title: CC_Kidney_049_SNP_Hind

description:
GR049T
Hybridized to 50K Hind

value: W

tag: tumor grade

value: III


title: HGF TG Mouse Whole Lung #2 (40wks) Cancer

status: Public on Dec 31 2010

type: RNA

city: Pittsburgh

first: Jill

middle: M

last: Siegfried

state: PA

address: The Hillman Cancer Center, UPCI Research Pavilion Suite 2.18, 5117 Centre Avenue

department: Pharmacology and Chemical Biology

country: USA

institute: University of Pittsburgh

description: Positive and negative controls are included within the array. Final images were saved in either .tiff or .jpg, and uploaded for further analysis as described below.

hyb_protocol: Hybridization was completed following the GEArray® protocol (SABiosciences) for HybTube. In brief: prehybridization was carried out 60°C for 2 hours followed by an overnight hybridization with labeled cDNA probe (4μg). On the second day two 15 minute washes at 60°C were completed before blocking and detection of spot signal. http://www.sabiosciences.com/support_manual.php

scan_protocol: X-ray film, exposed to the chemiluminescent array, was scanned on a flatbed scanner to obtain a digital image.

data_processing: Data analysis was conducted using online with GEArray Expression Analysis Suite at www.SuperArray.com. Absolute and comparison analyses were conducted using the following settings: average density, clover off, and no background correction. Data in the Value column are presented as relative induction of each gene normalized to the housekeeping gene GAPDH.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: whole lung

label_protocol:
cDNA template was reverse-transcribed from total RNA followed by amplification and biotin-16-labeling using the Oligo GEArray TrueLabeling-AMP™ 2.0 Kit (SABiosciences) according to the manufacturers protocol. Resulting cDNA was further purified using cRNA clean-up kit (SABiosciences) following the manufacturers procedure.
http://www.sabiosciences.com/support_manual.php

extract_protocol:
Total RNA was isolated from whole lung tissue in TRIzol (Invitrogen) following the manufacturers instructions. RNA was resuspended in RNase-free water and further purified using the RT² qPCR-Grade RNA Isolation Kit (SABiosciences) by following the manufacturers protocol.
http://www.sabiosciences.com/support_manual.php

tag: strain

tag: gender

value: Male/Female (equal numbers)

tag: age

value: 40 weeks

tag: tissue

value: Whole Lung

tag: genome/variation

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways


title: HGF TG Mouse Whole Lung #1 (40wks) Cancer


title: 16h_LPS_pIC_lipofected

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

country: France

institute: CIML - CNRS - INSERM

description: For each condition 100 ng total RNA were used to synthesize double-stranded cDNA in two successive reverse-transcription reactions according to standard Affymetrix protocols (GeneChip Two-Cycle Target Labelling, Affymetrix)

hyb_protocol: Standard Affymetrix hybridization procedure

scan_protocol: Scanning via an Affymetrix GCS 3000 GeneArray Scanner. Standard Affymetrix scanning procedure

data_processing: The data generated from the scan were analyzed using the MicroArray Suite software (MAS 5.0, Affymetrix).

source_name: DC, 16h LPS, pIC lipofected

label_protocol: Standard Affymetrix labelling procedure

extract_protocol: Total RNA was purified using the RNeasy kit (Qiagen) including a DNase digestion according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).

