title: blood-LPS-control-2

city: Davis

first: Kevin

last: Dawson

address: 2795 Second Street, Suite 400

department: CCM

institute: UC Davis

description:
LPS-stimulated control.
202-0-L

hyb_protocol: The arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000.

data_processing: Affymetrix .CEL files were imported into the Bioconductor Affy R package and subjected to baseline correction, normalization, and calculation of gene expression values using the Robust Multichip Average (RMA) procedure. Genes were considered for further analyses if they were detected in at least 50% of the microarrays (p<0.05 of the signed rank test). Gene expression values were exported into Cluster for hierarchical clustering (HC) and self organizing map (SOM) procedure and visualized as heat maps in Java TreeView. DHA and LPS-specific changes were determined using paired t test. False discovery rate (FDR) was controlled using Bonferroni. Lists of probe sets that were significantly differentially regulated by DHA or LPS or any combinations thereof were exported into the Database for Annotation, Visualization and Integrated Discovery (DAVID) (http://david.abcc.ncifcrf.gov). Gene Ontology (GO) categories and BioCarta and KEGG pathway maps were evaluated against the lists of probe sets.

source_name: blood, LPS, control

label_protocol: Purified total RNA (5 microg) was used for cDNA synthesis (SuperScript III First Strand Synthesis System; Invitrogen, Carlsbad, CA) followed by in vitro transcription to incorporate biotin labels and subsequent hybridization to Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA), which represents 38,500 well-characterized genes, per manufacturer’s protocol.

extract_protocol: Blood cells from four subjects in the DHA supplementation group were collected for either lipopolysaccharide (LPS) treatment or no treatment (vehicle) and subsequent RNA isolation. For each subject, two 10 mL heparinized venous blood were collected on days 0 and 91. Whole blood was then diluted 1:2 with sterile RPMI 1640 culture medium containing 25mM HEPES and L-glutamine (Gibco Invitrogen, Carlsbad, CA), then split into two 30 mL and incubated with either 10 microg/mL ultra pure LPS (E. coli O157:H7; List Biological Laboratories, Inc., Campbell, CA) or sterile endotoxin-free water alone for 4 h at 37°C, 5% CO2. To simplify RNA isolation, erythrocytes were lysed by a two-step process (Buffer EL; Qiagen, Valencia, CA) and the resulting leukocyte pellets were lysed with Buffer RLT (Qiagen), homogenized with QIAshredder spin columns (Qiagen), and stored at -80°C. Total cellular RNA from leukocytes was isolated using RNeasy Midi Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Forty moderately hyperlipidemic but otherwise healthy men were enrolled into a double-blind, placebo-controlled, parallel study with 2 metabolic periods – baseline (first 8 d) and intervention (last 90 d). Participants were randomized into one of two groups, where one received 7.5 g/day DHA oil capsules containing 3.0 g/day DHA, produced in Crypthecodinium cohinii (Martek Biosciences Corp., Columbia, MD), and no EPA, and the other group received 7.5 g/day extra virgin olive oil capsules. During the baseline period, participants did not receive supplements.

value: blood

tag: disease

value: hypertriglyceridemia

tag: lps

value: LPS

tag: dha


title: pcDNA3 transfection, experiment 1

status: Public on Jan 30 2010

type: RNA

city: Iowa City

first: Christopher

last: Adams

state: IA

address: 540G EMRB, 200 Hawkins Drive

country: USA

institute: University of Iowa

description: RNA from skeletal muscle transfected with empty plasmid vector

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Mouse Exon 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.  Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
RMA normalization
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.d1.1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.  Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Skeletal muscles were transfected in vivo with plasmid DNA, and RNA was harvested from transfected muscles (under nonfasting conditions) 11 days later.

tag: age

value: 8 weeks

tag: sex

value: male

tag: tissue

value: tibialis anterior


title: blood-LPS-control-4

state: CA

description:
LPS-stimulated control.
418-0-L

organism: Homo sapiens

value: control


title: diploid strain_7% ethanol_rep2

city: Tianjin

first: Bing-Zhi

last: Li

address: Weijin Road 92#

country: China

institute: Tianjin University

description: gene expression at exponential phase

hyb_protocol: The biotin-labeled cRNA was hybridized to the GeneChip® Yeast Genome 2.0 Array from Affymetrix (California, US) after dilution and fragmentation according to Affymetrix’s protocol

scan_protocol: Microarrays were scanned with the Genechip Scanner 3000

data_processing: The data were analyzed with GeneChip Operation System (GCOS) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Saccharomyces cerevisiae

source_name: diploid strain, 7% ethanol, exponential stage

label_protocol: Total RNA labeling was conducted according to the Affymetrix GeneChip Expression analysis technical manual (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: strains were incubated in 5-L fermentors with a 3-L working volume. YPD medium (10 g/L yeast extract, 20 g/L peptone, 100 g/L glucose) with different ethanol concentration were used. The initial cell density was OD600 of 0.5.

extract_protocol: Total RNA was isolated according to the hot phenol method

treatment_protocol: Cultures for microarray analysis were collected at mid-exponential phase

tag: strain

value: ethanol tolerant strain, diploid


title: diploid strain_3% ethanol_rep1

description: gene expression at exponential phase

source_name: diploid strain, 3% ethanol, exponential stage


title: diploid strain_3% ethanol_rep2

description: gene expression at exponential phase


title: blood-vehicle-DHA-3

description:
Unstimulated cells, DHA supplementation.
203-91-V

source_name: blood, vehicle, DHA

value: vehicle

value: DHA


title: diploid strain_0% ethanol_rep2

description: gene expression at exponential phase

source_name: diploid strain, 0% ethanol, exponential stage


title: blood-LPS-control-3

description:
LPS-stimulated control.
203-0-L


title: blood-LPS-DHA-2

description:
LPS-stimulated cells, DHA supplementation.
202-91-L

source_name: blood, LPS, DHA


title: blood-LPS-DHA-1

description:
LPS-stimulated cells, DHA supplementation.
101-91-L


title: blood-vehicle-DHA-4

description:
Unstimulated cells, DHA supplementation.
418-91-V


title: blood-LPS-DHA-3

description:
LPS-stimulated cells, DHA supplementation.
203-91-L


title: blood-LPS-control-1

description:
LPS-stimulated control.
101-0-L


title: FAIRE performed in human pancreatic islet cells, sample 1 (ENCODE regions)

status: Public on Jan 31 2010

type: genomic

city: San Diego

first: Kyle

middle: Jeffrie

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

description: Samples were amplified using ligation mediated (LM) PCR.

hyb_protocol: Hybridizations were performed in a MAUI hybridization station for 16 h at 42°C

scan_protocol: Arrays were scanned with an Axon Scanner 4000B

data_processing: log2 ratios of Cy5/Cy3 normalized so that the mean ratio is 0

molecule: genomic DNA

source_name: FAIRE processed DNA from pancreatic islets

label_protocol: Sample labeled by incorporation of cyanine dyes by polymerization with Klenow fragment primed by random nonomers

extract_protocol: DNA extracted using phenol-chloroform

tag: sample type

value: Human pancreatic islet chromatin crosslinked with 1% formaldehyde solution for 10 min and then sheared by sonication.

tag: cell type

value: pancreatic islet

source_name: Input DNA from pancreatic islets

value: Human pancreatic islet DNA sheared by sonication.


title: blood-vehicle-DHA-2

description:
Unstimulated cells, DHA supplementation.
202-91-V


title: diploid strain_0% ethanol_rep1

description: gene expression at exponential phase


title: blood-vehicle-DHA-1

description:
Unstimulated cells, DHA supplementation.
101-91-V


title: blood-vehicle-control-4

description:
Unstimulated control.
418-0-V

source_name: blood, vehicle, control


title: haploid Mat a strain_3% ethanol_rep1

description: gene expression at exponential phase

source_name: haploid Mat a strain, 3% ethanol, exponential stage

value: ethanol tolerant strain, haploid


title: haploid Mat a strain_3% ethanol_rep2

description: gene expression at exponential phase


title: haploid Mat a strain_7% ethanol_rep2

description: gene expression at exponential phase

source_name: haploid Mat a strain, 7% ethanol, exponential stage


title: haploid Mat alpha strain_0% ethanol_rep1

description: gene expression at exponential phase

source_name: haploid Mat alpha strain, 0% ethanol, exponential stage


title: haploid Mat alpha strain_7% ethanol_rep1

description: gene expression at exponential phase

source_name: haploid Mat alpha strain, 7% ethanol, exponential stage


title: FL5-12 miR-19b replicate C

city: New York

first: Andrew

middle: L

last: Wolfe

state: NY

address: 1275 York Ave

department: Cancer Biology and Genetics

institute: Memorial Sloan-Kettering Cancer Center

description: Total RNA from pure populations of FL5-12 cells expressing miR-19b/GFP replicate 3

hyb_protocol: 15ug of labeled cRNA were hybridized on the MOE 430A2.0 arrays

scan_protocol: Scan was performed according to standard protocols and manufacturer (Affymetrix)

data_processing: GCOS1.4 and Partek® Genomic Suite™ 6.4 were used for data analysis. Overall intensity was targetted to 500. Signal intensities were generated using GCOS1.4.

label: Biotin

source_name: FL5-12 cells with miR-19b growing in culture

label_protocol: 1ug total RNA was labeled using the Megascript Ambion kit (cat#AM1334)

growth_protocol: FL5-12 cells were grown in RPMI-1640 media supplemented with 10% FBS, 10% Wehi, and 400 pM Interleukin-3.

extract_protocol: Total RNA was extracted following the manufacturer's standard Trizol protocol.

treatment_protocol: FL5-12 cells were retrovirally infected with either Vector/GFP or miR-19b/GFP. The cells were puromycin selected until virtually all cells expressed the construct, as measured by flow cytometry.

tag: cell line

value: FL5-12 lymphocytic line


title: haploid Mat alpha strain_3% ethanol_rep1

description: gene expression at exponential phase

source_name: haploid Mat alpha strain, 3% ethanol, exponential stage


title: haploid Mat alpha strain_0% ethanol_rep2

description: gene expression at exponential phase


title: haploid Mat alpha strain_3% ethanol_rep2

description: gene expression at exponential phase


title: haploid Mat a strain_7% ethanol_rep1

description: gene expression at exponential phase


title: haploid Mat a strain_0% ethanol_rep1

description: gene expression at exponential phase

source_name: haploid Mat a strain, 0% ethanol, exponential stage


title: haploid Mat a strain_0% ethanol_rep2

description: gene expression at exponential phase


title: blood-vehicle-control-3

description:
Unstimulated control.
203-0-V


title: blood-vehicle-control-2

description:
Unstimulated control.
202-0-V


title: FL5-12 miR-19b replicate A

description: Total RNA from pure populations of FL5-12 cells expressing miR-19b/GFP replicate 1


title: haploid Mat alpha strain_7% ethanol_rep2

description: gene expression at exponential phase


title: FL5-12 vector replicate B

description: Total RNA from pure populations of FL5-12 cells expressing vector/GFP replicate 2

source_name: FL5-12 cells with vector growing in culture


title: FL5-12 vector replicate A

description: Total RNA from pure populations of FL5-12 cells expressing vector/GFP replicate 1


title: nas_17dpi_VT3

status: Public on Jan 29 2010

city: Athens

first: Cecilia

last: McGregor

state: GA

address: Miller Plant Sciences

department: Horticulture

institute: University of Georgia

hyb_protocol: Pronto hybridization kit (Corning Inc., Life Sciences, Corning, NY)

scan_protocol: After hybridization the arrays were scanned with a GenePix Personal 4100A scanner (Molecular Devices, Sunnyvale, CA) and quantified using GenePix Pro 6 (Molecular Devices)

data_processing: The microarray gene expression data were normalized to remove potential dye intensity biases using the locally weighted regression and smoothing scatter plot (LOWESS) procedure.

