protocol: Scanned using GenePix® 4000B microarray scanner (Molecular Devices, USA).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Dye-normalized values generated in the FE software data files were used to upload the Express Converter v. 2.1, to convert Agilent files to MeV files. After, data were processed using TIGR platform, with stringent one bad channel tolerance policy.The signal/noise threshold applied was 2.0 and the cross file cutoff percentage of 0.5. Data were visualized using TMeV from TIGR, and the same software has been used for statistical analysis (t test), where differentially expressed genes were statiscally identified using a one-class t-test. More details about data processing cold be find at de Souza WR et al., 2011 (Biotechnology for Biofuels, 4:40).

organism: Aspergillus nidulans

source_name: A. nidulans mycelia in YAG+CaCl2 for 30 min

label_protocol: Prior to labelling, cDNA was synthesized from 5 µg of RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent™ Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for SES-treated samples) for 2 hours at 40 C.

growth_protocol: A. nidulans strains (WT, ΔcrzA or ΔcrzA/scrA-) were initially grown on YAG medium for 16 hours at 30 oC and 150 rpm.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions, followed by DNAse treatment and purification using RNeasy® Mini Kit  (Qiagen).

treatment_protocol: Mycelia from A. nidulans wild-type, ΔcrzA and ΔcrzA/scrA- strains with 200 mM CaCl2 for 10 and 30 min at 30°C and 150 rpm in 25 mL YAG medium.

value: ΔcrzA/scrA-

value: mycelia

tag: treated with

value: 200 mM CaCl2 for 30min

source_name: A. nidulans mycelia without calcium treatment, labeled with Cyanine-3

tag: sample type

value: control (preculture in YAG medium)


title: URMITE_homo sapiens_44K_HMEC_251485041071_1_2_HF_Chlo

source_name: chloramphenicol treatment


title: WT 30min Replicate 2

description: Biological replicate 2 of 2. WT A. nidulans treated with calcium for 30 min

value: WT


title: ΔcrzA/scrA 10min Replicate 2

description: Biological replicate 2 of 2. ΔcrzA/scrA- A. nidulans treated with calcium for 10 min

source_name: A. nidulans mycelia in YAG+CaCl2 for 10 min

value: 200 mM CaCl2 for 10min


title: ΔcrzA/scrA 30min Replicate 1

description: Biological replicate 1 of 2. ΔcrzA/scrA- A. nidulans treated with calcium for 30 min


title: WT 30min Replicate 1

description: Biological replicate 1 of 2. WT A. nidulans treated with calcium for 30 min


title: ΔcrzA 10min Replicate 3

description: Biological replicate 3 of 3. ΔcrzA A. nidulans treated with calcium for 10 min

value: ΔcrzA


title: ΔcrzA/scrA 10min Replicate 1

description: Biological replicate 1 of 2. ΔcrzA/scrA- A. nidulans treated with calcium for 10 min


title: ΔcrzA 10min Replicate 1

description: Biological replicate 1 of 3. ΔcrzA A. nidulans treated with calcium for 10 min


title: ΔcrzA 30min Replicate 1

description: Biological replicate 1 of 1. ΔcrzA A. nidulans treated with calcium for 30 min


title: ChIP-chip of K562 cells; array 2 of 4

type: genomic

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

description: ChIP-chip mapping of HP1g locations in K562 cells

hyb_protocol: NimbleGen protocol

scan_protocol: NimbleGen protocol

data_processing: Normalization was performed using Model-based Analysis of 2-Color Arrays (MA2C) software package using default parameters (Robust C=2)

molecule: genomic DNA

source_name: ChIP DNA from K562 cells

label_protocol: NimbleGen protocol

growth_protocol: K562 cells were grown in Iscove’s Modified Dulbecco’s media, supplemented with 10% FBS and 1% pen-strep.

extract_protocol: Chromatin were isolated from cells crosslinked with 1% formaldehyde and chromatin immunoprecipitation was performed using specific antibodies. Resulting ChIP DNA and input DNA were isolated and amplified following NimbleGen protocol.

tag: antibody

value: HP1 gamma

tag: antibody vendor

value: Millipore

tag: antibody catalog number

tag: antibody lot numbers

source_name: Input DNA from K562 cells

tag: fraction

value: input


title: ΔcrzA 10min Replicate 2

description: Biological replicate 2 of 3. ΔcrzA A. nidulans treated with calcium for 10 min

tag: strain


title: ChIP-chip of MDA-MB-231 cells; array 2 of 4

description: ChIP-chip mapping of HP1g locations in MDA-MB-231 cells

source_name: ChIP DNA from MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were grown in Leibowitz media, supplemented with 10% FBS and 1% pen-strep.

source_name: Input DNA from MDA-MB-231 cells


title: Head_Control Population 3_Day 5_Rep 2

city: Urbana

first: Silvia

last: Remolina

state: IL

address: 505 S Goodwin Ave

institute: University of Illinois

description: SAMPLE 118

hyb_protocol: Hybridization was performed by Florida State University NimbleGen Systems Inc. approved facility following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Florida State University NimbleGen Systems Inc. approved facility following their standard operating protocol. See www.nimblegen.com.

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

label: Cy 3

organism: Drosophila melanogaster

source_name: Head_control_5 days of age

label_protocol: Labeling was performed by Florida State University NimbleGen Systems Inc. approved facility following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Drosophila melanogaster flies were maintained in an incubator at 25 degrees celsius on a 12L:12D light cycle and transferred to fresh cornmeal media every week.

extract_protocol: Total RNA was extracted using the PicoPure RNA isolation kit (Arcturus), and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was amplified using Ambion's Message AMpII RNA amplification Kit (Ambion). RNA was then reversed trasncribed to cDNA using SuperScript III (Invitrogen).

treatment_protocol:
We established three independent pairs of selection-control populations originally derived from an ancestral population of wild-caught female flies collected in New Jersey in 1998. Flies in the control populations were raised in single-sex vials and allowed to mate at 14 days of age.
Flies in the selection populations were also raised in single sex vials and allowed to mate initially at 28 days of age and later at 40 days of age as flies evolved longer reproductive lifespans.
After 35 generations of imposing selection for longer reproductive lifespan, unmated female offspring of control and selection populations were allowed to age to 5 different age classes and were collected, frozen and dissected into two separate tissues for gene expression analysis.

value: female

tag: group

value: control populations

value: Head

tag: population

tag: age (day)

tag: biological replicate


title: WT 10min Replicate 1

description: Biological replicate 1 of 2. WT A. nidulans treated with calcium for 10 min


title: Head_Selection Population 3_Day 50_Rep 2

description: SAMPLE 119

source_name: Head_selection_50 days of age

value: selection populations (for longer reproductive lifespans)


title: PA14 WT with adenosine after 7hr at 37C

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

hyb_protocol: Following affymetrix protocol. cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS)

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa

source_name: Channel 1

extract_protocol: Cells were harvested after incubating for 7 h, and RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) using a bead beater (Biospec, Bartlesville, OK ) with RNAlater buffer (Applied Biosystems, Foster City, CA) to stabilize the RNA.

value: PA14 WT

tag: growth time

value: 7 h

tag: medium

value: LB+10 mM adenosine


title: Head_Selection Population 3_Day 15_Rep 2

description: SAMPLE 116

source_name: Head_selection_15 days of age


title: Head_Control Population 3_Day 50_Rep 2

description: SAMPLE 120

source_name: Head_control_50 days of age


title: Head_Control Population 3_Day 15_Rep 2

description: SAMPLE 114

source_name: Head_control_15 days of age


title: Head_Selection Population 3_Day 5_Rep 2

description: SAMPLE 115

source_name: Head_selection_5 days of age


title: PA14 WT after 7hr at 37C

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

value: LB


title: WT 10min Replicate 2

description: Biological replicate 2 of 2. WT A. nidulans treated with calcium for 10 min

value: mycelia


title: Melanoma culture M080214

source_name: subcutaneous metastasis, intermammary

tag: cell line

tag: braf

value: wt

tag: nras

tag: cell culture phenotype

value: invasive


title: ChIP-chip of HCT116 cells; array 2 of 4

description: ChIP-chip mapping of HP1g locations in HCT116 cells

source_name: ChIP DNA from HCT116 cells

growth_protocol: HCT116 cells were grown in McCoys media, supplemented with 10% FBS and 1% pen-strep.

source_name: Input DNA from HCT116 cells


title: HOXA13 Gain Of Funstion, biological rep2

city: ILLKIRCH

first: philippe

last: moncuquet

address: 1 rue laurent fries

institute: IGBMC

description: Gene expression data from PSM precursors stage 9 somite chicken embryo

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hours at 45oC on GeneChip® Chicken Genome arrays.  Each microarray was then washed and stained on a GeneChip® fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.