tag: cell type

value: bone-marrow derived dendritic cell


title: CC_Kidney_034_SNP_Hind

type: genomic

city: Grand Rapids

first: Bin

middle: Tean

last: Teh

state: MI

address: 330 Bostwick Av

department: Cancer Genetics

institute: Van Andel Institute

description:
GR034T
Hybridized to 50K Hind

hyb_protocol: Following fragmentation, 40 ug of genomic DNA was hybridized for 16 hr at 48C on Affymetrix GeneChip Human Mapping 50K chip, either Xba Array or Hind array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Starting from the CEL files, we used the R package oligo (48) to read the raw SNP data set. The result is an object containing the summarized signals of either A or B allele, of sense or antisense strand for each SNP on the array. The SNP's A or B allele signal was averaged by its sense and antisense signals respectively. To obtain SNP raw copy numbers, we used a total of 56 normal references either downloaded from Affymetrix (n = 48) or obtained by our own scan on normal kidney tissues (n = 8) to calculate the reference signals for each SNP's A and B alleles. The overall signal for the SNP was the sum of its A and B signals. The raw copy number for a SNP of a target sample was its overall signal subtracted by the averaged overall signals from the normal references (as all signals are in logarithm scale). We then used a divide-and-conquer algorithm to partition the raw copy numbers into segments based on the maximum likelihood estimate of the break points. It is a top-down algorithm to speed up the segmentation process. The raw copy numbers of SNPs within any identified segment will be regarded identical. The (one-sided t-) test score (to test location=0) would replace the raw copy numbers within the identified segment and was reported thereafter. A segment identified in an individual sample would be declared either a gain or a loss if the score for the segment was larger or smaller than a preselected cutoff value (e.g., 10). The actual segmentation algorithm was a two round algorithm. In the first round, the algorithm identifies segments with unusual large or small test scores (e.g., 5 standard deviations away from the mean), will mark the segment as outliers. The reported scores were actually the output from the second round of segmentation based on the raw copy numbers after removal of the outliers identified from the first round.
Table containing t-test scores of identified segmental gains or losses is provided as a supplementary file on the Series record.

label: R-Phycoerythrin Streptavidin (SAPE)

molecule: genomic DNA

organism: Homo sapiens

source_name: Clear cell renal cell caricinoma

label_protocol: 40 ug per Xba1 chip and 40 ug per HindIII chip. Purified pooled 3 Xba1 PCRs with 3 pooled HindIII PCRs. R-Phycoerythrin Streptavidin (SAPE), from Molecular Probes, 1 mg/ml (we use 6ul per reaction).

extract_protocol: extraction of total Genomic DNA was performed using Genomed JETquick tissue DNA Maxi Kit (part # 452050), according to manufacturers instructions.

value: Clear cell renal cell caricinoma

value: F

tag: ethnicity

tag: tumor stage

tag: tumor size(cm)


title: CC_Kidney_055_SNP_Hind

description:
GR055T
Hybridized to 50K Hind

value: M

value: IV


title: HGF WT Mouse Whole Lung #2 (20wks) Cancer

value: 20 weeks


title: 16h_LPS

source_name: DC, 16h LPS


title: HGF WT Mouse Whole Lung #1 (20wks) Cancer


title: 16h_LPS_pIC_soluble

source_name: DC, 16h LPS, pIC soluble


title: CC_Kidney_025_SNP_Hind

description:
GR025T
Hybridized to 50K Hind

value: II


title: HGF TG Mouse Whole Lung #2 (20wks) Cancer


title: Control-1

city: Houston

first: April

middle: Burant

last: Hall

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation inorder to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies)

source_name: lymphobast cell lines

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours then incubated at 65°C for10 minutes to inactivate the enzyme.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

growth_protocol: Lymphoblastoid cell lines were establihsed and maintained by Rutgers University for the NIMH

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

value: lymphoblast cell line

tag: disease state

value: control

tag: id (rutgers)

tag: nimh identifier

tag: sex

source_name: blood

tag: sample type

value: blood


title: 16h_LPS_ctrl_lipofected

source_name: DC, 16h LPS, only lipofectamine


title: 0h_no_LPS

source_name: DC, 0h, no LPS


title: Gene expression between bone marrow, 2

city: College Station

first: Huaijun

last: Zhou

address: Rm 418D Kleberg Center,Texas A&M University

institute: Texas A&M University

description: Four arrays are included in one slide.

hyb_protocol: 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each array in Agilent 4x44K microarrays. Arrays were incubated at 65℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Slides were scanned at 5-μm resolution using GenePix Personal 4100A (Molecular Devices Corporation, Sunnyvale, CA) and were saved as TIFF images. Auto Photomultiplier tube (PMT) were selected and adjusted to get the ratio of the overall intensities between the two channels (Cy3 and Cy5) was 0.9~1.1. The intensities of the spots on each image were quantified by Genepix pro 6.0 software (Molecular Devices Corporation, Downingtown, PA), and data were saved as .txt files for further analyses.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R 2.9.0 (Yang et al, 2002).