organism: Ipomoea batatas

source_name: Cultivar Naspot 1, 9 days post infection, Virus Tested control, Replicate 3

label_protocol: 10 μg of total RNA was labeled using the SuperScript Indirect cDNA Labeling System for DNA Microarrays (Invitrogen, Carlsbad, CA). Samples were labeled with Cy3 or Cy5 fluorescent labels (Amersham Biosciences, Piscataway, NJ).

growth_protocol: Plants were grown under standard greenhouse conditions in 17-cm-diameter ITML Elite Azalea pots (ITLM Horticultural Products Inc., Brantford, ON, Canada) containing autoclaved soil mix consisting of 1 part river silt, 1 part sand, 1 part Redi-earth® Plug and Seedling Mix Series (Sun Gro Horticulture Distribution Inc., Bellevue, WA) and 3.5g per pot of Osmocote® 14N-6.1P-11.6K (Scotts-Sierra Horticultural Products Company, Marysville, OH). Aphids and whiteflies were controlled by a weekly insecticide spray program.

extract_protocol: RNeasy Maxi Kit (Qiagen)

treatment_protocol: I. batatas cv. Beauregard plants previously graft inoculated with the russet crack strain of SPFMV (SPFMV-RC, isolate 95-2) and the U.S. strain of SPCSV (isolate BWFT-3) were used as the source of SPVD scions for this experiment. VT sweetpotato cuttings of the cultivars Bx and Nas were graft inoculated 2 weeks after planting with scions affected with SPVD (Bx_SPVD and Nas_SPVD). Control plants were grafted with scions originating from VT plants (Bx_VT and Nas_VT)

tag: disease resistance

value: Resistant

tag: cultivar

value: Naspot 1


title: FL5-12 vector replicate C

description: Total RNA from pure populations of FL5-12 cells expressing vector/GFP replicate 3


title: bx_17dpi_VT4

source_name: Cultivar Beauregard, 17 days post infection, Virus Tested control, Replicate 4

value: Susceptible

value: Beauregard


title: FL5-12 miR-19b replicate B

description: Total RNA from pure populations of FL5-12 cells expressing miR-19b/GFP replicate 2


title: bx_17dpi_VT3

source_name: Cultivar Beauregard, 17 days post infection, Virus Tested control, Replicate 3


title: blood-vehicle-control-1

description:
Unstimulated control.
101-0-V

value: blood

value: hypertriglyceridemia


title: nas_17dpi_SPVD3

source_name: Cultivar Naspot 1, 17 days post infection, SPVD affected, Replicate 3


title: bx_17dpi_SPVD3

source_name: Cultivar Beauregard, 17 days post infection, SPVD affected, Replicate 3


title: bx_9dpi_VT3

source_name: Cultivar Beauregard, 9 days post infection, Virus Tested control, Replicate 3


title: bx_9dpi_SPVD3

source_name: Cultivar Beauregard, 9 days post infection, SPVD affected, Replicate 3


title: bx_9dpi_SPVD4

source_name: Cultivar Beauregard, 9 days post infection, SPVD affected, Replicate 4


title: bx_13dpi_SPVD4

source_name: Cultivar Beauregard, 13 days post infection, SPVD affected, Replicate 4


title: nas_13dpi_VT3

source_name: Cultivar Naspot 1, 13 days post infection, Virus Tested control, Replicate 3


title: bx_9dpi_VT4

source_name: Cultivar Beauregard, 9 days post infection, Virus Tested control, Replicate 4


title: bx_13dpi_SPVD3

source_name: Cultivar Beauregard, 13 days post infection, SPVD affected, Replicate 3


title: nas_13dpi_SPVD4

source_name: Cultivar Naspot 1, 13 days post infection, SPVD affected, Replicate 4


title: nas_17dpi_VT4

source_name: Cultivar Naspot 1, 17 days post infection, Virus Tested control, Replicate 4


title: nas_9dpi_SPVD4

source_name: Cultivar Naspot 1, 9 days post infection, SPVD affected, Replicate 4


title: nas_9dpi_VT4

source_name: Cultivar Naspot 1, 9 days post infection, Virus Tested control, Replicate 4


title: bx_5dpi_SPVD3

source_name: Cultivar Beauregard, 5 days post infection, SPVD affected, Replicate 3


title: nas_9dpi_SPVD3

source_name: Cultivar Naspot 1, 9 days post infection, SPVD affected, Replicate 3


title: bx_13dpi_VT3

source_name: Cultivar Beauregard, 13 days post infection, Virus Tested control, Replicate 3


title: nas_9dpi_VT3

source_name: Cultivar Naspot 1, 9 days post infection, Virus Tested control, Replicate 3


title: bx_13dpi_VT4

source_name: Cultivar Beauregard, 13 days post infection, Virus Tested control, Replicate 4


title: nas_13dpi_SPVD3

source_name: Cultivar Naspot 1, 13 days post infection, SPVD affected, Replicate 3


title: bx_5dpi_VT3

source_name: Cultivar Beauregard, 5 days post infection, Virus Tested control, Replicate 3


title: bx_17dpi_SPVD4

source_name: Cultivar Beauregard, 17 days post infection, SPVD affected, Replicate 4


title: nas_13dpi_VT4

source_name: Cultivar Naspot 1, 13 days post infection, Virus Tested control, Replicate 4


title: bx_5dpi_SPVD4

source_name: Cultivar Beauregard, 5 days post infection, Virus Tested control, Replicate 4


title: nas_5dpi_SPVD4

source_name: Cultivar Naspot 1, 5 days post infection, Virus Tested control, Replicate 4


title: BN_SHR

city: Utrecht

first: Victor

last: Guryev

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: BN represents Brown Norway; SHR represents spontaneously hypertensive

hyb_protocol: Hybridization was done at 37C according to Nimblegen standard aCGH protocol

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

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 SegMNT data extraction.

organism: Rattus norvegicus

source_name: BN rat

label_protocol: Labelling was done using standard Nimblegen protocol for aCGH

extract_protocol: DNA was extracted from 100 milligrams of liver tissue using Qiagen DNAEasy blood and tissue DNA isolation kit

value: BN

source_name: SHR rat

value: SHR


title: nas_5dpi_SPVD3

source_name: Cultivar Naspot 1, 5 days post infection, SPVD affected, Replicate 3


title: nas_5dpi_VT3

source_name: Cultivar Naspot 1, 5 days post infection, Virus Tested control, Replicate 3


title: SHR_BN


title: nas_5dpi_SPVD1

source_name: Cultivar Naspot 1, 5 days post infection, SPVD affected, Replicate 1


title: bx_13dpi_SPVD1

source_name: Cultivar Beauregard, 13 days post infection, SPVD affected, Replicate 1


title: bx_5dpi_SPVD2

source_name: Cultivar Beauregard, 5 days post infection, SPVD affected, Replicate 2


title: nas_5dpi_SPVD2

source_name: Cultivar Naspot 1, 5 days post infection, SPVD affected, Replicate 2


title: nas_13dpi_SPVD2

source_name: Cultivar Naspot 1, 13 days post infection, SPVD affected, Replicate 2


title: bx_13dpi_SPVD2

source_name: Cultivar Beauregard, 13 days post infection, SPVD affected, Replicate 2


title: bx_9dpi_SPVD2

source_name: Cultivar Beauregard, 9 days post infection, SPVD affected, Replicate 2


title: bx_9dpi_SPVD1

source_name: Cultivar Beauregard, 9 days post infection, SPVD affected, Replicate 1


title: nas_5dpi_VT4


title: bx_5dpi_VT4


title: bx_17dpi_SPVD1

source_name: Cultivar Beauregard, 17 days post infection, SPVD affected, Replicate 1


title: Jurkat-complete-rep2

city: Madrid

first: Sergio

last: Callejas

address: Melchor Fernández Almagro, 3

department: Genomics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were dried out using a centrifuge.

scan_protocol: Arrays were scanned at 5 um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays

data_processing: Images provided by the scanner were analyzed using Feature Extraction software version 9.5.3.1 (Agilent Technologies). Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe. Probes were also flagged (Present, Marginal, Absent) using GeneSpring® default settings. Probes that were flagged as Present or Marginal in all three replicates for the two experimental conditions to be compared on each contrast were selected for further analysis.  Filtered data were loaded into SAM (Significance Analysis of Microarrays), a supervised learning software for genomic expression data mining developed at Stanford University Labs and based on the paper by Tusher, Tibshirani and Chu (2001) (PNAS 2001 98: 5116-5121). SAM uses the FDR and q-value method presented in Storey (2002) (J. Roy. Stat. Soc. Ser. B, 64:479-498).  Expression ratios (log2) were calculated using TetOff condition values as baseline. q-value cutoff to consider a fold change as statistically significant was set at 5%.

source_name: Jurkat cell line of T lymphocyte cells stably transfected with TetOff and pTRE2hyg-Tat101 plasmids. These cells show a constitutive intracellular expression of the complete HIV-1 transactivator protein Tat (101aa).

label_protocol: 1 ug of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP

growth_protocol: Jurkat cell lines were cultured in RPMI 1640 medium (Biowhitaker, Walkersville, MD) with 10% fetal calf serum (PAN Biotech GmbH, Aidenbach, Germany), 2 mM L-glutamine, 100 ug/ml streptomycin and 100 U/ml penicillin, at 37ºC. Jurkat TetOff cell line was purchased from BD Biosciences Clontech (Mountain View, CA) and cultured according to manufacturer’s instructions. Jurkat TetOff cells stably transfected with HIV-1 Tat101 or Tat72 proteins were maintained in 200 ug/ml geneticin (Sigma-Aldrich, St. Louis, MO) and 200 ug/ml hygromycin B (BD Biosciences Clontech).

extract_protocol: Total RNA from cells was isolated with RNeasy Maxi kit (Qiagen) following manufacturer’s instructions

value: Jurkat


title: bx_5dpi_SPVD1

source_name: Cultivar Beauregard, 5 days post infection, SPVD affected, Replicate 1


title: nas_13dpi_SPVD1

source_name: Cultivar Naspot 1, 13 days post infection, SPVD affected, Replicate 1


title: Jurkat-complete-rep3


title: Hnf1-CDX2-GATA4rep4

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

description: HIEC expressing Hnf1+CDX2+GATA4: Biological replicate 4

hyb_protocol: Arabidopsis cDNA and hybridization buffer (formamide 50%, SSC 5X, SDS 0.1%) were added, and samples were applied to microarrays enclosed in hybridization chambers overnight at 42°C. After hybridization, slides were washed sequential

scan_protocol: Scanned on an ScanArray Express (Packard Bioscience).

data_processing: Images were quantified using Spotfinder 3 Software (The Institute for Genomic Research: www.tigr.org). Then LOWESS normalized, background subtracted data were obtained from log2 of processed Red signal/processed Green signal. TIGR package software was used.

source_name: HIEC pTetON + DOX

label_protocol:
aRNA amplified using TargetAmp 1-round aRNA amplification kit 103 following manufacturer's instructions (Epicentre Biotechnologies, Madison, WI)
1 µg of aRNA was primed with 3 µl of 2 µg/µL hexamer random primers at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 500 µM each dATP, dCTP, dGTP, 200µM dTTP and 300µM aa-dUTP.