data_processing: Initial filtering and preprocessing, including background correction, quantile normalization and summarization, was performed using MAS approach with the R bioconductor package (R version 2.12.1, Bioconductor version 2.8 ). Expression set were then filtered according to Calls information and to probes intensities.

organism: Gallus gallus

source_name: Chicken embryos PSM progenitors at Stage 9 Somites with a vector coding for both HoxA13 and an H2B-Venus reporter

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip® Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

growth_protocol: Chicken eggs were incubated for 24h at 38°C in a controlled humidified incubator until they reach the stage 5 HH, embryos were then cultured ex-ovo on filter paper and electroporated, after electroporation embryos were cultured on albumin/agar solution and re-incubated in humidified incubators at 38°C for 14 hours until they reached the stage 9 somites.

treatment_protocol: Primitive streak aera corresponding to PSM precursors were dissected in Stage 9 somites chicken embryo overexpressing HoxA13 or a control H2B-Venus.

tag: cell type

value: PSM precursors cells

tag: developmental stage

value: Stage 9 somites


title: Control, biological rep2

source_name: Chicken embryos PSM progenitors at Stage 9 Somites with a vector coding for H2B-Venus reporter alone


title: HOXA13 Gain Of Funstion, biological rep1


title: Head_Selection Population 3_Day 50_Rep 1

description: SAMPLE 110

tag: gender

tag: tissue


title: Head_Control Population 3_Day 1_Rep 2

description: SAMPLE 111

source_name: Head_control_1 day of age


title: Head Selection Population 3_Day 15_Rep 1

description: SAMPLE 109


title: Head_Control Population 3_Day 30_Rep 2

description: SAMPLE 112

source_name: Head_control_30 days of age


title: Control, biological rep1


title: Head_Selection Population 3_Day 30_Rep 2

description: SAMPLE 113

source_name: Head_selection_30 days of age


title: cDNA array  TM-1/Hai7124 10 DPA fiber set3(dye-swap)

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 10DPA

source_name: 10 DPA cotton fiber

tag: tissue type

value: fibers

value: 10 days post anthesis (DPA)

tag: cultivar


title: Head_Selection Population 3_Day 1_Rep 1

description: SAMPLE 106

source_name: Head_selection_1 day of age


title: Head_Control Population 3_Day 30_Rep 1

description: SAMPLE 104


title: HSC-3 cells treated with siRNA for HSF1-2

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. HSC-3 cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co) containing 20 nM siRNA (for HSF1) and Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C. Six hours after transfection, the medium was exchanged for E-MEM medium supplemented with 10% FBS, and the cells were maintained at 37°C for 2 days.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: program-name = Expression Console; affymetrix-algorithm-name = rma

source_name: Human oral squamous carcinoma cell line HSC-3

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3’ IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.8 and 10.

value: male

tag: age

value: tongue

tag: tumor stage

value: squamous carcinoma with high metastatic potential

value: oral squamous carcinoma cell line HSC-3

tag: genotype/variation

value: HSF1 knockdown


title: Head_Control Population 3_Day 1_Rep 1

description: SAMPLE 105

value: female

tag: group

value: control populations

value: Head

tag: population

tag: age (day)


title: Head_Selection Population 3_Day 5_Rep 1

description: SAMPLE 107

value: selection populations (for longer reproductive lifespans)

tag: biological replicate


title: Head_Selection Population 3_Day 1_Rep 2

description: SAMPLE 117


title: Head_Control Population 3_Day 5_Rep 1

description: SAMPLE 108

source_name: Head_control_5 days of age


title: HSC-3 cells treated with siRNA for HSF1-1

tag: cell line


title: ChIP-chip of MDA-MB-231 cells; array 3 of 4

source_name: ChIP DNA from MDA-MB-231 cells

tag: antibody

value: HP1 gamma

tag: antibody vendor

value: Millipore

tag: antibody catalog number

tag: antibody lot numbers

source_name: Input DNA from MDA-MB-231 cells

tag: fraction

value: input


title: HSC-3 cells treated with siRNA for luciferase-2

description: HSC-3 cells, a human oral squamous carcinoma cell line, were cultured at 37°C. HSC-3 cells were incubated in Opti-MEM® I Reduced Serum Medium (Life Technologies Co) containing 20 nM siRNA (for luciferase) and Lipofectamine™ RNAiMAX (Life Technologies Co.) at 37°C. Six hours after transfection, the medium was exchanged for E-MEM medium supplemented with 10% FBS, and the cells were maintained at 37°C for 2 days.

tag: gender

value: control


title: HSC-3 cells treated with siRNA for luciferase-1

tag: tissue


title: C990557A

city: Chapel Hill

first: Felix

last: Araujo-Perez

state: NC

address: 103 Mason Farm Road-MBRB 7336

institute: University of North Carolina

hyb_protocol: Overnight incubation at 65 degrees Celsius.

scan_protocol: Agilent scanner C.

data_processing: Data for both channels were Lowess-normalized using the R package "Statistics for Microarray Analysis", and then the log(2) ratio was generated.

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID 15679094).

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: Human Reference B

source_name: Macrodissected snap-frozen healthy tissue sample, AA

extract_protocol: RNeasy Protect Mini Kit (Qiagen).

treatment_protocol: Sample stored in RNAlater.

value: healthy colon

tag: race

value: black


title: Head_Selection Population 2_Day 15_Rep 2

description: SAMPLE 99

source_name: Head_selection_15 days of age


title: C990465A

source_name: Macrodissected snap-frozen healthy tissue sample, EA

value: white


title: Head_Selection Population 3_Day 30_Rep 1

description: SAMPLE 101


title: Head_Control Population 3 Day 15_Rep 3

description: SAMPLE 102

source_name: Head_control_15 days of age


title: C990272A rpt


title: Head_Control Population 2_Day 15_Rep 2

description: SAMPLE 98


title: C990252A


title: HaCaTEGFR_EGF_gefitinib_8hr_rep1

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description: Gene expression data

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G

data_processing: fRMA normalization and removal of date effect estimated with a limma linear model

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with gefitinib

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: HaCaT

tag: forced expression

value: EGFR

tag: media

tag: media stimulation

value: EGF

tag: treatment

value: gefitinib

tag: treatment time

tag: batch


title: HaCaTEGFR_serum_gefitinib_8hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in serum, stimulated with none, treated with gefitinib

value: serum


title: Head_Selection Population 2_Day 50_Rep 2

description: SAMPLE 96

source_name: Head_selection_50 days of age

value: female

tag: group

tag: population

tag: age (day)

tag: biological replicate


title: Head_Control Population 2_Day 30_Rep 2

description: SAMPLE 97

value: control populations


title: Head_Selection Population 2_Day 5_Rep 2

description: SAMPLE 100

source_name: Head_selection_5 days of age

value: Head


title: URMITE_homo sapiens_44K_HMEC_251485041071_1_3_HF_Chlo

description: Rickettsia felis-infected (HMEC) human epithelial cells

source_name: chloramphenicol treatment

tag: cell type


title: ChIP-chip of K562 cells; array 3 of 4

source_name: ChIP DNA from K562 cells

tag: antibody

tag: antibody vendor

tag: antibody catalog number

tag: antibody lot numbers

tag: cell line

source_name: Input DNA from K562 cells


title: HaCaTEGFR_serum_none_8hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in serum, stimulated with none, treated with none


title: C990167A

tag: sample type

tag: tissue

tag: race


title: ChIP-chip of HCT116 cells; array 3 of 4

source_name: ChIP DNA from HCT116 cells

source_name: Input DNA from HCT116 cells

tag: fraction


title: Head_Control Population 2_Day 50_Rep 2

description: SAMPLE 95

source_name: Head_control_50 days of age

tag: gender


title: HaCaTEGFR_none_none_8hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with none, treated with none

tag: forced expression

tag: media

tag: media stimulation

tag: treatment

tag: treatment time


title: C990091A

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: C982109A


title: Head_Control Population 2 _Day 5_Rep 2

description: SAMPLE 93

source_name: Head_control_5 days of age

tag: group

tag: population

tag: age (day)

tag: biological replicate


title: HaCaTEGFR_EGF_none_8hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with none

tag: batch


title: Head_Control Population 2_Day 30_Rep 1

description: SAMPLE 89

source_name: Head_control_30 days of age


title: Head_Selection Population 2_Day 1_Rep 2

description: SAMPLE 92

source_name: Head_selection_1 day of age

value: selection populations (for longer reproductive lifespans)