organism: Gallus gallus

source_name: Bone marrow

label_protocol: A 400 ng of aliquot of total RNA was reverse transcribed into cDNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA labeled with one of two cyanine-labeled nucleotides (Perkin Elmer, Wellesley, MA). Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity measured with ND-100 spectrophotometer (NanoDrop Technologies).

extract_protocol: Tissue sample was homogenized within lysis buffer (Qiagen RNeasy mini RNA extraction kit, Qiagen Inc., Valencia, CA). Total RNA was extracted from the homogenized lysate according to the manufacturer’s instructions, eluted with 30 µl RNase-free water and stored at -80°C.

tag: type

value: broiler

value: 4 weeks

value: bone marrow

tag: biological replicate


title: CC_Kidney_015_SNP_Hind

description:
GR015T
Hybridized to 50K Hind

tag: tumor grade

value: II~III


title: 4h_LPS

source_name: DC, 4h LPS

tag: strain


title: CC_Kidney_011_SNP_Hind

description:
GR011T
Hybridized to 50K Hind

tag: gender

value: W

value: III


title: CC_Kidney_010_SNP_Hind

description:
GR010T
Hybridized to 50K Hind


title: ZM_4dpi_dfox1_2

city: Karlsruhe

first: Jörg

middle: Thomas

last: Kämper

address: Hertzstrasse 16, Geb. 06.40

department: Department for Applied Biosciences

country: Germany

institute: Karlsruhe Institute of Technology

description:
3. leaf of maize seedlings 4 days post Ustilago maydis infection. Infection was performed 7 days post sowing. Dissected leaf tissue from 30 plants was pooled. Samples were harvested in the evening.
Identification of differentially regulated maize genes in maize leaves infected with the SG200∆fox1 strain 4 days post infection. The experiments GSM253265	(ZM_4d_SG200_3inf_I), GSM253266 (ZM_4d_SG200_3inf_II), GSM253267 (ZM_4d_SG200_3inf_III) of series GSE10023 (	Maize gene expression during infection with Ustilago maydis) were used as wild-type controls.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (Expression Analysis Technical Manual, 2001, Affymetrix)

scan_protocol: Microarrays were scanned on an Affymetrix GSC3000.

data_processing: Data were analyzed with Microarray Suite version 5.1 (MAS 5.1) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

label: biotin/phycoerythrin

organism: Zea mays

source_name: Maize leaf tissue 4 days post infection with Ustilago maydis strain SG200∆fox1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Maize plants of the cultivar Early Golden Bantam were grown in a phytochamber in a 15 h / 9 h light-dark cycle; light period started with a continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28°C and 20°C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.

extract_protocol: For RNA isolation, material from 30 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.

treatment_protocol: U. maydis strain SG200∆fox1 was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6–7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period. Samples were taken 4 days post infection at 1 h before end of the light period.

value: leaf


title: HGF TG Mouse Whole Lung #1 (20wks) Cancer

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways

value: Male/Female (equal numbers)

tag: age

value: Whole Lung


title: 4h_LPS_pIC_lipofected

source_name: DC, 4h LPS, pIC lipofected

value: bone-marrow derived dendritic cell


title: CC_Kidney_528_SNP_Hind

description:
CHTN528
Hybridized to 50K Hind

tag: tissue

value: Clear cell renal cell caricinoma

value: M


title: ZM_4dpi_dfox1_1


title: STA-NB-10_aCGH

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: aCGH analysis of untreated cell line

hyb_protocol: Labelled DNAs were hybridized to whole-genome oligonucleotide 1x244K microarrays (Agilent Technologies) following the manufacture's instructions (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNAs (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 1x244k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100%) . Microarray performance was assessed by QC metric tool.