extract_protocol: Total RNA from reference pool was isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp 1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

tag: HIEC stably infected with pTetON plasmid (Clontech)

extract_protocol: Total RNA from HIEC pTetON stably infected with pRevTRE-Hnf1 and pRevTRE-CDX2 treated with DOX and transfected with pLenti-GATA4 five days later was isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

treatment_protocol: treated with doxycycline for 5 days, then transfected with pLenti-GATA4 and treated up to 30 days

tag: HIEC pTetON stably infected with pRevTRE-Hnf1 and pRevTRE-CDX2 and transfected with pLenti-GATA4


title: nas_9dpi_SPVD1

source_name: Cultivar Naspot 1, 9 days post infection, SPVD affected, Replicate 1


title: nas_17dpi_SPVD2

source_name: Cultivar Naspot 1, 17 days post infection, SPVD affected, Replicate 2


title: bx_17dpi_SPVD2

source_name: Cultivar Beauregard, 17 days post infection, SPVD affected, Replicate 2


title: Hnf1-CDX2-GATA4rep3

description: HIEC expressing Hnf1+CDX2+GATA4: Biological replicate 3


title: Jurkat-Exon1-rep2

source_name: Jurkat cell line of T lymphocyte cells stably transfected with TetOff and pTRE2hyg-Tat72 plasmids. These cells show a constitutive intracellular expression of the first exon of HIV-1 transactivator protein Tat (72aa).


title: Jurkat-TetOff-rep3

source_name: Jurkat cell line of T lymphocyte cells stably transfected with TetOff and pTRE2hyg plasmids

tag: treatment

value: TetOff-pTRE2hyg cells (basal control)


title: Jurkat-Exon1-rep3


title: Jurkat-TetOff-rep2

value: transfected with TetOff-pTRE2hyg cells (basal control)


title: nas_9dpi_SPVD2

source_name: Cultivar Naspot 1, 9 days post infection, SPVD affected, Replicate 2


title: Hnf1-CDX2-GATA4rep1

description: HIEC expressing Hnf1+CDX2+GATA4: Biological replicate 1


title: Hnf1-CDX2rep3

description: HIEC expressing Hnf1 and CDX2:  Biological replicate 3

extract_protocol: Total RNA from HIEC pTetON stably infected with pRevTRE-Hnf1 and pRevTRE-CDX2 treated with DOX was isolated by phenol/chloroform extraction (Trizol, Invitrogen), then amplified with TargetAmp1-round aRNA amplification kit (Epicentre Biotechnologies, Madison, WI)

treatment_protocol: treated with doxycycline for 30 days


title: Hnf1-CDX2rep2

description: HIEC expressing Hnf1 and CDX2:  Biological replicate 2

tag: HIEC pTetON stably infected with pRevTRE-Hnf1 and pRevTRE-CDX2


title: nas_17dpi_SPVD1

source_name: Cultivar Naspot 1, 17 days post infection, SPVD affected, Replicate 1


title: Hnf1-CDX2rep4

description: HIEC expressing Hnf1 and CDX2:  Biological replicate 4


title: Hnf1-CDX2rep1

description: HIEC expressing Hnf1 and CDX2:  Biological replicate 1


title: nas_17dpi_VT1

source_name: Cultivar Naspot 1, 17 days post infection, Virus Tested control, Replicate 1


title: Hnf1-CDX2-GATA4rep2

description: HIEC expressing Hnf1+CDX2+GATA4: Biological replicate 2


title: Jurkat-Exon1-rep1


title: nas_17dpi_VT2

source_name: Cultivar Naspot 1, 17 days post infection, Virus Tested control, Replicate 2


title: MALKO macrophages, LPS vs. Mock control, mouse 8, dye swap

city: Dublin

first: Stephen

middle: Francis

last: Madden

address: Glasnevin

department: National Institute for Cellular Biotechnology

country: Ireland

institute: Dublin City University

description: Biological replicate 4 of 4. MALKO mouse macrophages treated with LPS vs. no treatment.

hyb_protocol: Labelled samples were hybridized overnight using an automated hybridization station (Genomic Solutions; Perkin-Elmer, Boston MA).

scan_protocol: Fluorescent images from the arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments). Images were quantified with the GenePix Pro 3.0 software.

data_processing: The raw gene expression data were read, background corrected with the “normexp” option and quantile normalised using the Bioconductor package limma.

source_name: Macrophages from MALKO mouse 8 treated with 10 ng/mL LPS for 2 hours

label_protocol: 8µg of RNA from both test and reference samples was reverse transcribed and differentially labelled with Cy3 and Cy5 dyes (Amersham) using the Atlas Powerscript fluorescent labeling kit (BD Biosciences).

growth_protocol: Mice were anaesthetized with CO2 inhalation and then killed by cervical dislocation. Bone marrow was isolated from 6- to 8-week-old C57BL/6 MAL-deficient mice. Macrophages from these marrows were cultured in DMEM media supplemented with 10% FBS and 15% L929 conditioned media (a source for colony-stimulating factor CSF-1) for 10 days.

extract_protocol: Total RNA for microarray analysis was isolated using an RNeasy extraction kit (Qiagen, Valencia, CA) according to the manufacturer’s recommendations.

treatment_protocol: Bone marrow-derived macrophage cells were treated at day 10 ex vivo for 2 hours with 10 ng/ml lipopolysaccharide and their gene expression profiles were compared with that of mock-treated cells incubated for the same time.

tag: genotype

value: MAL knockout

value: 6-8 weeks

value: bone marrow

value: macrophage

value: lipopolysaccharide (LPS)

tag: treatment time

value: 2 hours

source_name: Macrophages from MALKO mouse 8 treated with media only for 2 hours

treatment_protocol: Bone marrow-derived macrophage cells for the mock control were untreated.

value: mock


title: MALKO macrophages, LPS vs. Mock control, mouse 7, dye swap

description: Biological replicate 3 of 4. MALKO mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from MALKO mouse 7 treated with 10 ng/mL LPS for 2 hours

source_name: Macrophages from MALKO mouse 7 treated with media only for 2 hours


title: nas_9dpi_VT1

source_name: Cultivar Naspot 1, 9 days post infection, Virus Tested control, Replicate 1

value: Resistant

value: Naspot 1


title: nas_13dpi_VT1

source_name: Cultivar Naspot 1, 13 days post infection, Virus Tested control, Replicate 1


title: nas_13dpi_VT2

source_name: Cultivar Naspot 1, 13 days post infection, Virus Tested control, Replicate 2


title: nas_9dpi_VT2

source_name: Cultivar Naspot 1, 9 days post infection, Virus Tested control, Replicate 2


title: bx_17dpi_VT2

source_name: Cultivar Beauregard, 17 days post infection, Virus Tested control, Replicate 2

value: Susceptible

value: Beauregard


title: nas_17dpi_SPVD4

source_name: Cultivar Naspot 1, 17 days post infection, SPVD affected, Replicate 4


title: bx_5dpi_VT1

source_name: Cultivar Beauregard, 5 days post infection, Virus Tested control, Replicate 1


title: Jurkat-complete-rep1

source_name: Jurkat cell line of T lymphocyte cells stably transfected with TetOff and pTRE2hyg-Tat101 plasmids. These cells show a constitutive intracellular expression of the complete HIV-1 transactivator protein Tat (101aa).


title: nas_5dpi_VT1

source_name: Cultivar Naspot 1, 5 days post infection, Virus Tested control, Replicate 1


title: Jurkat-TetOff-rep1

source_name: Jurkat cell line of T lymphocyte cells stably transfected with TetOff and pTRE2hyg plasmids


title: MALKO macrophages, LPS vs. Mock control, mouse 6

description: Biological replicate 2 of 4. MALKO mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from MALKO mouse 6 treated with media only for 2 hours

source_name: Macrophages from MALKO mouse 6 treated with 10 ng/mL LPS for 2 hours


title: nas_5dpi_VT2

source_name: Cultivar Naspot 1, 5 days post infection, Virus Tested control, Replicate 2


title: carcinoma-associated fibroblast_case8

city: Madison

first: Andreas

last: Friedl

state: WI

address: 1111 Highland Avenue

department: Pathology

institute: University of Wisconsin

hyb_protocol: After fragmentation, 10 µg of cRNA were hybridized at 45 °C for 16 h to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays containing probes to >47 000 transcripts.  After inhibition of endogenous peroxidase and blocking, the slides were incubated with primary antibody for 60 min. The following primary antibodies were used: Goat anti-WISP1/CCN4 (1:50; R&D Systems, Minneapolis, MN, USA), mouse anti-TGF?2 (1:500; Abcam) and goat anti-KLF4 (1:100; R&D Systems). This was followed by incubation with an appropriate horseradish peroxidase-based detection reagent (Biocare, Concord, CA, USA) and DAB+ chromogenic substrate (Dako). The slides were counterstained with hematoxylin and coverslipped.

data_processing: The data were analyzed with R language and environment using Affymetrix default analysis settings and RMA as normalization method.  The expression levels were compared using empirical Bayes methods and a lognormal-normal model.

source_name: Fibroblast isolated from breast carcinoma

label_protocol: Ambion MessageAmp II-Biotin Enhanced kit

growth_protocol: CAF and NF were routinely maintained in DMEM and 10% fetal bovine serum at 37 °C in a humidified atmosphere containing 5% CO2. RNA was extracted from confluent cultures as soon as epithelial cells had disappeared. This criterion was met typically after one to three passages. The purity of the fibroblasts was assessed in parallel cultures by immunolabeling for the epithelial cell marker pan-cytokeratin (mouse monoclonal antibody, dilution 1:100; Lab Vision, Fremont, CA, USA) and the endothelial cell marker von Willebrand factor (rabbit polyclonal antibody, dilution 1:1000; Dako, Carpinteria, CA, USA) and the mesenchymal marker vimentin (mouse monoclonal antibody, dilution 1:100; Lab Vision). For further characterization, the fibroblast cultures were labeled with antibodies to ?-SMA (mouse monoclonal antibody ?SMA, dilution 1:100, Sigma) and fibroblast-specific protein FSP1/S100A4 (rabbit polyclonal, dilution 1:50, Abcam, Cambridge, MA, USA).

extract_protocol: Total RNA from CAF and NF was isolated using the RNeasy Micro kit according to the manufacturer's instructions (Qiagen, Alameda, CA, USA).

value: breast carcinoma

value: carcinoma-associated fibroblast


title: carcinoma-associated fibroblast_case6


title: bx_17dpi_VT1

source_name: Cultivar Beauregard, 17 days post infection, Virus Tested control, Replicate 1


title: carcinoma-associated fibroblast_case2


title: bx_13dpi_VT1

source_name: Cultivar Beauregard, 13 days post infection, Virus Tested control, Replicate 1


title: B.proteoclasticus_M.ruminantium_Coculture_vs_Pooled Monocultures

status: Public on Jan 28 2010

city: Urbana

first: Carl

middle: James

last: Yeoman

state: IL

address: 1207 W Gregory ave

department: Institute for Genomic Biology

institute: University of Illinois

description: Each slide was scanned at a high, medium and low PMT gain settings (High PMT settings were deemed most useful and were subsequently used).