title: Head_Selection Population 2_Day 50_Rep 1

description: SAMPLE 90


title: Head_Control Population 2_Day 1_Rep 2

description: SAMPLE 91

source_name: Head_control_1 day of age


title: Head_Control Population 2_Day 15_Rep 1

description: SAMPLE 88

source_name: Head_control_15 days of age


title: Head_Control Population 2_Day 5_Rep 1

description: SAMPLE 81


title: Head_Selection Population 2_Day 30_Rep 1

description: SAMPLE 87

source_name: Head_selection_30 days of age


title: Head_Selection Population 2_Day 30_Rep 2

description: SAMPLE 94


title: Head_Selection Population 2_Day 15_Rep 1

description: SAMPLE 83

source_name: Head_selection_15 days of age


title: HaCaTEGFR_none_none_4hr_rep2

description: Gene expression data


title: Head_Selection Population 2_Day 5_Rep 1

description: SAMPLE 86

source_name: Head_selection_5 days of age


title: C982074A

source_name: Macrodissected snap-frozen healthy tissue sample, EA


title: HaCaTEGFR_serum_gefitinib_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in serum, stimulated with none, treated with gefitinib


title: C061330A


title: HaCaTEGFR_EGF_none_4hr_rep2

description: Gene expression data


title: Head Selection Population 1_Day 15_Rep 2

description: SAMPLE 80


title: HaCaTEGFR_serum_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in serum, stimulated with none, treated with none


title: Head_Control Population 2_Day 50_Rep 1

description: SAMPLE 85


title: C980227A


title: C060375A


title: HaCaTEGFR_EGF_U1026_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with U1026


title: Head_Selection Population 2_Day 1_Rep 1

description: SAMPLE 82


title: Head_Control Population 2_Day 1_Rep 1

description: SAMPLE 84


title: Head_Control Population 1_Day 30_Rep 2

description: SAMPLE 79


title: HaCaTEGFR_EGF_LY294002_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with LY294002


title: HaCaTEGFR_none_none_4hr_rep1

description: Gene expression data


title: HaCaTEGFR_EGF_none_4hr_rep1

description: Gene expression data


title: Head_Control Population 1_Day 1_Rep 2

description: SAMPLE 78


title: C040045A


title: C050197A


title: C050334A

source_name: Macrodissected snap-frozen healthy tissue sample, AA


title: C050813A replicate


title: Head_Control Population 1_Day 5_Rep 2

description: SAMPLE 77


title: Head_Control Population 3_Day 50_Rep 1

description: SAMPLE 103

source_name: Head_control_50 days of age


title: Head_Selection Population 1_Day 50_Rep 2

description: SAMPLE 76

source_name: Head_selection_50 days of age


title: Head_Selection Population 1_Day 30_Rep 2

description: SAMPLE 75


title: Head_Selection Population 1_Day 15_Rep 1

description: SAMPLE 67


title: Head_Selection Population 1_Day 30_Rep 1

description: SAMPLE 69


title: HaCaTvector_EGF_U1026_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with EGF, treated with U1026

value: mock


title: Head_Control Population 1_Day 1_Rep 1

description: SAMPLE 68


title: Head_Selection Population 1_Day 1_Rep 2

description: SAMPLE 71


title: Head_Control Population 1_Day 15_Rep 2

description: SAMPLE 73


title: Head_Control Population 1_Day 5_Rep 1

description: SAMPLE 66

source_name: Head_control_5 days of age


title: HaCaTvector_none_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with none, treated with none


title: C030358A

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: HaCaTvector_EGF_LY294002_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with EGF, treated with LY294002


title: Head_Control Population 1_Day 30_Rep 1

description: SAMPLE 70

source_name: Head_control_30 days of age


title: Head_Control Population 1_Day 50_Rep 2

description: SAMPLE 74


title: Head_Selection Population 1_Day 5_Rep 1

description: SAMPLE 64


title: C030444A


title: Head_Selection Population 1_day 50_Rep 1

description: SAMPLE 65


title: C030538A


title: C010210A


title: C010295A


title: C000527A


title: C000595A


title: CH_HaCaTvector_EGF_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with EGF, treated with none


title: Head_Control Population 1_Day 50_Rep 1

description: SAMPLE 62


title: Head_Control Population 1_Day 15_Rep 1

description: SAMPLE 61

source_name: Head_control_15 days of age


title: Abdomen_Selection Population 3_Day 30_Rep 2

description: SAMPLE 60

source_name: Abdomen_selection_30 days of age

value: Abdomen


title: HaCaTvector_TNF_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with TNF, treated with none

value: TNF


title: Abdomen_Selection Population 3_Day 15_rep 2

description: SAMPLE 59

source_name: Abdomen_selection_15 days of age


title: Abdomen_Control Population 3_Day 5_Rep 2

description: SAMPLE 58

source_name: Abdomen_control_5 days of age


title: Abdomen_Control Population 3_Day 1_Rep 2

description: SAMPLE 57

source_name: Abdomen_control_1 day of age


title: C000526A

source_name: Macrodissected snap-frozen healthy tissue sample, EA


title: HaCaTvector_none_none_4hr_rep3

description: Gene expression data


title: CH_HaCaTvector_none_none_4hr_rep1

description: Gene expression data


title: C000389A


title: C000451A


title: Abdomen_Control Population 3_Day 15_Rep 2

description: SAMPLE 56

source_name: Abdomen_control_15 days of age


title: Abdomen_Selection Population 3_Day 5_Rep 2

description: SAMPLE 53

source_name: Abdomen_selection_5 days of age


title: HaCaTvector_TNF_none_4hr_rep2

description: Gene expression data


title: CH_HaCaTvector_EGF_none_4hr_rep2

description: Gene expression data


title: Abdomen_Control Population 3_Day 30_Rep 2

description: SAMPLE 54

source_name: Abdomen_control_30 days of age


title: HaCaTvector_TNF_none_4hr_rep3

description: Gene expression data


title: C000339A


title: HaCaTvector_EGF_none_4hr_rep3

description: Gene expression data


title: C000220A

source_name: Macrodissected snap-frozen healthy tissue sample, AA


title: C000240A


title: HaCaTEGFR_EGF_gefitinib_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with gefitinib


title: Abdomen_Selection Population 3_Day 30_Rep 1

description: SAMPLE 50


title: Abdomen_Selection Population 3_Day 50_Rep 2

description: SAMPLE 51

source_name: Abdomen_selection_50 days of age


title: Abdomen_Control Population 3_Day 30_Rep 1

description: SAMPLE 49


title: Abdomen_Control Population 3_Day 50_Rep 2

description: SAMPLE 55

source_name: Abdomen_control_50 days of age


title: C000215A

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: Abdomen_Control Population 3_Day 1_Rep 1

description: SAMPLE 45


title: Abdomen_Selection Population 3_Day 1_Rep 1

description: SAMPLE 46

source_name: Abdomen_selection_1 day of age


title: Abdomen_Selection Population 3_Day 1_Rep 2

description: SAMPLE 52


title: Abdomen_Control Population 3_Day 50_Rep 1

description: SAMPLE 47


title: Abdomen_Selection Population 3_Day 5_Rep 1

description: SAMPLE 48


title: HaCaTEGFR_none_none_4hr_rep3

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with none, treated with none


title: Abdomen_Control Population 3_Day 15_Rep 1

description: SAMPLE 44


title: HaCaTp65_TNF_none_4hr_rep3

description: Gene expression data

source_name: HaCaT cell line with RELA/p65 forced over expression, grown in none, stimulated with TNF, treated with none


title: Abdomen_Selection Population 3_Day 50_Rep 1

description: SAMPLE 42


title: HaCaTEGFR_EGF_none_4hr_rep3

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with none


title: Head_Selection Population 1_Day 5_Rep 2

description: SAMPLE 72

source_name: Head_selection_5 days of age


title: C000175A


title: Abdomen_Control Population 3_Day 5_Rep 1

description: SAMPLE 43


title: HaCaTvector_EGF_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with EGF, treated with none


title: HaCaTp65_TNF_none_4hr_rep2

description: Gene expression data


title: C000117A


title: Abdomen_Selection Population 3_Day 15_Rep 1

description: SAMPLE 41

source_name: Abdomen_selection_15 days of age


title: C000063A


title: CH_ HaCaTEGFR_EGF_none_4hr_rep2

description: Gene expression data


title: HaCaTp65_none_none_4hr_rep2

description: Gene expression data

source_name: HaCaT cell line with RELA/p65 forced over expression, grown in none, stimulated with none, treated with none