data_processing: The scanned TIFF images were loaded into the R software environment for statistical computing (http://www.r-project.org/) with the limma package. Signal intensities were segmented by the CBS method within the CGHcall package, after control of raw data for local spatial bias, low signal-to-noise ratio, low replicates consistency and intensity effects had been conducted by means of the MANOR package. The aberration status for each segment across the fourteen cell lines was determined with the KCsmart package at the significance threshold of 0.05 using 1000 permutations-based testing.

source_name: human neuroblastoma cell line

label_protocol: We followed the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 3 ug of test and reference genomic DNAs were separately digested with AluI/RsaI restriction enzyme mix (Promega). After purification with QIAprep MiniPrep kit (Qiagen), fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elme) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by Biophotometer (Eppendorf) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

growth_protocol: See specific description in additional description column Characteristics. Growth conditions in the SAMPLE section.

extract_protocol: Total DNA was isolated by using the DNA Blood and Tissue Extraction Kit (Qiagen) according to manufacturer’s protocol.

treatment_protocol: All samples were untreated cell lines

tag: cell line

source_name: Human Genomic DNA: female Cat G1521,Promega, Madison, WI

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: ZM_4dpi_dfox1_3


title: CC_Kidney_503_SNP_Hind

description:
CHTN503
Hybridized to 50K Hind

value: F


title: SIMA_aCGH

description: aCGH analysis of untreated cell line

value: SIMA

source_name: Human Genomic DNA: male Cat G1471,Promega, Madison, WI

value: Human Genomic DNA:male Cat G1471,Promega, Madison, WI


title: YS Liver, biological rep 4

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

description: Gene expression profile

hyb_protocol: Ten micrograms of fragmented cRNA.  45 degrees C for 16 hours.

scan_protocol: GeneChip scanner 3000G following the Affymetrix standard protocols

data_processing: GCOS 1.3 following the Affymetrix standard protocols

label: biotin

organism: Sus scrofa

source_name: Yorkshire Liver

label_protocol: Affymetrix standard methods using GeneChip reagents

growth_protocol: The pigs were raised under the same conditions. The details of conditions and feeding were fully described in the supplementary material of Moon et al., Anim. Genet. 40(1): 115-8 (2009).

extract_protocol: Trizol reagent following the manufacturer's instruction

treatment_protocol: Tip of the largest lobe of liver was taken for the RNA extraction.

value: Liver

tag: breed

value: Yorkshire (YS)

value: 6 month old


title: 4h_LPS_pIC_soluble

source_name: DC, 4h LPS, pIC soluble

tag: cell type


title: IMR-32_aCGH

description: aCGH analysis of untreated cell line


title: Pt 5_Ballif et al._17q23.2

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

hyb_protocol: Hybridization and washing were perfomed with Agilent reagents per manufacturer's instructions

scan_protocol: Scanned on Axon 4000B scanner (Molecular Devices)

data_processing: Agilent Feature Extraction software v9.5.3.1 and Agilent CGH Analytics software v3.5.14 and displayed using oligonucleotide aCGH analysis software Genoglyphix

source_name: test genomic DNA, extracted from blood

label_protocol: 500 ng of sonicated DNA was labeled with AF5 (patient) and AF3 (control) using BioPrime Total labeling kit (Invitrogen) per manufacturer's instructions

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines, peripheral blood, or cultured tissues of the subjects and phenotypically normal male and female references using MagAttract DNA Mini M48 following the manufacture's instructions.

value: Female

tag: test

value: Patient 5

source_name: control genomic DNA, extracted from blood

tag: reference

value: phenotypically normal female


title: CC_Kidney_029_SNP_Hind

description:
CHTN029
Hybridized to 50K Hind

source_name: Clear cell renal cell caricinoma


title: YS Liver, biological rep 2

description: Gene expression profile


title: CC_Kidney_012_SNP_Hind

description:
CHTN012T
Hybridized to 50K Hind


title: YS Liver, biological rep 3

description: Gene expression profile


title: CC_Kidney_219_SNP_Hind

description:
CHTN219
Hybridized to 50K Hind

tag: ethnicity

value: W

tag: tumor size(cm)