hyb_protocol: Microarray slides were transferred to pre-warmed (50º C) microarray prehybridisation buffer and incubated at 50 °C for 30 min. The microarray slides were then rinsed in two 50 ml volumes of 0.22 μm filter-sterilised MilliQ water. The slides were subsequently washed with 50 ml of isopropanol and air dried. Once dry, the slides were transferred into hybridisation chambers (Corning, Lowell, MA, USA) and lifter cover slips (Erie Scientific, Portsmouth, NH, USA) were carefully laid over the probe areas. Samples to be compared (e.g. Cy3 Co-culture versus combined Cy5 individual mono-cultures) were combined in 0.2 ml PCR tubes. The combined sample was denatured by incubation at 95 °C for 10 min and mixed with 60 μl of pre-warmed (68° C) Slide Hyb buffer #1 (Ambion, Austin, TX, USA). The mixture was loaded onto the pre-hybridised slide at the edge of the cover slip and allowed to diffuse beneath it. Sterile MilliQ water (30 μl) was added to the wells at each end of the hybridisation chambers to ensure the chambers did not dry out during hybridisation. The hybridisation chambers were then sealed and incubated in a water bath at 50 °C for 24 h. Following hybridisation, the cover slip was carefully removed and microarray slides were transferred sequentially to each of 3 pre-warmed (50º C) microarray wash solutions. The microarray slides were incubated for 7 min in each Wash solution with extremely vigorous shaking. Following the third wash the slide was transferred to a fresh 50 ml Falcon tube containing a small amount of lint-free paper towel at the bottom and centrifuged for 4 min at 1,500 x g at 20º C. The slide was transferred to a fresh 50 ml Falcon tube and dried by incubation in a 37 °C vacuum oven (Contherm) with the lid removed for 20 min and stored in the dark until scanned.

scan_protocol: Microarray slides were scanned using a GenePix® Professional 4200 scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). The excitation wavelengths and emission filters were selected for optimal analysis of Cy3 and Cy5 dyes (excitation at 532 and 635 nm and emission detection between 655 to 695 nm and 550 to 600 nm, respectively). An image of the entire microarray slide was acquired using a low-resolution (40 μm/pixel) preview scan. The arrayed DNA portion of the slide was identified and an area encompassing these features was selected for scanning at high resolution (5 μm/pixel). The Photo Multiplier Tube (PMT) gains of each channel were adjusted between test scans, to balance the Cy5 and Cy3 signals, until a red to green ratio of 0.95 to 1.05 was achieved to ensure sufficient signal was obtained from each fluorophore. The software was set to scan each line twice, extracting the average value to maximise the signal to noise ratio (Axon Instruments, 2004). The gene names associated with each spot on the microarray were uploaded and traced via a grid with parameters set to overlay the features of the scanned microarray (grid settings Appendix III, Table A6). Features were aligned to the grid automatically using the automatic GenePix Pro 6.0 software function and then refined manually. Some features on the array were not uniformly printed, therefore the „find irregular features‟ option was selected. Each feature was checked and any poor regions were flagged for exclusion before signal data were extracted using the option „analyse‟ resulting in a GenePix results (GPR) file.

data_processing: The data were analysed using the limma package in Bioconductor (Smyth, 2005). Bioconductor was operated through the R platform, using the R editor Tinn-R. The signal to noise ratio was analysed by comparing the foreground and background intensities by calculating the intensity of each feature and that of the region around that feature (outside of a 2 pixel circular exclusion zone). To determine if there was any hybridisation spatial bias, the foreground and background densities were plotted individually for each of the 16 slide scans to get an overall impression of the data. To ensure there was no bias to either fluorophore‟s detection through the increasing signal intensities an MA plot was produced. Density plots were produced to show the proportion of features at each intensity and the signal distribution across a microarray slide. Boxplots were produced to give an overview of the range of values observed for each of the spot types (B. proteoclasticus, M. ruminantium, controls. The blank spots and those flagged as being of poor quality were removed from subsequent analysis. Normalisation was performed within each microarray using the „print-tip loess‟ method to remove any spatial trends within the slide. As some spatial variation was observed in the backgrounds which is not reflected in the foregrounds it was determined that background subtraction would unfairly bias the results therefore this was not performed. To determine the efficacy of normalisation, density plots were repeated following normalisation and compared to the raw data and boxplots were produced of the intensity distribution of each feature by category. Statistical data analyses were carried out using the limma package of the Bioconductor software. Data were log2 transformed prior to analysis and the mean difference was calculated using this scale, resulting in a log ratio for each feature. The log ratios for each probes replicates (biological and technical) were averaged prior to further analysis. Each feature was then adjusted for the technical slide replication by determining the average correlation between technical replicates using the „duplicateCorrelation‟ function, and accounting for this when fitting the linear model. Empirical Bayes moderated t-statistics (Robbins, 1956, Smyth, 2004) were then calculated for each gene. The moderated t-statistics were adjusted to give an FDR (False Discovery Rate; (Benjamini & Yekutieli, 2005) value.

label: Cy3 (Samples with suffix A) Cy5 (Samples with suffix B)

organism:
Butyrivibrio proteoclasticus B316
Methanobrevibacter ruminantium M1

source_name: Monocultures

label_protocol: Dimethyl sulphoxide (DMSO, 45 μl) was mixed with both Cy3 and Cy5 dye vials (GE Healthcare, Uppsala, Sweden) using a Labinco L46 vortex. Each cDNA sample was divided into equal volumes and 5 μl of the appropriate Dye-DMSO solution was added to each cDNA sample (one volume with Cy3, one volume with Cy5) and incubated in the dark for 2 h, after which the labeled cDNA was purified using a SNAP column (invitrogen) and resuspended in DEPC-treated MilliQ water.

growth_protocol: 100 ml cultures were grown independent from one another at 39 deg c on a shaker set to 100 rpm in BY+ media. M. ruminantium m1 cultures were supplemented with 25 psi of 80% hydrogen: 20% CO2 gas. When M. ruminantium cultures reached mid-maximum density they were flushed with O2-free CO2 gas until hydrogen was not detectible by gas chromatography and then supplemented with Oat spelts xylan (final concentration 0.2%). Monocultured M. ruminantium M1 cultures were then re-supplemented with 25 psi of 80% hydrogen:20% CO2 gas to replace biologically derived hydrogen from B. proteoclasticus B316, while cocultures were inoculated with 0.5 ml of a late exponential phase B. proteoclasticus. At the same time a further three 100 ml volumes of pre-warmed (39ºC) BY+ medium supplemented with 0.2% Xylan solution were also inoculated with 0.5 ml of the same late exponential phase B. proteoclasticus culture. Cultures were grown to mid-exponential phase and RNA was extracted.

extract_protocol: Cultures were pooled into pre-chilled (-20º C) 250 ml centrifuge tubes and pelleted at 10,000 x g for 5 min at 4º C. The supernatant was discarded and the resulting cell pellet was resuspended in 10 ml of BY+ medium and 20 ml of RNAprotect reagent (Qiagen). The culture was transferred to a 50 ml Oakridge tube and incubated for 5 min at room temperature. The cells were again pelleted then dried and frozen using liquid nitrogen. The frozen pellet was ground with a sterile pre-chilled (-20º C) mortar and pestle under liquid nitrogen. The ground sample was then resuspended in an excess of TRIzol reagent and subsequently transferred in 1 ml aliquots to Eppendorf tubes and incubated at 20º C in a waterbath for 5 min to permit complete dissociation of nucleoprotein complexes. Chloroform (200 μl) was added to each tube and mixed vigorously and incubated at 20º C in a waterbath for 3 min. The sample was centrifuged at 4 ºC to separate the TRIzol-Chloroform and protein phases from the aqueous phase containing the RNA. The aqueous phase was transferred to a sterile Oakridge tube and mixed with 0.5 volumes isopropanol. This mixture was incubated at -20º C for 30 min to precipitate the RNA, which was subsequently pelleted by centrifugation. The RNA pellet was washed in 75% ethanol before the ethanol was removed and the pellet was allowed to air dry on ice. RNA pellets were resuspended in DEPC-treated milliQ water. Extracted RNA was purified using an RNeasy Midi kit (Qiagen, Hilden, Germany) and integrity was analysed by RNA 6000 Nano assay (Agilent Technologies, Santa Clara, CA, USA) and the RNA concentration was quantified by spectrophotometry using a nanodrop.

tag: cultures

value: Pooled Monocultures

label: Cy5 (Samples with suffix A) Cy3 (Samples with suffix B)

source_name: Cocultures

treatment_protocol: The relative quantities of RNA contributed by each organism to the co-culture samples were then determined by qPCR using primers designed, to the B. proteoclasticus butyryl-CoA dehydrogenase (bcd) gene and the M. ruminantium gene encoding N5,N10-methenyl-H4MPT cyclohydrolase (mch) (both genes are constitutively expressed). The mono-culture RNAs were then combined appropriately


title: carcinoma-associated fibroblast_case7


title: bx_9dpi_VT2

source_name: Cultivar Beauregard, 9 days post infection, Virus Tested control, Replicate 2


title: carcinoma-associated fibroblast_case1


title: bx_9dpi_VT1

data_processing:
The microarray gene expression data were normalized to remove potential dye intensity biases using the locally weighted regression and smoothing scatter plot (LOWESS) procedure.The data was further normalized
within the two-step mixed model proposed by Wolfinger at al. (2001)

source_name: Cultivar Beauregard, 9 days post infection, Virus Tested control, Replicate 1


title: prostate, 300 ng/kg TCDD, 3

city: Kagoshima

first: Akihiro

last: Arima

address: 2438 Miyanoura

country: Japan

institute: Shin Nippon Biomedical Laboratories, Ltd.

description: Gene expression in the prostate of Macaca mulatta (rhesus monkey) offspring necropsied 7 years after in utero and lactational exposure to TCDD.

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides .

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v1_95) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The normalization algorithm (GeneSpring GX 7.3.1 software) we used is as follows:
1. Data Transformation: Set measurements less than 0.01 to 0.01
2. Per Chip: Normalize to 50 percentile
3. Per Gene Normalization: Normalize to Specific Samples

organism: Macaca mulatta

source_name: prostate, 300 ng/kg TCDD, No. 66

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

extract_protocol: Total RNA was isolated from homogenized frozen prostate tissue using theTrizol (Invitrogen, Carlsbad, USA) and RNeasy columns (QIAGEN, Valencia, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Dam received 0 (vehicle), 30 or 300 ng/kg TCDD subcutaneously on Day 20 of gestation, and then 5 % of the initial dose was injected evry 30 days during the gestation and lactation periods until Day 90 after delivery, to maintain the desired body burden in accordance with the biological half-life of TCDD in rhesus monkeys.

value: prostate glands

tag: agent

value: TCDD

tag: initial tcdd dose

value: 300 ng/kg


title: Wildtype macrophages, LPS vs. Mock control, mouse 1

description: Biological replicate 1 of 4. Wildtype mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from wildtype mouse 1 treated with media only for 2 hours

growth_protocol: Mice were anaesthetized with CO2 inhalation and then killed by cervical dislocation. Bone marrow was isolated from 6- to 8-week-old C57BL/6 wild type mice. Macrophages from these marrows were cultured in DMEM media supplemented with 10% FBS and 15% L929 conditioned media (a source for colony-stimulating factor CSF-1) for 10 days.

value: WT

tag: age

source_name: Macrophages from wildtype mouse 1 treated with 10 ng/mL LPS for 2 hours


title: carcinoma-associated fibroblast_case5

tag: tissue


title: MALKO macrophages, LPS vs. Mock control, mouse 5

description: Biological replicate 1 of 4. MALKO mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from MALKO mouse 5 treated with media only for 2 hours

tag: strain

value: MAL knockout

value: 6-8 weeks

source_name: Macrophages from MALKO mouse 5 treated with 10 ng/mL LPS for 2 hours


title: Wildtype macrophages, LPS vs. Mock control, mouse 3, dye swap

description: Biological replicate 3 of 4. Wildtype mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from wildtype mouse 3 treated with 10 ng/mL LPS for 2 hours

value: bone marrow

value: macrophage

source_name: Macrophages from wildtype mouse 3 treated with media only for 2 hours


title: bx_5dpi_VT2

data_processing: The microarray gene expression data were normalized to remove potential dye intensity biases using the locally weighted regression and smoothing scatter plot (LOWESS) procedure. The data was further normalized within the two-step mixed model proposed by Wolfinger at al. (2001).