title: Abdomen_Control Population 2_Day 5_Rep 2

description: SAMPLE 40

source_name: Abdomen_control_5 days of age


title: C000123A

source_name: Macrodissected snap-frozen healthy tissue sample, EA


title: C000020A


title: Abdomen_Selection Population 2_Day 30_Rep 2

description: SAMPLE 38

source_name: Abdomen_selection_30 days of age


title: CH_HaCaTEGFR_none_none_4hr_rep2

description: Gene expression data


title: Abdomen_Selection Population 2_Day 5_Rep 2

description: SAMPLE 39

source_name: Abdomen_selection_5 days of age


title: Abdomen_Control Population 2_Day 15_Rep 2

description: SAMPLE 37

source_name: Abdomen_control_15 days of age


title: Abdomen_Selection Population 2_Day 15_Rep 2

description: SAMPLE 35


title: 104_HaCaTp65_TNF_none_4hr_rep2

description: Gene expression data


title: HaCaTp65_TNF_none_8hr_rep1

description: Gene expression data


title: Head_Selection Population 1_Day 1_Rep 1

description: SAMPLE 63

source_name: Head_selection_1 day of age


title: C060375B

source_name: Macrodissected snap-frozen tumor sample, EA

value: colon tumor

tag: Sex

tag: age


title: Abdomen_Control Population 2_Day 30_Rep 2

description: SAMPLE 36

source_name: Abdomen_control_30 days of age


title: Abdomen_Selection Population 2_Day 1_Rep 2

description: SAMPLE 34


title: C050334B

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

tag: sample type

value: Human Reference B

source_name: Macrodissected snap-frozen tumor sample, AA

value: male


title: HaCaTvector_none_none_4hr_rep2

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in none, stimulated with none, treated with none

tag: cell line


title: C020309B replicate (RNA)

tag: tissue

tag: race

value: black


title: HaCaTp65_none_none_8hr_rep1

description: Gene expression data


title: Abdomen_Control Population 2_Day 5_Rep 1

description: SAMPLE 30

tag: gender


title: Abdomen_Control Population 2_Day 50_Rep 1

description: SAMPLE 28

source_name: Abdomen_control_50 days of age


title: CH_HaCaTEGFR_none_none_8hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with none, treated with none

tag: forced expression


title: Abdomen_Selection Population 2_Day 50_Rep 2

description: SAMPLE 33

source_name: Abdomen_selection_50 days of age


title: C000287B replicate (RNA)


title: C030538B


title: Abdomen_Control Population 2_Day 50_Rep 2

description: SAMPLE 31


title: HaCaTp65_TNF_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with RELA/p65 forced over expression, grown in none, stimulated with TNF, treated with none

tag: media


title: Abdomen_Selection Population 2_Day 50_Rep 1

description: SAMPLE 27


title: Abdomen_Control Population 2_Day 15_Rep 1

description: SAMPLE 29


title: Abdomen_Selection Population 2_Day 30_Rep 1

description: SAMPLE 26


title: CH_HaCaTEGFR_EGF_none_8hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in none, stimulated with EGF, treated with none

tag: media stimulation


title: Abdomen_Selection Population 2_Day 15_Rep 1

description: SAMPLE 24

source_name: Abdomen_selection_15 days of age


title: C030444B


title: Abdomen_Selection Population 2_Day 1_Rep 1

description: SAMPLE 25

source_name: Abdomen_selection_1 day of age


title: C030358B


title: Abdomen_Control Population 2_Day 1_Rep 2

description: SAMPLE 32

source_name: Abdomen_control_1 day of age


title: CH_HaCaTEGFR_EGF_none_4hr_rep1

description: Gene expression data

tag: treatment


title: Abdomen_Selection Population 2_Day 5_Rep 1

description: SAMPLE 22


title: HaCaTp65_none_none_4hr_rep1

description: Gene expression data

source_name: HaCaT cell line with RELA/p65 forced over expression, grown in none, stimulated with none, treated with none

tag: treatment time


title: C030202B

value: white


title: C020498B


title: Abdomen_Control Population 1_Day 5_Rep 2

description: SAMPLE 19

source_name: Abdomen_control_5 days of age

tag: group


title: Abdomen_Control Population 2_Day 1_Rep 1

description: SAMPLE 23

tag: population


title: HaCaTp65_serum_none_0hr_rep3

description: Gene expression data

source_name: HaCaT cell line with RELA/p65 forced over expression, grown in serum, stimulated with none, treated with none

value: HaCaT


title: Abdomen_Selection Population 1_Day 1_Rep 2

description: SAMPLE 16

tag: age (day)


title: Abdomen_Control Population 2_Day 30_Rep 1

description: SAMPLE 21

tag: biological replicate


title: Abdomen_Selection Population 1_Day 30_Rep 2

description: SAMPLE 14

source_name: Abdomen_selection_30 days of age


title: Abdomen_Selection Population 1_Day 15_Rep 2

description: SAMPLE 17


title: C010210B

source_name: Macrodissected snap-frozen tumor sample, EA


title: C000595B


title: Abdomen_Selection Population 1_Day 5_Rep 2

description: SAMPLE 18

source_name: Abdomen_selection_5 days of age


title: HaCaTEGFR_serum_none_0hr_rep3

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in serum, stimulated with none, treated with none

value: EGFR

tag: batch


title: CH_HaCaTEGFR_none_none_4hr_rep1

description: Gene expression data


title: C010295B

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Macrodissected snap-frozen tumor sample, AA

tag: Sex


title: Abdomen_Control Population 1_Day 15_Rep 2

description: SAMPLE 15

source_name: Abdomen_control_15 days of age


title: Abdomen_Control Population 1_Day 50_Rep 2

description: SAMPLE 12

source_name: Abdomen_control_50 days of age


title: C000175B replicate (RNA)

tag: age


title: Abdomen_Control Population 1_Day 1_Rep 2

description: SAMPLE 13


title: Abdomen_Selection Population 1_Day 50_Rep 2

description: SAMPLE 20

source_name: Abdomen_selection_50 days of age


title: HaCaTvector_serum_none_0hr_rep3

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in serum, stimulated with none, treated with none


title: HaCaTras_serum_none_0hr_rep3

description: Gene expression data

source_name: HaCaT cell line with HRAS-VAL12D forced over expression, grown in serum, stimulated with none, treated with none


title: Abdomen_Control Population 1_Day 30_Rep 2

description: SAMPLE 11

source_name: Abdomen_control_30 days of age


title: HaCaTnone_serum_none_0hr_rep3

description: Gene expression data

source_name: HaCaT cell line with none forced over expression, grown in serum, stimulated with none, treated with none


title: Abdomen_Selection Population 1_Day 5_Rep 1

description: SAMPLE 10


title: C990557B

tag: sample type


title: Abdomen_Selection Population 1_Day 15_Rep 1

description: SAMPLE 9

source_name: Abdomen_selection_15 days of age


title: Abdomen_Control Population 1_Day 15_Rep 1

description: SAMPLE 8


title: C070076B


title: Abdomen_Control Population 1_Day 50_Rep 1

description: SAMPLE 6


title: Abdomen_Control Population 1_Day 1_Rep 1

description: SAMPLE 4

source_name: Abdomen_control_1 day of age


title: C050107B


title: HaCaTp65_serum_none_0hr_rep2

description: Gene expression data

tag: cell line


title: Abdomen_Selection Population 1_Day 30_Rep 1

description: SAMPLE 5

tag: tissue


title: Abdomen_Control Population 1_Day 30_Rep 1

description: SAMPLE 7


title: Abdomen_Selection Population 1_Day 1_Rep 1

description: SAMPLE 1

source_name: Abdomen_selection_1 day of age


title: HaCaTras_serum_none_0hr_rep2

description: Gene expression data


title: Abdomen_Selection Population 1_Day 50_Rep 1

description: SAMPLE 2


title: C000451B replicate

tag: race


title: HaCaTnone_serum_none_0hr_rep2

description: Gene expression data


title: HaCaTp65_serum_none_0hr_rep1

description: Gene expression data

source_name: HaCaT cell line with RELA/p65 forced over expression, grown in serum, stimulated with none, treated with none


title: C000545B


title: WA53

city: Ann Arbor

first: Scott

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

department: Pathology

institute: University of Michigan

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 1x44k or 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1).  Spot values were normalized using the default linear-lowess normalization. LogRatio for all probes, which were used for subsequent analysis, were converted to log(2). Although the 1x44k and 4x44k arrays have the same probes, the 4x44k arrays have 10 replicates of some probes. Thus, to generate a final data set, the median value of replicated probes was used for 4x44k arrays. The final data set (including benign prostate, localized prostate cancer and CRPC) was uploaded into a custom instance of Oncomine  for automated analysis. In Oncomine, the dataset was median centered (per array) prior to indicated analyses.

source_name: pooled benign prostate tissue (Clontech)

label_protocol: One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions

value: reference

source_name: metastatic prostate cancer (obtained at rapid [warm] autopsy)

value: metastatic castrate resistant prostate cancer (WA)


title: HaCaTEGFR_serum_none_0hr_rep2

description: Gene expression data

value: serum


title: C000339B replicate

source_name: Macrodissected snap-frozen tumor sample, EA

value: female


title: Abdomen_Control Population 1_Day 5_Rep 1

description: SAMPLE 3

source_name: Abdomen_control_5 days of age

tag: gender

value: control populations


title: HaCaTvector_serum_none_0hr_rep2

description: Gene expression data

tag: forced expression


title: C000259B

source_name: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs


title: HaCaTEGFR_serum_none_0hr_rep1

description: Gene expression data

source_name: HaCaT cell line with EGFR forced over expression, grown in serum, stimulated with none, treated with none

tag: media


title: WA54


title: WA55


title: C000527B replicate


title: C000323B


title: WA23


title: WA30


title: WA10


title: C000249B


title: HaCaTras_serum_none_0hr_rep1

description: Gene expression data

tag: media stimulation


title: WA29


title: WA26


title: C000220B replicate

source_name: Macrodissected snap-frozen tumor sample, AA


title: WA28


title: HaCaTnone_serum_none_0hr_rep1

description: Gene expression data

tag: treatment


title: HeLa_control_48hours

city: Greifswald

first: Sabine

last: Ameling

address: Felix-Hausdorff.Str 8

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

institute: Universitätsmedizin Greifswald

hyb_protocol: Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA, USA) were employed.

scan_protocol: After hybridization and washing, arrays were scanned using the GeneChip System Confocal Scanner 3000 (Affymetrix)

data_processing: Affymetrix default parameters were used for data extraction (GCOS, MAS5.0). Expression data were transferred to GeneSpring GX version 7.3.1. (Agilent Technologies) and per-chip normalized. Genes which were flagged as present or marginal and exceeding a fold change of 2 in comparison to control were further analysed.

source_name: human cervix carcinoma cell line HeLa_control

label_protocol: T7-RNA polymerase-mediated linear amplification was performed starting with 1µg RNA (One cycle Target labelling protocol; Affymetrix, Santa Clara, CA, USA).

growth_protocol: The human cervix carcinoma cell line HeLa were obtained from the American Type Culture Collection and maintained by culture in RPMI 1640 or DMEM medium supplemented with 10% FCS, 1% glutamine, 50 U/ml penicillin, and 50 µg/ml streptomycin.

extract_protocol: Total RNA of one batch Doxorubicin treated and untreated (DMSO) HeLa cells for two timepoints (24h, 48h) was extracted using Trizol PeqGold RNA Pure (Peqlab, Erlangen, Germany) according to the manufacturer`s protocol.

treatment_protocol: For expression analysis, cells were seeded 24 h before drug treatment in 6-Well plates (300,000 cells per well) and were cultured for the respective time points with doxorubicin, DMSO as solvent respectively.

value: HeLa


title: HeLa_doxorubicin_48hours

source_name: human cervix carcinoma cell line HeLa_treatment with doxorubicin for 48h

value: doxorubicin for 48h


title: C000117B replicate


title: WA19


title: C000240B replicate


title: WA7


title: HeLa_control_24hours


title: WA2


title: WA6


title: WA40


title: C000178B


title: WA42


title: WA37


title: WA47


title: WA39


title: HeLa_doxorubicin_24hours

source_name: human cervix carcinoma cell line HeLa_treatment with doxorubicin for 24h

value: doxorubicin for 24h


title: C000111B


title: WA46


title: WA35


title: HaCaTvector_serum_none_0hr_rep1

description: Gene expression data

source_name: HaCaT cell line with mock forced over expression, grown in serum, stimulated with none, treated with none

value: mock

tag: treatment time


title: C000020B replicate


title: C990512A

source_name: Macrodissected snap-frozen healthy tissue sample, EA

value: healthy colon


title: C050813B replicate

value: colon tumor


title: C060003B

value: Human Reference B


title: WA31


title: C040186A


title: C050813A

source_name: Macrodissected snap-frozen healthy tissue sample, AA


title: C000287A


title: WA33


title: C010342A


title: WA25


title: WA18


title: C010095A


title: T75

source_name: prostate tissue (radical prostatectomy specimen)

value: localized prostate cancer (T)


title: T83


title: C050571B

value: male


title: T82


title: C060096

value: black


title: WA32


title: T85


title: T69


title: T70


title: C050301B


title: C050134B


title: T73


title: T67


title: C050282B


title: C050197B

value: white


title: T68


title: C050813B


title: C030461B


title: C040186B


title: T63


title: T66


title: T64


title: T62


title: C010342B


title: C030263B


title: WA11


title: T59


title: C000287B


title: C030090B


title: C020449B


title: T60


title: Gastric cancer tissue sample [800T]

city: Shanghai

first: Cheng

last: Lei

address: 151 Li Bing Road

institute: National Engineering Center for Biochip at Shanghai

description: tumor stomach sample

hyb_protocol: Five micrograms of labeled ss-cDNA was used to hybridize the Human Exon 1.0 ST microarray for 16 hours. Staining and washing were all processed with Affymetrix’s protocols.

scan_protocol: The arrays were scanned on the GeneChip Scanner 3000 7G with GeneChip Operating Software v 1.3 (Affymetrix) to generate .CEL intensity files.

data_processing:
Expression Consol software (v 1.0) (Affymetrix) integrated robust multiarray analysis (RMA) algorithm was applied to extract gene-level expression signal and detection above background (DABG) P-value for each probe set of the samples. Probe sets with P<0.05 were considered as present, and an expression signal cutoff was set as 3.9, as minimum number of falsely called probes. Only the genes with signal above cutoff were used in later analysis.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: stomach

label_protocol: One hundred nanograms of starting total RNAs was used in first round double strand (ds)-cDNA synthesis and cRNA synthesis; 8-10 μg of cRNA could be got and then used in second round single-strand (ss)-cDNA synthesis. ss-cDNA fragmentation and labeling were finished according to the Whole Transcript Sense Target Labeling Assay manual (Affymetrix).

growth_protocol: not applicable

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

treatment_protocol: 25 pairs of gastric tissues were collected immediately after surgical resection and snap-frozen in liquid nitrogen. Microdissection was performed using MMI CellCut LCM system (MMI), under 100 × magnification. Tumor or non-malignant cells were captured from cancerous or adjacent noncancerous tissues using LCM macro caps (MMI), respectively.

tag: tissue type

value: Gastric Cancer Tissue

tag: disease state

value: tumor

tag: histopathology

value: adenocarcinoma

tag: tumor stage

tag: differentiation

value: MD


title: T61

value: reference


title: WA14

value: metastatic castrate resistant prostate cancer (WA)


title: C010095B

tag: Sex


title: Gastric cancer tissue sample [791T]

description: tumor stomach sample

value: female

tag: age

value: adenocarcinoma, partial signet-ring cell carcinoma

value: PD


title: Gastric cancer tissue sample [766T]

description: tumor stomach sample


title: C030485B

tag: sample type


title: C020122B


title: Gastric cancer tissue sample [787T]

description: tumor stomach sample

value: M-PD


title: T58


title: T57


title: C030457B


title: T54


title: T56


title: Gastric cancer tissue sample [740T]

description: tumor stomach sample


title: T53


title: C030411B


title: Gastric cancer tissue sample [737T]

description: tumor stomach sample


title: T50


title: Gastric cancer tissue sample [729T]

description: tumor stomach sample


title: Gastric cancer tissue sample [736T]

description: tumor stomach sample


title: C030369B


title: T47


title: T51


title: T49


title: T43


title: T52


title: T48


title: C030225B


title: T46


title: C030144B


title: T42


title: Gastric cancer tissue sample [726T]

description: tumor stomach sample


title: Gastric cancer tissue sample [723T]

description: tumor stomach sample


title: C030111B


title: T40


title: T41


title: Gastric cancer tissue sample [575T]

description: tumor stomach sample


title: T45


title: T44


title: T39


title: C010322B


title: T37


title: C010335B


title: C010331B


title: T29


title: Gastric cancer tissue sample [543T]

description: tumor stomach sample


title: Gastric cancer tissue sample [553T]

description: tumor stomach sample


title: Gastric cancer tissue sample [554T]

description: tumor stomach sample


title: T31


title: Gastric cancer tissue sample [442T]

description: tumor stomach sample


title: Gastric cancer tissue sample [574T]

description: tumor stomach sample


title: C040427B


title: T25


title: T32


title: C040140B


title: T27


title: T65


title: C010341B


title: T24


title: C010156B


title: Gastric cancer tissue sample [414T]

description: tumor stomach sample

value: tubular adenocarcinoma


title: Gastric cancer tissue sample [439T]

description: tumor stomach sample


title: T21


title: T17


title: T19


title: C010209B

value: colon tumor


title: T26


title: T20


title: N29

value: benign prostate tissue (N)


title: C010104B

value: Human Reference B


title: Gastric cancer tissue sample [395T]

description: tumor stomach sample


title: Gastric cancer tissue sample [384T]

description: tumor stomach sample

value: male


title: N27


title: C000584B


title: N28


title: C010054B

value: black


title: Gastric cancer tissue sample [177T]

description: tumor stomach sample


title: Gastric cancer tissue sample [175T]

description: tumor stomach sample


title: Gastric cancer tissue sample [159T]

description: tumor stomach sample


title: Gastric cancer tissue sample [168T]

description: tumor stomach sample


title: N23


title: Gastric cancer tissue sample [134T]

description: tumor stomach sample


title: N20


title: N25


title: C000591B

value: white


title: T55

value: localized prostate cancer (T)


title: N24


title: N22


title: N21


title: C000158B


title: N19


title: N18


title: WA29

hyb_protocol: Cy-5 (test channel) and Cy-3 (reference channel) labeled DNA was purified using Microcon YM-30 columns and hybridized for 40 hours at 65o C. Post-hybridization wash was performed with acetonitrile wash and Agilent Stabilization and Drying Solution wash.

scan_protocol: Scanning was performed on an Agilent scanner Model G2505B (5 micron scan with software v7.0).