source_name: Cultivar Beauregard, 5 days post infection, Virus Tested control, Replicate 2


title: Wildtype macrophages, LPS vs. Mock control, mouse 4, dye swap

description: Biological replicate 4 of 4. Wildtype mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from wildtype mouse 4 treated with 10 ng/mL LPS for 2 hours

value: lipopolysaccharide (LPS)

value: 2 hours

source_name: Macrophages from wildtype mouse 4 treated with media only for 2 hours


title: prostate, 300 ng/kg TCDD, 1

source_name: prostate, 300 ng/kg TCDD, No. 33


title: prostate, 30 ng/kg TCDD, 1

source_name: prostate, 30 ng/kg TCDD, No. 19

value: 30 ng/kg


title: prostate, 300 ng/kg TCDD, 2

source_name: prostate, 300 ng/kg TCDD, No. 39


title: prostate, 0 ng/kg TCDD, 3

source_name: prostate, 0 ng/kg TCDD, No. 64

value: vehicle

value: 0 ng/kg


title: prostate, 30 ng/kg TCDD, 3

source_name: prostate, 30 ng/kg TCDD, No. 53


title: Wildtype macrophages, LPS vs. Mock control, mouse 2

description: Biological replicate 2 of 4. Wildtype mouse macrophages treated with LPS vs. no treatment.

source_name: Macrophages from wildtype mouse 2 treated with media only for 2 hours

value: mock

source_name: Macrophages from wildtype mouse 2 treated with 10 ng/mL LPS for 2 hours


title: Flag Chromatin IP in Cyclin D1 Flag-HA tagged E.14.5 embryos versus Flag Chromatin IP in wildtype E.14.5 embryos, 2

city: Boston

first: Frederic

middle: Emile

last: Bienvenu

state: MA

address: 1 Jimmy Fund Way

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Cyclin D1 was immunoprecipitated using anti-FLAG antibody (M2 Sigma) from 1/5 of 10 pooled E14.5 knock-in (or for control wild-type) embryos and hybridized onto tiled Agilent arrays.

hyb_protocol: Regular Whitehead Institute Hybrydization protocol. Labeled and purified DNA was combined (4–5 ug each of immunoenriched or whole cell extract DNA) and hybridized to arrays in Agilent hybridization chambers for 40 hours at 40°C. Arrays were then washed and scanned.

scan_protocol: Slides were scanned using an Agilent DNA microarray scanner with 5 micron scan resolution.

data_processing: Data was extracted and normalized using Agilent’s Feature Extraction version 9.1., using settings CGH-v4_91.  Pvalues and generation of bound gene lists was performed using Agilent’s ChIP Analytics software with the MIT algorithm and a gap size of 500bp allowed between neighbor probes.

source_name: Flag Ip from E.14.5 cyclin D1 Flag-HA tagged embryos

label_protocol:
invitrogen bioprime labeling kit #18094-011
Standard labelling.

growth_protocol: Normal embryo development in state-of-the-art mouse facility.

extract_protocol: Flag antibody Immunoprecipitation followed by standard washing procedure and RNase A, proteinase K treatment.

treatment_protocol:
3% Paraformaldehyde fixation for 10 minutes at 37 degrees Celsius.
Whole embryos cells were homogenized during crosslinking step.
Further 1x PBS washes 2 times on ice.
Lysis and sonication unsing standard protocol.

tag: C57BL/6 129SV Mixed genetic background

source_name: Flag Ip from E.14.5 wildtype embryos


title: prostate, 30 ng/kg TCDD, 2

source_name: prostate, 30 ng/kg TCDD, No. 25


title: prostate, 0 ng/kg TCDD, 1

source_name: prostate, 0 ng/kg TCDD, No. 4


title: BM5 Replicate1

city: Ferrara

first: Matteo

last: Bovolenta

address: 74, Fossato di Mortara

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol v5.0

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1). Scanned on an Agilent G2565AA scanner.

data_processing: Agilent's DNA Analytics 4.0.76 software (default settings)

source_name: DNA from blood

extract_protocol: Nucleon™ BACC Genomic DNA Extraction Kit (GE Healthcare)

tag: gender

value: Male

tag: phenotype (disease state)

value: Bethlem Myopathy

tag: mutation

value: none identified by sequencing

source_name: Promega Male reference DNA

tag: sample type

value: reference


title: bx_13dpi_VT2

source_name: Cultivar Beauregard, 13 days post infection, Virus Tested control, Replicate 2

tag: disease resistance

value: Susceptible

tag: cultivar

value: Beauregard


title: Control Replicate1

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol v5.0

value: Wild Type


title: BM5 Replicate2


title: Control Replicate2


title: prostate, 0 ng/kg TCDD, 2

source_name: prostate, 0 ng/kg TCDD, No. 13

value: prostate glands


title: BM1 Replicate1

value: Female

value: Recessive Bethlem Myopathy

source_name: Promega Female reference DNA


title: BM1 Replicate2


title: BM4 Replicate2


title: BM4 Replicate1


title: H32B s1.s2.e2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: E2, SAFB1 SiRNA, SAFB2 SiRNA in MCF-7

hyb_protocol: Labeled RNAs were hybridized and washed according to manufacturer's recommendations (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data was analyzed using the dChip software (www.dchip.org) for gene expression estimation (with PM _Perfect Match only) model.

source_name: MCF-7 breast cancer cells

label_protocol: Five micrograms of total RNA from each sample were labeled using the bioarray high-yield transcript kit according to manufacturer's conditions (ENZO, Farmingdale, NY).

growth_protocol: MCF-7 was grown in FBS (Invitrogen, Carlsbad, CA) supplemented with 5% fetal bovine serum and 1% penicillin and streptomycin in a 5% CO2 atmosphere at 37C. Before treatments or transfections, the cells were maintained in phenol red-free minimal essential medium containing 5% charcoal-stripped calf serum for a minimum of 2 days.

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

treatment_protocol: Cells were transfected with either control siRNA (NS) (Dharmacon, siGenome non targeting siRNA #2, catalog no. D-00121002-20), SAFB1 (siGENOME SMARTpool, catalog no. L-005150-00) and/or SAFB2 (siGENOME SMARTpool, catalog no. L-020373-01) siRNA, using LipofectAMINE 2000 (Invitrogen).

tag: cell line

value: MCF-7 cells

tag: treatment

value: SAFB1 and SAFB2 siRNA

value: E2 treated


title: H24As1.s2.e2

description: E2, SAFB1 SiRNA, SAFB2 SiRNA in MCF-7


title: H8Ds1.s2.e2

description: E2, SAFB1 SiRNA, SAFB2 SiRNA in MCF-7


title: Flag Chromatin IP in Cyclin D1 Flag-HA tagged E.14.5 embryos versus Flag Chromatin IP in wildtype E.14.5 embryos, 1


title: H31B s1.s2

description: SAFB1 SiRNA, SAFB2 SiRNA in MCF-7

value: untreated


title: H23As1.s2

description: SAFB1 SiRNA, SAFB2 SiRNA in MCF-7


title: H15Ds1.s2

description: SAFB1 SiRNA, SAFB2 SiRNA in MCF-7


title: H3Cs1

description: SAFB1 SiRNA in MCF-7

value: SAFB1 siRNA


title: H11Ds1

description: SAFB1 SiRNA in MCF-7


title: H27B s1

description: SAFB1 SiRNA in MCF-7


title: H7Cs1.s2

description: SAFB1 SiRNA, SAFB2 SiRNA in MCF-7


title: H22As2.e2

description: E2, SAFB2 SiRNA in MCF-7

value: SAFB2 siRNA


title: H14Cs2.e2

description: E2, SAFB2 SiRNA in MCF-7


title: H5Cs2

description: SAFB2 SiRNA in MCF-7


title: H30B s2.e2

description: E2, SAFB2 SiRNA in MCF-7


title: H6Ds2.e2

description: E2, SAFB2 SiRNA in MCF-7


title: H13Ds2

description: SAFB2 SiRNA in MCF-7


title: H12Cs1.e2

description: E2, SAFB1 SiRNA in MCF-7


title: H26B ns.e2

description: E2, control SiRNA in MCF-7

value: control siRNA


title: H28B s1.e2

description: E2, SAFB1 SiRNA in MCF-7


title: H21As2

description: SAFB2 SiRNA in MCF-7


title: H29B s2

description: SAFB2 SiRNA in MCF-7


title: H16Cs1.s2.e2

description: E2, SAFB1 SiRNA, SAFB2 SiRNA in MCF-7


title: H4Ds1.e2

description: E2, SAFB1 SiRNA in MCF-7


title: H1Cns

description: control SiRNA in MCF-7


title: H2Dns.e2

description: E2, control SiRNA in MCF-7


title: H17Ans

description: control SiRNA in MCF-7


title: H18Ans.e2

description: E2, control SiRNA in MCF-7


title: H25B ns

description: control SiRNA in MCF-7


title: negative control inhibitor_17-6

description: negative control inhibitor (mir-182 knockdown control), biological rep2

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: The image data were compiled into a project using  Beadstudio software gene expression module version 3.2.7.  No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.

source_name: ES2 ovarian cancer cell line

label_protocol: According to Illumina protocol.

growth_protocol: ES-2 cells were cultured in DMEM/F12 (Invitrogen), with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

extract_protocol: Cells were harvested 48 hours after transfection. Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). ES-2 cells were transfected in 6-well plates (2.5 x 105 cells/well) using 10 μl X-tremeGENE siRNA Transfection Reagent (Roche) and 2 μg hsa-mir-182 hairpin inhibitor (50 nM final concentration) (Dharmacon). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).

tag: protocol

value: control


title: negative control inhibitor_17-5

description: negative control inhibitor (mir-182 knockdown control), biological rep1


title: hsa-mir-182 inhibitor_17-2

description: hsa-mir-182 inhibitor (mir-182 knockdown in ES2), biological rep2

value: hsa-mir-182 depletion


title: negative control mimic (NTC2)_21-8

description: negative control mimic (mir-100 knockup control), biological rep3

source_name: OVSAYO ovarian cancer cell line

growth_protocol: OVSAYO cells were cultured in RPMI 1640 (Invitrogen), with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

treatment_protocol: Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). OVSAYO cells were transfected in 6-well plates (3.0 x 105 cells/well) using 3 μl Invitrogen Lipofectamine 2000 and 3 μg total hairpin inhibitor (66 nM). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).


title: hsa-mir-182 inhibitor_17-1

description: hsa-mir-182 inhibitor (mir-182 knockdown in ES2), biological rep1


title: OVSAYO clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, OVSAYO

source_name: OVSAYO clear cell culture, confluent

growth_protocol: Primary cultures of normal ovarian surface epithelium (NOSE) were performed as previously described. Briefly, brushings of the ovarian surface were performed in pre- and postmenopausal women undergoing clinically indicated surgery. NOSE cells were cultured in 1:1 MCDB105/M199 (Sigma). The epithelial origin of cultured cells was confirmed using immunohistochemistry to examine the expression of vimentin and cytokeratins, and only cultures containing >90% epithelial cells were used.  ES-2 cells were cultured in DMEM/F12 (Invitrogen). TOV-21G cells were cultured in 1:1 MCDB105/M199 (Sigma). RMG-I cells were cultured in Ham’s F-12 (Invitrogen). OVMANA, OVISE, OVAS, OVTOKO, OVSAYO, KK, and SMOV-2d cells were cultured in RPMI 1640 (Invitrogen). NOSE and cancer cell lines were cultured with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).

extract_protocol: Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).