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (v9.5) using protocol CGH-v4_95_Feb07.  For data analysis, probes on all arrays were limited to those on the 105K array. Log(2) ratios for each probe were determined as rProcessedSignal/gProcessedSignal. To remove copy number variants, all probes with log(2) values >1 or <-1 in any of the 28 benign prostate samples were excluded. The final dataset (consisting of localized prostate cancer and castrate resistant metastatic samples) was uploaded into a custom instance of Oncomine for automated copy number analysis. In Oncomine, circular binary segmentation was performed on the dataset using the DNACopy package (v1.18) available via the Bioconductor project. Agilent Probe IDs are mapped to segments and reporter values are used to generate segment values (mean of reporters). Resulting segments are mapped to hg18 (NCBI 36.1) RefSeq coordinates (UCSC refGene) as provided by UCSC (UCSC refGene, July 2009, hg18, NCBI 36.1, March 2006) and segment values are assigned to each gene. Copy number profiles were visualized using Oncomine Power Tools.

source_name: normal human male DNA (Promega)

label_protocol: 1.5 - 3 ug of gDNA from prostate specimens (test channel) or Human Male Genomic DNA (Promega, reference channel), was restriction digested with AluI and RsaI, and labeled with Cy-5 (test channel) or Cy-3 (reference channel).

extract_protocol: gDNA was isolated using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.


title: N26


title: Matched adjacent noncancerous tissue sample [800N]

description: normal stomach sample

value: gastric cancer adjacent noncancerous tissue

value: normal


title: C000397B


title: WA23


title: WA30


title: C000014B


title: C000575B


title: WA10


title: C000381B


title: WA7


title: WA26


title: Matched adjacent noncancerous tissue sample [740N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [737N]

description: normal stomach sample


title: C000389B


title: Matched adjacent noncancerous tissue sample [736N]

description: normal stomach sample


title: WA11


title: Matched adjacent noncancerous tissue sample [766N]

description: normal stomach sample


title: WA19


title: WA28


title: Matched adjacent noncancerous tissue sample [787N]

description: normal stomach sample


title: WA14


title: C000123B


title: WA2


title: WA42


title: C000526B


title: WA47


title: WA6


title: C000451B


title: WA35


title: Matched adjacent noncancerous tissue sample [729N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [791N]

description: normal stomach sample


title: C000527B


title: WA40


title: WA39


title: WA46


title: C000339B


title: C000240B


title: Matched adjacent noncancerous tissue sample [726N]

description: normal stomach sample


title: C000220B


title: WA37


title: Matched adjacent noncancerous tissue sample [723N]

description: normal stomach sample


title: WA32


title: WA33


title: WA22


title: Matched adjacent noncancerous tissue sample [554N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [575N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [553N]

description: normal stomach sample


title: WA25


title: WA18


title: WA31


title: C040461B


title: C000063B


title: WA3


title: WA5


title: Matched adjacent noncancerous tissue sample [574N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [543N]

description: normal stomach sample


title: WA20


title: WA4


title: C000020B


title: WA16


title: C020309B


title: T83


title: WA13


title: C000117B


title: WA24


title: C000215B


title: T85


title: C000175B


title: Matched adjacent noncancerous tissue sample [442N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [439N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [414N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [384N]

description: normal stomach sample


title: T82


title: 21_muscle in barrow with beef tallow

city: Suwon

first: Bong-Hwan

last: Choi

address: 77 chuksan-gil

department: Animal Genomics & Bioinformatics Division

country: South Korea

institute: National Institute of Animal Science

description: Gene expression data from muscle treated for dietary fat sources in pig

hyb_protocol: Hybridization cocktail (200L) containing 15g of fragmented cRNA were injected into the porcine genome array chip

scan_protocol: The array was scanned with a GeneChip® Scanner 3000 (Affymetrix Inc.).

data_processing: The GeneChip® porcine genome array contains 23,937 probe sets to interrogate 23,256 transcripts in pigs, which represents 20,201 genes. Fold change and Welch’s t-test were applied to select the genes for further analysis. The genes showing 2-fold differential expression were clustered using hierarchical clustering with Pearson’s correlation as a similarity measure and complete linkage as a linkage method.

organism: Sus scrofa

source_name: muscle

label_protocol: Aliquots of 1 g of mRNA were converted into double-stranded cDNA using a Genechip® Expression 3'-Amplification One Cycle Synthesis kit (Affymetrix Inc.).

growth_protocol: Seventy-two crossbred pigs (Landrace × Large White × Duroc) were used. The animals, at 71 ± 1 kg body weight (about 130 days of age), were randomly allocated into 24 pens (320 × 150 cm with solid concrete flooring) in a confined pig house, with three pigs per pen and six replicate pens per treatment.

extract_protocol: The muscle was powdered with liquid nitrogen, and total RNA was extracted from 1 mg of muscle tissue using 3 mL of TRIzol® reagent (Invitrogen, Inc., Carlsbad, CA).

treatment_protocol: Fat sources used in the present study were beef tallow, coconut oil, olive oil, and soybean oil, which were added to a concentration of 3.0% in feed. 24 longissimus dorsi muscle samples were taken for meat quality and used for gene expression.

tag: dietary fat sources

value: beef tallow

value: barrow

value: longissimus dorsi muscle

tag: breed

value: Landrace × Large White × Duroc


title: Matched adjacent noncancerous tissue sample [395N]

description: normal stomach sample

value: female


title: T75

value: reference

tag: tissue


title: T69


title: 23_muscle in barrow with cocont oil

value: coconut oil

tag: gender


title: T68


title: 24_muscle in barrow with beef tallow


title: 20_muscle in barrow with cocont oil


title: Matched adjacent noncancerous tissue sample [168N]

description: normal stomach sample


title: Matched adjacent noncancerous tissue sample [175N]

description: normal stomach sample


title: 22_muscle in barrow with olive oil

value: olive oil


title: T73


title: T65


title: T70


title: Matched adjacent noncancerous tissue sample [177N]

description: normal stomach sample


title: 19_muscle in barrow with soybean oil

value: soybean oil


title: T66


title: T67


title: T63


title: T64


title: 18_muscle in barrow with olive oil


title: 17_muscle in barrow with olive oil


title: T60


title: T59


title: T61


title: T62


title: Matched adjacent noncancerous tissue sample [159N]

description: normal stomach sample


title: T58


title: Matched adjacent noncancerous tissue sample [134N]

description: normal stomach sample


title: WA55

value: metastatic castrate resistant prostate cancer (WA)


title: 16_muscle in barrow with beef tallow


title: T57


title: 15_muscle in barrow with cocont oil


title: WA54


title: WA53


title: T56


title: T54


title: 12_muscle in gilt with olive oil

value: gilt (female)


title: T47


title: T53


title: T52


title: 14_muscle in barrow with soybean oil


title: T50


title: 10_muscle in gilt with beef tallow


title: 11_muscle in gilt with soybean oil


title: T49


title: 9_muscle in gilt with soybean oil


title: 13_muscle in barrow with soybean oil


title: T51


title: T48


title: T44


title: T45


title: T46


title: Gastric Tissue [800]

description: a pair of gastric tissues

hyb_protocol: Equal amount of the labeled sample pairs were mixed and hybridized on CGH microarrays by using Oligo aCGH Hybridization Kit and the SureHyb chambers, for 40 hours at 60°C. After hybridization, slides were washed sequentially using Oligo aCGH Wash Buffer 1 and 2 set (Agilent Technologies).

scan_protocol: The microarray slides were scanned on an Agilent G2655AA scanner, and raw data were extracted using Feature Extraction Software (v 9.5.3) at the default CGH parameter settings (Agilent Technologies).

data_processing: Putative CNV intervals in each sample were identified using Agilent CGH Analytics software ver. 4.0.76. Cy5/Cy3 ratios were converted into log2-transformed values. Centralization and fuzzy zero corrections were applied to the microarray.

source_name: gastric cancer tissues

label_protocol: The genomic DNA (500 ng) was digested using AluI and RsaI restriction enzymes (Promega, Madison, WI), and labeled with either Cy5- or Cy3-dUTP fluorescent dyes for cancerous and adjacent noncancerous samples respectively, using Agilent Genomic DNA Labeling Kit Plus (Agilent Technologies).