title: negative control mimic (NTC2)_21-6

description: negative control mimic (mir-100 knockup control), biological rep2


title: hsa-mir-100 mimic_21-4

description: hsa-mir-100 mimic (mir-100 knockup in OVSAYO), biological rep3

value: hsa-mir-100 overexpression


title: negative control inhibitor_17-8

description: negative control inhibitor (mir-182 knockdown control), biological rep3


title: hsa-mir-182 inhibitor_17-3

description: hsa-mir-182 inhibitor (mir-182 knockdown in ES2), biological rep3


title: negative control mimic (NTC2)_21-5

description: negative control mimic (mir-100 knockup control), biological rep1


title: SMOV2 clear cell culture, subconfluent

description: Ovarian cancer (clear cell) cell line, SMOV2

source_name: SMOV2 clear cell culture, subconfluent


title: NOSE cell culture, biological rep6

description: Normal ovarian surface epithelium (NOSE) cell culture, biological rep6

value: Normal ovarian surface epithelial (NOSE) cells


title: hsa-mir-100 mimic_21-2

description: hsa-mir-100 mimic (mir-100 knockup in OVSAYO), biological rep1


title: H19As1

description: SAFB1 SiRNA in MCF-7


title: KK clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, KK

source_name: KK clear cell culture, confluent


title: OVISE clear cell culture, subconfluent

description: Ovarian cancer (clear cell) cell line, OVISE

source_name: OVISE clear cell culture, subconfluent


title: negative control siRNA

city: Halifax

first: Paul

middle: R

last: Murphy

state: Nova Scotia

address: 5850 College Street

department: Physiology and Biophysics

institute: Dalhousie University

description: Seg-1 cells transfected with negative control siRNA for 72hrs

hyb_protocol: 15 μg of Biotin-labeled cRNA in 250 μl hybridization cocktail was injected into each array and hybridized at 45oC for 16 hours with rotation of 60 rpm in an Affymetrix GeneChip Hybridization Oven 640. After hybridization, the staining and washing of each array was performed on Affymetrix GeneChip Fluidics Station 450 using Streptavidin Phycoerythrin, goat IgG, and Biotinylated anti-streptavidin antibody.

scan_protocol: Each array was scanned with an Affymetrix GeneChip 7G  2 Plus Scanner.

data_processing: Expression values were processed using GeneChip Operating Software (GCOS) v 1.4, MAS5, Baseline level: 100 fluorescence unit.

source_name: Seg-1 cells

label_protocol: Total RNA (5 μg) was used for 1st- and 2nd -strand cDNA synthesis with oligo-dT containing T7 promoter from the One-Cycle Target Labeling and Control Reagents kit (Affymetrix Cat. No. 900493).  Synthesized double stranded cDNA was used as template to generate Biotin-labeled cRNA which was then fragmented to 35-200 bases in size using fragmentation buffer (Affymetrix Cat. No. 900493).

growth_protocol: Adherent human Seg-1 cells (generously provided by David Beer, Ph.D., University of Michigan, Ann Arbor, MI) were cultured in DMEM supplemented with 8% fetal bovine serum at 37°C with 5% CO2. Although originally believed to be an esophageal adenocarcinoma cell line, Seg-1 has recently been confirmed to be the human lung adenocarcinoma cell line H460 (Dr. David Beer, personal communication).

extract_protocol: Total RNA was extracted with the Qiagen Rneasy mini RNA extraction kit.

treatment_protocol: Seg-1 cells were reverse transfected with pre-designed siRNA from Ambion according to Invitrogen’s Lipofectamine™ RNAiMAX Reverse Transfection protocol. Briefly, transfection complexes were formed in 6-well culture plates in OPTI-1 MEM culture media to give final siRNA concentrations of 25-200 nM. A control siRNA, with no homology to any known gene sequence, was included as a negative control.  Cell suspensions were added to formed complexes to give a seeding density of 1.0x105 cells per well and incubated at 37°C with 5% C02 for 72 hours. Cells were then harvested for RNA.

tag: cell type

value: lung adenocarcinoma cell line

tag: sirna

value: negative control


title: OVAS clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, OVAS

source_name: OVAS clear cell culture, confluent


title: OVMANA clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, OVMANA

source_name: OVMANA clear cell culture, confluent


title: TOV21G clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, TOV21G

source_name: TOV21G clear cell culture, confluent


title: OVTOKO clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, OVTOKO

source_name: OVTOKO clear cell culture, confluent


title: NOSE cell culture, biological rep5

description: Normal ovarian surface epithelium (NOSE) cell culture, biological rep5


title: RMG1 clear cell culture, confluent

description: Ovarian cancer (clear cell) cell line, RMG1

source_name: RMG1 clear cell culture, confluent


title: ES2 clear cell culture, subconfluent

description: Ovarian cancer (clear cell) cell line, ES2

source_name: ES2 clear cell culture, subconfluent


title: FGF-AS siRNA

description: Seg-1 cells transfected with FGF-AS siRNA for 72hrs

value: FGF-AS


title: hsa-mir-100 mimic_21-3

description: hsa-mir-100 mimic (mir-100 knockup in OVSAYO), biological rep2


title: NOSE cell culture, biological rep3

description: Normal ovarian surface epithelium (NOSE) cell culture, biological rep3


title: hESC-4_GSM348004

city: Stanford

first: Kitchener

middle: D.

last: Wilson

address: S140 Grant Bldg

institute: Stanford University

description: raw data file: GSM348004.txt

hyb_protocol: 825 ng of Cy3- and Cy5- labeled and amplified cRNA was mixed and fragmented according to the Agilent technology protocol. cRNA was hybridized to 4x44K whole human genome microarray slides from Agilent (Part G4112F) according to the manufacturer’s instructions. The hybridization was carried in a rotating hybridization chamber in the dark at 65°C for 17 h.

scan_protocol: The arrays were scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.5.1 applying LOWESS background subtraction and dye-normalization.

source_name: hESC

label_protocol: Using Low RNA Input Fluorescent Linear Amplification Kits (Agilent), cDNA was reverse transcribed from each RNA sample, as well as from a pooled reference control, and cRNA then transcribed and fluorescently labeled with Cy5/Cy3. cRNA was purified using an RNeasy kit (Qiagen).

growth_protocol: hESCs were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). To induce endothelial differentiation, undifferentiated hESCs were cultured in differentiation medium containing Iscove’s modified Dulbecco’s medium (IMDM) and 15% Knockout TM Serum Replacement (KnockoutTM SR) (Invitrogen, Carlsbad, CA), 16 BIT (BSA, insulin, transferring; Stem Cell Technologies), 0.1 mM nonessential amino acids, 2 mM Lglutamine, 450 mM monothioglycerol (Sigma, St. Louis, MO), 50 U/ml penicillin, and 50 mg/ml streptomycin, supplemented with 20 ng/ml bFGF (R&D Systems Inc., Minneapolis) and 50 ng/ml VEGF (R&D Systems Inc.), in ultra-low attachment plates (Corning Incorporated, Corning, NY) for the formation of suspended embryoid bodies (EBs).12 days-old EBs were harvested, and then suspended into rat tail collagen type I (Becton Dickinson, San Jose, CA) at a final concentration of 1.5 mg/ml collagen. After thoroughly mixing EBs into collagen, 1.5 ml/well of mixture was added into six-well plate. The plates were incubated at 37C for 30 min, allowing gel polymerization prior to addition of medium. After gel formation, each dish was supplemented with EGM-2 medium (Lonza, Basel, Switzerland) and 5% KnockoutTM SR with additional 50 ng/ml VEGF and 20 ng/ml bFGF. The cultures were then incubated for 3 days without media change.

extract_protocol: Total RNA was isolated as described previously in Trizol (Invitrogen) followed by purification over a Qiagen RNeasy column (Qiagen).

value: embryonic stem cells

tag: developmental stage

value: Undifferentiated hESCs

source_name: Pooled RNA reference

value: pool of undifferentiated and differentiated hESCs, as well as fetal and neonatal tissues


title: HUVEC-3

description: Human umbilical vein endothelial cells replicate 3

source_name: HUVEC

growth_protocol: hESCs were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes  with mTESR-1 human ES Growth Medium (StemCell Technologies). To induce endothelial differentiation, undifferentiated hESCs were cultured in differentiation medium containing Iscove’s modified Dulbecco’s medium (IMDM) and 15% Knockout TM Serum Replacement (KnockoutTM SR) (Invitrogen, Carlsbad, CA), 16 BIT (BSA, insulin, transferring; Stem Cell Technologies), 0.1 mM nonessential amino acids, 2 mM Lglutamine, 450 mM monothioglycerol (Sigma, St. Louis, MO), 50 U/ml penicillin, and 50 mg/ml streptomycin, supplemented with 20 ng/ml bFGF (R&D Systems Inc., Minneapolis) and 50 ng/ml VEGF (R&D Systems Inc.), in ultra-low attachment plates (Corning Incorporated, Corning, NY) for the formation of suspended embryoid bodies (EBs).12 days-old EBs were harvested, and then suspended into rat tail collagen type I (Becton Dickinson, San Jose, CA) at a final concentration of 1.5 mg/ml collagen. After thoroughly mixing EBs into collagen, 1.5 ml/well of mixture was added into six-well plate. The plates were incubated at 37C for 30 min, allowing gel polymerization prior to addition of medium. After gel formation, each dish was supplemented with EGM-2 medium (Lonza, Basel, Switzerland) and 5% KnockoutTM SR with additional 50 ng/ml VEGF and 20 ng/ml bFGF. The cultures were then incubated for 3 days without media change.

extract_protocol: Total RNA was prepared using RNeasy Mini Kit (Qiagen)

value: Human umbilical vein endothelial cells

value: Neonatal:cells obtained from human embilical vein


title: HUVEC-4

description: Human umbilical vein endothelial cells replicate 4


title: hsa-mir-30a/30d inhibitor_24-8

description: hsa-mir-30a/30d inhibitor (mir-30a knockdown in OVSAYO), biological rep3

treatment_protocol: Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). OVSAYO cells were transfected in 6-well plates (3.0 x 105 cells/well) using 3 μl Invitrogen Lipofectamine 2000 and 3 μg total hairpin inhibitor (66 nM). Knockdown of hsa-mir-30 family miRNAs was achieved using a mix of 2 μg hsa-mir-30a inhibitor (44 nM) and 1 μg hsa-mir-30d inhibitor (22 nM). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).

value: hsa-mir-30a/30d depletion


title: hESC-1_GSM348001

description: raw data file: GSM348001.txt


title: negative control inhibitor (NTC1)_24-9

description: negative control inhibitor (mir-30a knockdown control), biological rep3


title: hsa-mir-30a/30d inhibitor_24-6

description: hsa-mir-30a/30d inhibitor (mir-30a knockdown in OVSAYO), biological rep2


title: hESC-EC-2

description: Endothelial cells derived from H9 hESCs replicate 2

source_name: hESC-EC

value: Endothelial cells derived from H9 hESCs

value: Progenitor-type cell:Flow sorted for CD31 and CD144, then extended culture


title: NOSE cell culture, biological rep2

description: Normal ovarian surface epithelium (NOSE) cell culture, biological rep2


title: hESC-3_GSM348003

description: raw data file: GSM348003.txt


title: hESC-2_GSM348002

description: raw data file: GSM348002.txt


title: HUVEC-2

description: Human umbilical vein endothelial cells replicate 2


title: hsa-mir-30a/30d inhibitor_24-5

description: hsa-mir-30a/30d inhibitor (mir-30a knockdown in OVSAYO), biological rep1


title: negative control inhibitor (NTC1)_24-12

description: negative control inhibitor (mir-30a knockdown control), biological rep2


title: hESC-EC-4

description: Endothelial cells derived from H9 hESCs replicate 4


title: hESC-EC-3

description: Endothelial cells derived from H9 hESCs replicate 3


title: CEBPb wildtype, CD24+CD29hi cells, biological rep 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and quantile normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values

source_name: CD24+CD29hi cells from mouse mammary epithelial cells

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

growth_protocol: Mammary epithlial cells (MECs) were isolated from two paired sets of wildtype and germline C/EBPb-/- glands (10 mice per group).  Cells were FACS sorted based on CD24, CD29 and LIN expression.

extract_protocol: Total RNA was isolated using the Arcturus Pico Pure RNA isolation kit (Molecular Devices, Sunnyvale, CA).  The mRNA was then amplified using a NuGEN FFPE amplification kit (NuGEN, San Carlos, CA).

tag: genotype/variation

value: CEBPb wildtype

value: Mammary epithlial cells (MECs)

tag: stem/progenitor cell subpopulation

value: CD24+CD29hi cells


title: negative control mimic_18-8

description: negative control mimic (mir-22 knockup control), biological rep3

source_name: ES2 ovarian cancer cell line

treatment_protocol: Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). ES-2 cells were transfected in 6-well plates (2.5 x 105 cells/well) using 10 μl X-tremeGENE siRNA Transfection Reagent (Roche) and 2 μg hsa-mir-22 mimic (65 nM) (Dharmacon). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).

value: control


title: NOSE cell culture, biological rep4

description: Normal ovarian surface epithelium (NOSE) cell culture, biological rep4


title: HUVEC-1

description: Human umbilical vein endothelial cells replicate 1


title: CEBPb wildtype, CD24hiCD29lo cells, biological rep 2

source_name: CD24hiCD29lo cells from mouse mammary epithelial cells

value: CD24hiCD29lo cells


title: CEBPb wildtype, CD24hiCD29lo cells, biological rep 1


title: negative control mimic_18-6

description: negative control mimic (mir-22 knockup control), biological rep2


title: negative control inhibitor (NTC1)_24-10

description: negative control inhibitor (mir-30a knockdown control), biological rep1

source_name: OVSAYO ovarian cancer cell line


title: hESC-EC-1

description: Endothelial cells derived from H9 hESCs replicate 1


title: NOSE cell culture, biological rep1

description: Normal ovarian surface epithelium (NOSE) cell culture, biological rep1

value: Normal ovarian surface epithelial (NOSE) cells


title: CEBPb wildtype, CD24+CD29hi cells, biological rep 1


title: hsa-mir-22 mimic_18-3

description: hsa-mir-22 mimic (mir-22 knockup in ES2), biological rep3

value: hsa-mir-22 overexpression


title: EB-2

description: Day 12 Embryoid Bodies differentiated from H9 hESCs replicate 2

source_name: EB

value: Day 12


title: EB-4

description: Day 12 Embryoid Bodies differentiated from H9 hESCs replicate 4


title: CEBPb knockout, CD24+CD29hi cells, biological rep 1

value: CEBPb knockout


title: CEBPb knockout, CD24hiCD29lo cells, biological rep 1


title: negative control mimic_18-5

description: negative control mimic (mir-22 knockup control), biological rep1


title: EB-1

description: Day 12 Embryoid Bodies differentiated from H9 hESCs replicate 1


title: hsa-mir-22 mimic_18-1

description: hsa-mir-22 mimic (mir-22 knockup in ES2), biological rep1


title: CEBPb knockout, CD24hiCD29lo cells, biological rep 2


title: CEBPb knockout, CD24+CD29hi cells, biological rep 2


title: EB-3

description: Day 12 Embryoid Bodies differentiated from H9 hESCs replicate 3


title: T cell_Afr_Fem_56y.o._Control_6h_Sample ID 096

status: Public on Jan 27 2010

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

hyb_protocol: 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing:
LOWESS normalized, background subtracted, batch adjusted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction. Batch effect removal was performed on 8 experimental array batches, matched for race, age, gender and treatment using Distance Weighted Discrimination, in three steps, as follows. Step1 A >80% presence call-filter was applied on all genes. Step 2 Missing expression values were added by KNN imputation (PMID: 11395428). Step 3 Batch effect was removed by the DWD method (PMID: 14693816)  merging batch pairs (1-2), (3-4), (5-6) and (7-8). Step 4; merging batch quadruplets (1-2-3-4) and (5-6-7-8). Step 5; merging all 8 batches together (1-2-3-4-5-6-7-8).
Sample table represents unfiltered data. The filtered data (ie, passed the 75% presence call filter) have been linked as a supplementary file on the Series GSE17952  record.

source_name: Magnetic bead-selected CD3+ T cells, untreated control, 6h

label_protocol: 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion).