extract_protocol: Genomic DNA extracted using QIAamp DNA Micro Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: 27 pairs of gastric tissues were collected immediately after surgical resection and snap-frozen in liquid nitrogen. Microdissection was performed using MMI CellCut LCM system (MMI), under 100 × magnification. Tumor or non-malignant cells were captured from cancerous or adjacent noncancerous tissues using LCM macro caps (MMI), respectively.

value: Gastric Cancer Tissue

value: tumor

value: adenocarcinoma

value: MD

source_name: matched adjacent noncancerous tissues

value: Matched Adjacent Noncancerous Tissue


title: Gastric Tissue [791]

description: a pair of gastric tissues

value: adenocarcinoma, partial signet-ring cell carcinoma

value: PD

value: normal


title: Gastric Tissue [787]

description: a pair of gastric tissues

value: male

value: M-PD


title: T40

value: localized prostate cancer (T)


title: 6_muscle in gilt with cocont oil

value: longissimus dorsi muscle

value: Landrace × Large White × Duroc


title: 7_muscle in gilt with olive oil

value: olive oil


title: 8_muscle in gilt with beef tallow

value: beef tallow


title: T41

value: reference


title: T39


title: 4_muscle in gilt with olive oil

value: gilt (female)


title: 5_muscle in gilt with cocont oil

value: coconut oil


title: T42


title: T37


title: T43


title: 3_muscle in gilt with soybean oil

value: soybean oil


title: T29


title: T25


title: T31


title: T27


title: Gastric Tissue [766]

description: a pair of gastric tissues

value: Gastric Cancer Tissue

value: tumor

value: adenocarcinoma


title: Gastric Tissue [779]

description: a pair of gastric tissues

value: female

value: Matched Adjacent Noncancerous Tissue


title: Gastric Tissue [736]

description: a pair of gastric tissues

value: MD

value: normal


title: Gastric Tissue [729]

description: a pair of gastric tissues

value: male

value: PD


title: T20

value: localized prostate cancer (T)


title: T24


title: T26


title: 2_muscle in gilt with beef tallow

value: longissimus dorsi muscle

value: Landrace × Large White × Duroc


title: Gastric Tissue [726]

description: a pair of gastric tissues

value: M-PD


title: Gastric Tissue [737]

description: a pair of gastric tissues


title: T19

value: reference


title: T11


title: Gastric Tissue [740]

description: a pair of gastric tissues

value: adenocarcinoma, partial signet-ring cell carcinoma


title: T21


title: T12


title: 1_muscle in gilt with cocont oil

value: coconut oil

value: gilt (female)


title: T10


title: T17


title: T8


title: liver_STZ 0.5% quercetin diet_rep4

city: Tsukuba

first: Masuko

last: Kobori

state: Ibaraki

address: 2-1-13 Kannondai

institute: Food Research Institute, National Agriculture and Food Research Organization

description: Gene expression data from STZ-treated mouce liver after 14 day feeding of 0.5% quercetin diet

hyb_protocol: Fifteen microgram aliquots of fragmented cRNA were hybridized to an array (Mouse Genome 430 2.0 array, Affymetrix) at 45°C for 16 h.

scan_protocol: After hybridization, the gene chips were washed and stained using a GeneChip Fluidics Station 450 (Affymetrix) and then scanned (GeneChip Scanner; Affymetrix) with the GeneChip Operation Software Ver. 1.3 (Affymetrix).

data_processing: Data analysis was performed with a GeneChip Operating Software (Ver. 1.3) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Mus musculus

source_name: liver, STZ-treated fed 0.5% quercetin diet for 14 days

label_protocol: Double-stranded cDNA was synthesized from the total RNA of each mouse using the One-Cycle cDNA Synthesis Kit (Affymetrix Japan KK, Tokyo, Japan) with a T7-(dT)24 primer. Biotin-labeled cRNA was then synthesized using an IVT Labeling Kit (Affymetrix). The biotin-labeled cRNA was further purified and fragmented using the Sample Cleanup Module (Affymetrix).

growth_protocol: Six-week-old male BALB/c mice were obtained from the Institute for Animal Reproduction, Charles River Japan Inc. (Ibaraki, Japan). The mice were housed under conditions of 24± 1°C, 55 ± 5% humidity, and 12 hour light/dark photocycles (dark period from 0800 to 2000) with free access to water and a standard nonpurified diet (NMF, Oriental Yeast Co., Tokyo, Japan) for a week prior to the experiment.

extract_protocol: The mice were killed under anesthesia with pentobarbital, and blood and liver tissue were immediately collected. Total RNA was extracted from liver tissues using an RNeasy Midi Kit (Qiagen KK, Tokyo, Japan) according to the manufacturer’s instructions.

treatment_protocol: The mice were then intraperitoneally injected with STZ (Wako Pure Chemical Industries, Osaka, Japan, 185 mg/kg in 0.05M citrate buffer, pH 4.5).  Mice (n=6) in the untreated control group did not receive any treatment.  Tail vein blood was sampled weekly and the blood glucose levels of the samples were immediately measured using a blood glucose test meter (Glucocard, Arkray, Kyoto, Japan).  After 1 week, 18 mice showing non-fasting blood glucose levels of 230-400 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% quercetin (Funakoshi, Tokyo, Japan) for 2 weeks. All mice had access to food and water ad libitum during the experimental period.

tag: strain

value: BALB/c

value: liver


title: T9a


title: T5


title: MGA3_Mannitol3

city: Trondheim

first: Tonje

middle: Marita Bjerkan

last: Heggeset

address: Postboks 4760 Torgarden

department: Industry

country: Norway

institute: SINTEF

description:
Gene expression grown on Mannitol
SAMPLE 6

hyb_protocol: Hybridizations were carried out using labeled cDNA and the in situ Hybridization Kit Plus (Agilent Technologies, Santa Clara CA). Arrays were incubated at 65°C for 17 h in Agilent's microarray hybridization chambers and subsequently washed according to Agilent protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The Agilent G2567AA Feature Extraction Software v.9.5.1.1 (Agilent Technologies, Santa Clara CA) was used for data extraction and quality control. Agilent standard scenario normalizations for FE1-colour arrays were applied to all data sets. Default parameters were used (GE1-v5_95_Feb07 and Grid: 022922_D_F_20090212) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bacillus methanolicus

source_name: MGA3_bacterial culture_Mannitol

label_protocol: Fluorescent cy3 labeled cDNA was generated using the SuperScript indirect labeling system (Invitrogen, Carlsbad, CA). Cy3 fluorescent dye (GE-Healtcare Bioscience, Buckinghamshire, UK) was coupled to the amino allyl-labeled cDNA.

growth_protocol: Bacterial culture of Bacillus methanolicus were grown in minimal media with either methanol or mannitol as carbon source and harvested at OD600=1.

extract_protocol: RNA was extracted using the RNAqueous kit (Ambion Inc., Auston TEX). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNAlater were added to the bacterial culture for preservation.

tag: carbon source

value: mannitol

tag: growth condition

value: non-methylotropic


title: T3


title: T7


title: Gastric Tissue [575]

description: a pair of gastric tissues

value: female

value: Gastric Cancer Tissue

value: tumor

value: adenocarcinoma

value: Matched Adjacent Noncancerous Tissue


title: liver_STZ 0.5% quercetin diet_rep5

value: male


title: Gastric Tissue [723]

description: a pair of gastric tissues

value: MD

value: normal


title: liver_STZ 0.5% quercetin diet_rep3


title: liver_STZ 0.5% quercetin diet_rep6


title: Gastric Tissue [574]

description: a pair of gastric tissues


title: Gastric Tissue [554]

description: a pair of gastric tissues

value: PD


title: Gastric Tissue [553]

description: a pair of gastric tissues


title: T32

value: reference

value: localized prostate cancer (T)


title: MGA3_Mannitol2

description:
Gene expression grown on Mannitol
SAMPLE 5


title: T55


title: Gastric Tissue [722]

description: a pair of gastric tissues

value: adenocarcinoma, partial mucinous


title: T1


title: N28

value: benign prostate tissue (N)


title: liver_STZ 0.5% quercetin diet_rep2

value: BALB/c


title: liver_STZ 0.1% quercetin diet_rep6

description: Gene expression data from STZ-treated mouce liver after 14 day feeding of 0.1% quercetin diet

source_name: liver, STZ-treated fed 0.1% quercetin diet for 14 days

value: liver


title: liver_STZ 0.1% quercetin diet_rep5


title: T6


title: MGA3_MeOH2

description:
Gene expression grown on Methanol
SAMPLE 2

source_name: MGA3_bacterial culture_MeOH

value: methanol

value: methylotropic


title: Gastric Tissue [543]

description: a pair of gastric tissues

value: M-PD


title: liver_STZ 0.5% quercetin diet_rep1


title: MGA3_MeOH3

description:
Gene expression grown on Methanol
SAMPLE 3


title: N26


title: N27


title: liver_STZ 0.1% quercetin diet_rep3


title: liver_STZ 0.1% quercetin diet_rep4


title: N25


title: N29


title: Gastric Tissue [439]

description: a pair of gastric tissues

value: female

value: Gastric Cancer Tissue


title: Gastric Tissue [442]

description: a pair of gastric tissues

value: tumor

value: adenocarcinoma


title: Ms4a8a-transfected RAW264.7 co3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression from Ms4a8a transfected Raw264.7 macrophages

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of Mouse430_2 -type from Affymetrix. A Custom CDF Version 13 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.