extract_protocol: Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions

value: test

tag: race

value: African American

value: F

tag: age

value: Control

tag: treatment pairs

tag: master set

value: No

tag: training set

tag: test set

tag: repeat set

value: Yes

tag: repeat samples derived from dentical donors

value: N

tag: array batch

value: Batch No.8

source_name: PBMCs, untreated control


title: T cell_Afr_Male_37y.o._Control_6h_Sample ID 093

tag: sample type

tag: gender

value: M


title: hsa-mir-22 mimic_18-2

description: hsa-mir-22 mimic (mir-22 knockup in ES2), biological rep2

tag: protocol


title: T cell_Afr_Fem_50y.o._IFNa_6h_Sample ID 098

source_name: Magnetic bead-selected CD3+ T cells, IFNa-treated, 6h

tag: treatment

value: IFNa


title: T cell_Afr_Male_47y.o._IFNa_6h_Sample ID 097


title: T cell_Afr_Fem_50y.o._Control_6h_Sample ID 098


title: T cell_Afr_Fem_56y.o._IFNa_6h_Sample ID 096


title: T cell_Afr_Male_60y.o._IFNa_6h_Sample ID 094


title: T cell_Afr_Male_37y.o._IFNa_6h_Sample ID 093


title: T cell_Afr_Fem_47y.o._Control_6h_Sample ID 095


title: T cell_Afr_Male_60y.o._Control_6h_Sample ID 094


title: T cell_Afr_Fem_47y.o._IFNa_6h_Sample ID 095


title: T cell_Afr_Male_47y.o._Control_6h_Sample ID 097


title: T cell_Eur_Male_61y.o._Control_6h_Sample ID 092

value: European American

value: O


title: T cell_Eur_Male_61y.o._IFNa_6h_Sample ID 092

value: control


title: T cell_Eur_Male_23y.o._IFNa_6h_Sample ID 086

value: Batch No.7


title: T cell_Eur_Fem_73y.o._IFNa_6h_Sample ID 087


title: T cell_Afr_Male_44y.o._IFNa_6h_Sample ID 090


title: T cell_Eur_Male_41y.o._IFNa_6h_Sample ID 089


title: T cell_Eur_Male_44y.o._Control_6h_Sample ID 091

value: B


title: T cell_Eur_Male_59y.o._IFNa_6h_Sample ID 085


title: T cell_Eur_Male_47y.o._IFNa_6h_Sample ID 084


title: T cell_Eur_Male_23y.o._Control_6h_Sample ID 086


title: T cell_Eur_Male_41y.o._Control_6h_Sample ID 089


title: T cell_Afr_Male_47y.o._IFNa_6h_Sample ID 083


title: T cell_Eur_Male_44y.o._IFNa_6h_Sample ID 091


title: T cell_Eur_Male_63y.o._Control_6h_Sample ID 088


title: T cell_Eur_Male_59y.o._Control_6h_Sample ID 085


title: T cell_Afr_Male_44y.o._Control_6h_Sample ID 090


title: T cell_Eur_Male_63y.o._IFNa_6h_Sample ID 088


title: T cell_Eur_Fem_73y.o._Control_6h_Sample ID 087


title: T cell_Afr_Male_47y.o._Control_6h_Sample ID 083


title: T cell_Eur_Male_24y.o._IFNa_6h_Sample ID 081


title: T cell_Eur_Fem_58y.o._Control_6h_Sample ID 082


title: T cell_Eur_Fem_58y.o._IFNa_6h_Sample ID 082


title: T cell_Eur_Male_47y.o._Control_6h_Sample ID 084


title: T cell_Eur_Male_31y.o._IFNa_6h_Sample ID 080


title: T cell_Eur_Male_31y.o._Control_6h_Sample ID 080


title: T cell_Eur_Male_24y.o._Control_6h_Sample ID 081


title: T cell_Afr_Male_36y.o._Control_6h_Sample ID 079


title: T cell_Afr_Male_49y.o._IFNa_6h_Sample ID 078


title: T cell_Afr_Male_36y.o._IFNa_6h_Sample ID 079


title: T cell_Afr_Male_49y.o._Control_6h_Sample ID 078


title: T cell_Eur_Fem_60y.o._Control_6h_Sample ID 074

value: Batch No.5


title: T cell_Eur_Male_61y.o._IFNa_6h_Sample ID 077


title: T cell_Eur_Fem_39y.o._Control_6h_Sample ID 075


title: T cell_Afr_Male_34y.o._Control_6h_Sample ID 071

value: Batch No.6


title: T cell_Afr_Male_48y.o._IFNa_6h_Sample ID 069

value: test


title: T cell_Eur_Male_61y.o._Control_6h_Sample ID 077


title: T cell_Eur_Male_68y.o._IFNa_6h_Sample ID 073


title: T cell_Eur_Male_64y.o._Control_6h_Sample ID 072

value: I


title: T cell_Afr_Fem_56y.o._IFNa_6h_Sample ID 070

value: African American

value: F


title: T cell_Afr_Male_45y.o._Control_6h_Sample ID 076

value: Control

value: No


title: T cell_Eur_Male_48y.o._IFNa_6h_Sample ID 067

value: Yes


title: T cell_Eur_Male_48y.o._Control_6h_Sample ID 067


title: T cell_Afr_Male_34y.o._IFNa_6h_Sample ID 071


title: T cell_Afr_Male_48y.o._Control_6h_Sample ID 069


title: T cell_Eur_Male_64y.o._IFNa_6h_Sample ID 072


title: T cell_Eur_Fem_60y.o._IFNa_6h_Sample ID 074


title: T cell_Eur_Male_68y.o._Control_6h_Sample ID 073


title: T cell_Afr_Fem_56y.o._Control_6h_Sample ID 070

value: N


title: T cell_Afr_Male_52y.o._IFNa_6h_Sample ID 066

value: M


title: T cell_Eur_Fem_39y.o._IFNa_6h_Sample ID 075

value: IFNa


title: T cell_Afr_Male_52y.o._Control_6h_Sample ID 066


title: T cell_Afr_Male_45y.o._IFNa_6h_Sample ID 076


title: T cell_Afr_Male_51y.o._IFNa_6h_Sample ID 064

value: L


title: T cell_Afr_Male_22y.o._Control_6h_Sample ID 065


title: T cell_Afr_Male_51y.o._Control_6h_Sample ID 064


title: T cell_Afr_Male_22y.o._IFNa_6h_Sample ID 065


title: T cell_Eur_Male_46y.o._Control_6h_Sample ID 062

value: European American


title: T cell_Eur_Male_67y.o._IFNa_6h_Sample ID 063

value: control


title: T cell_Eur_Male_67y.o._Control_6h_Sample ID 063


title: T cell_Eur_Male_19y.o._Control_6h_Sample ID 059


title: T cell_Eur_Male_50y.o._Control_6h_Sample ID 060


title: T cell_Eur_Male_36y.o._Control_6h_Sample ID 061


title: T cell_Eur_Male_46y.o._IFNa_6h_Sample ID 062


title: T cell_Eur_Male_23y.o._Control_6h_Sample ID 056

value: Batch No.4


title: T cell_Eur_Male_50y.o._IFNa_6h_Sample ID 060


title: T cell_Eur_Male_69y.o._Control_6h_Sample ID 053

value: Batch No.3


title: T cell_Eur_Male_36y.o._IFNa_6h_Sample ID 061


title: T cell_Eur_Male_43y.o._Control_6h_Sample ID 054


title: T cell_Eur_Male_67y.o._IFNa_6h_Sample ID 057

value: Batch No.5


title: T cell_Eur_Male_56y.o._IFNa_6h_Sample ID 058

value: Batch No.6


title: T cell_Eur_Male_54y.o._Control_6h_Sample ID 052

value: test


title: T cell_Eur_Male_43y.o._IFNa_6h_Sample ID 054


title: T cell_Afr_Male_39y.o._IFNa_6h_Sample ID 055


title: T cell_Eur_Male_23y.o._IFNa_6h_Sample ID 056


title: T cell_Afr_Male_39y.o._Control_6h_Sample ID 055


title: T cell_Eur_Male_19y.o._IFNa_6h_Sample ID 059


title: T cell_Eur_Male_67y.o._Control_6h_Sample ID 057


title: T cell_Eur_Male_56y.o._Control_6h_Sample ID 058


title: T cell_Afr_Male_43y.o._IFNa_6h_Sample ID 051


title: T cell_Eur_Male_69y.o._IFNa_6h_Sample ID 053


title: T cell_Afr_Male_43y.o._Control_6h_Sample ID 051


title: T cell_Eur_Male_54y.o._IFNa_6h_Sample ID 052


title: T cell_Eur_Male_57y.o._IFNa_6h_Sample ID 050


title: T cell_Eur_Male_56y.o._IFNa_6h_Sample ID 048


title: T cell_Eur_Male_57y.o._Control_6h_Sample ID 050


title: T cell_Eur_Male_53y.o._IFNa_6h_Sample ID 049

value: K


title: T cell_Eur_Male_56y.o._Control_6h_Sample ID 048


title: T cell_Eur_Male_53y.o._Control_6h_Sample ID 049


title: T cell_Afr_Fem_53y.o._IFNa_6h_Sample ID 047

value: African American


title: T cell_Afr_Fem_53y.o._Control_6h_Sample ID 047

value: F


title: T cell_Eur_Male_57y.o._IFNa_6h_Sample ID 046


title: T cell_Afr_Male_39y.o._IFNa_6h_Sample ID 041

value: J


title: T cell_Afr_Male_39y.o._Control_6h_Sample ID 041

value: Control

value: No


title: T cell_Afr_Male_47y.o._IFNa_6h_Sample ID 042

value: Yes


title: T cell_Afr_Male_41y.o._IFNa_6h_Sample ID 040

value: M

value: A


title: T cell_Afr_Male_41y.o._Control_6h_Sample ID 040


title: T cell_Eur_Male_50y.o._IFNa_6h_Sample ID 036

value: IFNa


title: T cell_Afr_Male_54y.o._Control_6h_Sample ID 038


title: T cell_Afr_Male_54y.o._IFNa_6h_Sample ID 038


title: T cell_Afr_Male_52y.o._Control_6h_Sample ID 039

value: L


title: T cell_Eur_Male_57y.o._Control_6h_Sample ID 046

value: European American

value: control


title: T cell_Afr_Fem_47y.o._IFNa_6h_Sample ID 045

value: Batch No.4


title: T cell_Afr_Fem_47y.o._Control_6h_Sample ID 045


title: T cell_Eur_Fem_44y.o._Control_6h_Sample ID 044

value: Batch No.3


title: T cell_Afr_Male_36y.o._Control_6h_Sample ID 043

value: G

value: Batch No.5


title: T cell_Eur_Fem_44y.o._IFNa_6h_Sample ID 044

value: test


title: T cell_Eur_Male_50y.o._Control_6h_Sample ID 036


title: T cell_Afr_Fem_40y.o._Control_6h_Sample ID 033

value: African American


title: T cell_Afr_Male_46y.o._IFNa_6h_Sample ID 035

value: C


title: T cell_Afr_Male_44y.o._IFNa_6h_Sample ID 034


title: T cell_Afr_Male_47y.o._Control_6h_Sample ID 042


title: T cell_Afr_Male_47y.o._IFNa_6h_Sample ID 032

value: E


title: T cell_Afr_Male_46y.o._Control_6h_Sample ID 035

value: Control


title: T cell_Afr_Male_44y.o._Control_6h_Sample ID 034

value: No


title: T cell_Afr_Male_47y.o._Control_6h_Sample ID 032

value: Yes


title: T cell_Eur_Fem_73y.o._Control_6h_Sample ID 029

value: F


title: T cell_Afr_Male_44y.o._IFNa_6h_Sample ID 028

value: M


title: T cell_Eur_Male_53y.o._Control_6h_Sample ID 027

value: K


title: T cell_Afr_Fem_40y.o._IFNa_6h_Sample ID 033

value: IFNa


title: T cell_Eur_Male_22y.o._Control_6h_Sample ID 031

value: European American


title: T cell_Afr_Fem_65y.o._Control_6h_Sample ID 026

value: control


title: T cell_Eur_Male_22y.o._IFNa_6h_Sample ID 031

value: Batch No.4


title: T cell_Afr_Male_51y.o._IFNa_6h_Sample ID 025


title: T cell_Eur_Male_25y.o._IFNa_6h_Sample ID 023

value: Batch No.1


title: T cell_Afr_Male_44y.o._Control_6h_Sample ID 028


title: T cell_Afr_Male_46y.o._IFNa_6h_Sample ID 024


title: T cell_Afr_Male_51y.o._Control_6h_Sample ID 025


title: T cell_Afr_Male_43y.o._IFNa_6h_Sample ID 030

value: D


title: T cell_Eur_Male_53y.o._IFNa_6h_Sample ID 027


title: T cell_Afr_Male_43y.o._Control_6h_Sample ID 030


title: T cell_Eur_Fem_73y.o._IFNa_6h_Sample ID 029


title: T cell_Afr_Fem_65y.o._IFNa_6h_Sample ID 026


title: T cell_Afr_Male_46y.o._Control_6h_Sample ID 024


title: T cell_Afr_Male_42y.o._Control_6h_Sample ID 022

value: Batch No.2


title: T cell_Eur_Male_25y.o._Control_6h_Sample ID 023

value: test


title: T cell_Afr_Male_42y.o._IFNa_6h_Sample ID 022

value: African American


title: T cell_Eur_Male_28y.o._IFNa_6h_Sample ID 021

value: H


title: T cell_Eur_Male_28y.o._Control_6h_Sample ID 021


title: T cell_Eur_Male_46y.o._Control_6h_Sample ID 018


title: T cell_Eur_Male_63y.o._Control_6h_Sample ID 017

value: I


title: T cell_Eur_Male_46y.o._IFNa_6h_Sample ID 018


title: T cell_Afr_Male_39y.o._IFNa_6h_Sample ID 020

value: J


title: T cell_Afr_Male_40y.o._IFNa_6h_Sample ID 019

value: No


title: T cell_Eur_Male_53y.o._Control_6h_Sample ID 016

value: Control

value: Yes


title: T cell_Eur_Male_29y.o._Control_6h_Sample ID 015

value: M


title: T cell_Eur_Male_29y.o._IFNa_6h_Sample ID 015


title: T cell_Eur_Fem_39y.o._Control_6h_Sample ID 014

value: F


title: T cell_Afr_Male_47y.o._Control_6h_Sample ID 012


title: T cell_Eur_Male_23y.o._Control_6h_Sample ID 011


title: T cell_Afr_Male_35y.o._Control_6h_Sample ID 013

value: G


title: T cell_Afr_Male_40y.o._Control_6h_Sample ID 019


title: T cell_Afr_Male_35y.o._IFNa_6h_Sample ID 013

value: IFNa


title: T cell_Eur_Fem_39y.o._IFNa_6h_Sample ID 014

value: European American

value: control


title: T cell_Eur_Male_23y.o._IFNa_6h_Sample ID 011

value: Batch No.1


title: T cell_Afr_Male_47y.o._IFNa_6h_Sample ID 012


title: T cell_Eur_Male_53y.o._IFNa_6h_Sample ID 016


title: T cell_Afr_Male_48y.o._IFNa_6h_Sample ID 009


title: T cell_Eur_Male_63y.o._IFNa_6h_Sample ID 017


title: T cell_Afr_Male_46y.o._Control_6h_Sample ID 010

value: E


title: T cell_Afr_Male_46y.o._IFNa_6h_Sample ID 010


title: T cell_Afr_Male_36y.o._IFNa_6h_Sample ID 043

value: Batch No.5


title: T cell_Afr_Male_48y.o._Control_6h_Sample ID 009

value: test

value: Batch No.2


title: T cell_Afr_Male_73y.o._IFNa_6h_Sample ID 008

value: African American


title: T cell_Afr_Male_52y.o._IFNa_6h_Sample ID 039

value: L

value: Batch No.6


title: T cell_Afr_Male_43y.o._Control_6h_Sample ID 006

value: No

value: D


title: T cell_Afr_Male_73y.o._Control_6h_Sample ID 008

value: Control

value: Yes


title: Male Hypox + GH (30 min) mouse liver/ Female Hypox + GH (30 min)/Replicate #2

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: The RNA expression profile for a Hypox + single GH injection (30 min) adult male liver pool (n = 3) and a Hypox  + single GH injection (30 min) adult female liver pool (n = 3) is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox + GH treated (30 min) mouse liver gene expression.

hyb_protocol: Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.

scan_protocol: Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).

data_processing: Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)

label: Alexa 647

source_name: Frozen adult mouse liver

label_protocol: RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI).  Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature.  Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA).  Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.

extract_protocol: Trizol extraction of RNA

tag: strain

value: ICR

value: Hypophysectomy ('Hypox') + GH injection (30 min)

tag: sex

value: Female

tag: tissue

value: Liver

value: 8 wks

label: Alexa 555

value: Male


title: T cell_Eur_Fem_41y.o._IFNa_6h_Sample ID 007

value: European American

value: F

value: IFNa

value: control


title: T cell_Afr_Male_33y.o._IFNa_6h_Sample ID 004

value: test

value: African American

value: M

value: Batch No.1


title: T cell_Afr_Male_46y.o._IFNa_6h_Sample ID 005

value: No

value: C

value: Batch No.2


title: T cell_Eur_Fem_41y.o._Control_6h_Sample ID 007

value: Control

value: Yes


title: T cell_Afr_Male_46y.o._Control_6h_Sample ID 005


title: T cell_Afr_Male_43y.o._IFNa_6h_Sample ID 006

value: D


title: Male Hypox + GH (30 min) mouse liver/ Female Hypox + GH (30 min)/Replicate #1

description: The RNA expression profile for a Hypox + single GH injection (30 min) adult male liver pool (n = 4) and a Hypox + single GH injection (30 min) adult female liver pool (n = 4) is given as a normalized ratio. The purpose of this comparison is to highlight sex-specific differences in Hypox + GH treated (30 min) mouse liver gene expression.

value: ICR

value: Hypophysectomy ('Hypox') + GH injection (30 min)

value: Female

value: Liver


title: T cell_Eur_Male_43y.o._IFNa_6h_Sample ID 002

value: European American

value: B


title: T cell_Eur_Fem_64y.o._IFNa_6h_Sample ID 003

value: F

value: IFNa

value: control


title: T cell_Afr_Male_33y.o._Control_6h_Sample ID 004

value: test

value: African American

value: M