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

growth_protocol: Raw 264.7 cells were cultivated with DMEM medium supplemented with 10%FCS, 100IU penicillin, 100 µg/ml penicillin, 100 µg/ml streptomycin, 1% pyruvic acid, 1% non essential amino acids. Authentication of cell lines was assured by regular morphology checks and growth curve analyses. Cells were regularly tested for mycoplasma infection by PCR.

extract_protocol: RNA was isolated from these cultures using Qiagen RNeasy Kit

treatment_protocol: Ms4a8a-transfected and empty vector-transfected RAW264.7 cells were incubated for 48 h in DMEM medium supplemented with 10% FCS, 100 IU penicillin, 100 µg/ml streptomycin, 1% pyruvic acid, 1% non essential amino acids.

tag: cell type

value: Raw264.7 macrophages

tag: transfector

tag: cloneid


title: MGA3_MeOH1

description:
Gene expression grown on Methanol
SAMPLE 1


title: Gastric Tissue [395]

description: a pair of gastric tissues

tag: tissue type

tag: disease state

value: Matched Adjacent Noncancerous Tissue


title: N24


title: vector-transfected RAW264.7 co3

description: Gene expression from empty vector transfected Raw264.7 macrophages

value: empty vector


title: MGA3_Mannitol1

description:
Gene expression grown on Mannitol
SAMPLE 4

value: mannitol

value: non-methylotropic


title: Ms4a8a-transfected RAW264.7 co1


title: Gastric Tissue [414]

description: a pair of gastric tissues

tag: histopathology

value: tubular adenocarcinoma

tag: tumor stage

value: MD

value: normal


title: Gastric Tissue [384]

description: a pair of gastric tissues

value: male

tag: differentiation


title: vector-transfected RAW264.7 co2


title: liver_STZ 0.1% quercetin diet_rep2

value: BALB/c

value: liver


title: N22

value: reference

value: benign prostate tissue (N)


title: N20


title: liver_STZ treated diabetic_rep4

description: Gene expression data from STZ-treated mouce liver after 14 day feeding of control AIN93G diet

source_name: liver, STZ-treated fed AIN93G diet for 14 days


title: vector-transfected RAW264.7 co1


title: Ms4a8a-transfected RAW264.7 co2


title: liver_STZ treated diabetic_rep5


title: liver_STZ treated diabetic_rep6


title: N23


title: Gastric Tissue [177]

description: a pair of gastric tissues

value: female

tag: age


title: liver_STZ 0.1% quercetin diet_rep1


title: N21

tag: sample type


title: Gastric Tissue [175]

description: a pair of gastric tissues

value: Gastric Cancer Tissue


title: N19


title: Gastric Tissue [168]

description: a pair of gastric tissues

value: tumor

value: PD


title: Gastric Tissue [159]

description: a pair of gastric tissues

value: adenocarcinoma


title: oxygen_limited_cjejuni_exposed_15min_to_0.010mM_NOC-5&7 (1)

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

hyb_protocol: The Cy3-dCTP-labelled sample was mixed with the Cy5-dCTP-labelled sample and re-suspended in 120 μl salt-based hybridization buffer (supplied with the microarray slides). This was heated at 95 ˚C for 3 min then cooled on ice for 3 min. The mixture was pipetted onto a microarray slide, sealed with a GeneFrame and coverslip in a hybridization chamber and incubated 18 h at 42˚C. Following hybridiztion, microarray slides (minus GeneFrame and coverslip) were washed in a series of pre-warmed (37 ˚C) SSC buffers for 5 min each at 37˚C: 1 x SSC/0.01% SDS, 1x SSC, 0.2x SSC and 0.01x SSC. Microarray slides were dried by centrifugation at 500 xg for 2 min before scanning.

scan_protocol: Slides were scanned on an Affymetrix 428 scanner. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, v 4.0 and GeneSight v 3.5)

data_processing: Spots automatically flagged as bad negative or poor in the Imagene software were removed  before the statistical analysis was carried out in GeneSight. The mean values from each channel were log2 transformed and normalised using the LOWESS method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

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

source_name: Microaerobic log phase cultured control sample

label_protocol: Approximately 12μg RNA was annealed to 4.5μg pd(N)6 random hexamers (Amersham Biosciences) by heating at 65˚C for 10 min, followed by 10 min at 22˚C and cooling on ice for 2 min. This was supplemented with 6μl of 5X First-strand buffer (Invitrogen), 2.5μl dNTP mixture (5mM each dATP, dTTP, dGTP and 2mM dCTP), 3μl 0.1 M DDT, 2μl 1mM Cy3 or Cy5 (Perkin elmer) and 1.5 μl Superscript III reverse transcriptase (200 U) (Invitrogen). This was incubated at 42˚C for 3 hours. The reaction was terminated by the addition of NaOH (7.5 μl of 1M) and HCl (7.5 μl of 1M) before the addition of TE buffer (300 μl). Labelled cDNA was purified using a Qiaquick purification kit (Qiagen)

growth_protocol: 3 to 5% of an overnight starter inoculated into 200 ml of Mueller Hinton Broth supplemented with vancomycin (10 µg/ml) in a 250 ml conical flask. Placed in a microaerobic workstation (80% N2, 10%O2, 10% CO2) and shaken at 125 rpm.

extract_protocol: Samples (30 ml) were harvested using phenol/ethanol to stabilize RNA and total RNA was purified using Qiagen's Rneasy Mini kit as recommended by the suppliers. RNA was quantified using a BioPhotometer (Eppendorf).

treatment_protocol: Stock solution of NOC-5 and NOC-7 enough to reach 10 μM was added when the OD(600 nm) of the culture was 0.3. After 15 min, 30 ml samples were taken and total RNA was extracted.  Control cultures had no NOC-s treatment.

source_name: Microaerobic log phase cultured, 10 μM NOC-5 & -7 exposed for 15 min sample


title: oxygen_limited_cjejuni_exposed_15min_to_0.010mM_NOC-5&7 (4)


title: oxygen_limited_cjejuni_exposed_15min_to_0.010mM_NOC-5&7 (3)


title: oxygen_limited_cjejuni_exposed_15min_to_0.010mM_NOC-5&7 (2)


title: N18


title: C26_Tumour

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Illumina BeadStudio

label: Cy5 and Cy3

source_name: Tumour

label_protocol: Illumina

extract_protocol: Qiagen Puregene Core kit

tag: disease status

value: colorectal carcinoma patient

value: colon tissue

value: Tumour


title: N17


title: C26_Normal

source_name: surrounding healthy tissue

value: surrounding healthy colonic mucosa


title: liver_STZ treated diabetic_rep3


title: liver_control_diet_rep6

description: Gene expression data from liver after 14 day feeding of control AIN93G diet

source_name: liver, fed control AIN93G diet for 14 days


title: liver_STZ treated diabetic_rep2


title: N16


title: microaerobic_cjejuni_exposed_15min_to_0.010mM_NOC-5&7

growth_protocol: 3 to 5% of an overnight starter inoculated into 100 ml of Mueller Hinton Broth supplemented with vancomycin (10 µg/ml) in a 250 ml conical flask. Placed in a microaerobic workstation (80% N2, 10%O2, 10% CO2) and shaken at 125 rpm.


title: liver_STZ treated diabetic_rep1


title: liver_control_diet_rep5


title: C25_Tumour


title: WA24

source_name: pooled benign prostate tissue (Clontech)

source_name: metastatic prostate cancer (obtained at rapid [warm] autopsy)

value: metastatic castrate resistant prostate cancer (WA)


title: C24_Tumour


title: C25_Normal


title: N15

source_name: prostate tissue (radical prostatectomy specimen)


title: Gastric Tissue [134]

description: a pair of gastric tissues

value: tubular adenocarcinoma

value: MD

value: Matched Adjacent Noncancerous Tissue


title: WA22


title: C23_Tumour


title: liver_control_diet_rep4

value: male

value: BALB/c


title: N13

source_name: normal human male DNA (Promega)

value: reference


title: N14

value: benign prostate tissue (N)


title: C24_Normal


title: liver_control_diet_rep1

value: liver


title: WA4


title: C22_Normal


title: liver_control_diet_rep2


title: liver_control_diet_rep3


title: WA20


title: C22_Tumour


title: WA13


title: C21_Tumour


title: WA5


title: N12


title: WA16


title: N10