title: STA-NB-7_aCGH

description: aCGH analysis of untreated cell line


title: CHP-212_aCGH

description: aCGH analysis of untreated cell line


title: KNP Liver, biological rep 3

description: Gene expression profile

source_name: Korean native pig Liver

value: Korean native pig (KNP)

value: 7 month old


title: CC_Kidney_009_SNP_Hind

description:
CHTN009T
Hybridized to 50K Hind


title: YS Liver, biological rep 1

description: Gene expression profile


title: SK-N-BE(2)_aCGH

description: aCGH analysis of untreated cell line


title: KNP Liver, biological rep 4

description: Gene expression profile


title: CC_Kidney_008_SNP_Hind

description:
CHTN008
Hybridized to 50K Hind


title: CHP-126_aCGH

description: aCGH analysis of untreated cell line


title: SK-N-SH_aCGH

description: aCGH analysis of untreated cell line

value: SK-N-SH


title: CC_Kidney_007_SNP_Hind

description:
CHTN007
Hybridized to 50K Hind


title: COLO 205

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland), for 16 hours followed by stringency washes.

scan_protocol: Subsequently, slides were dried and scanned. The analysis were performed using the relevant GenePix® Array Lists (GAL files) www.exiqon.com. The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA), to generate Tagged Image File Format (TIFF) images. The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.

data_processing: The text files, generated by Imagene v.8.0, were imported into Rosetta Resolver and normalized as previously described. The data used are median of replicate spots from normalized values using the Quantile normalization method in limma package in R version 11 as descriped in Søkilde et al. (MICRORNA EXPRESSION ANALYSIS BY LNA ENHANCED MICROARRAYS)

source_name: Cell line

label_protocol: A total of 1000 ng of total RNA was used for each sample. MiRCURY™ LNA microRNA Power labeling Kit (Exiqon, Vedbaek, Denmark) was used following the manufacturers’ recommendations. Spike-ins (used as control probes) were added in equal amounts to each reaction and labeled.

extract_protocol: Total RNA was isolated from the individual cell lines using Trizol (Invitrogen)

tag: barcode

tag: sample tag

value: COLO 205


title: OVCAR-3


title: A498


title: LAN-1_aCGH

description: aCGH analysis of untreated cell line

tag: sample type


title: KELLY_aCGH

description: aCGH analysis of untreated cell line

value: KELLY


title: T-47D


title: KNP Liver, biological rep 1

description: Gene expression profile


title: muscle at T3, biological rep3

city: Guang- zhou

first: song

middle: xiao

last: yan

state: Guang -dong

address: wu shan

country: China

institute: South China Agricultural University

description: Gene expression data from leg muscle in heat stress

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. An invariant set normalization procedure was performed to normalize the different arrays using DNA-chip analyzer [dChip].

source_name: leg muscle of chicken in heat stress (in 40℃)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA .

growth_protocol: The Chicken were maintained in a temperature controlled（28±1°C） for 8 days with water and food were available ad libitum .

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

treatment_protocol: The 8 days chicken were randomly divided into two groups to study the effects of heat stress on gene expression of brain, liver and leg muscle. Twenty-four birds (12 male and 12 female) were allocated to heat stress or post-heat stress group（40±1°C,3h） and control or pre-heat stress group（28±1°C）.

value: leg muscle


title: CHP-134_aCGH

description: aCGH analysis of untreated cell line


title: muscle at T3, biological rep2


title: SW-620


title: NCI-H23


title: SK-MEL-5


title: HOP-92


title: K-562


title: NB-69_aCGH

description: aCGH analysis of untreated cell line


title: strain DSY717; PDR1 with substitution L1081F DSY717_rep3

city: Lausanne

first: Dominique

last: Sanglard

address: Rue Bugnon 48

country: Switzerland

institute: University of Lausanne and University Hospital Center

hyb_protocol: Agilent gene expression hybridization kit protocol

scan_protocol: Agilent Scanning protocol on an Agilent DNA Microarray Scanner G2565BA  Other: Arrays were scanned at 5um resolution and 100/10% PMT XDR

data_processing: Data were extracted from the images with Feature Extraction (FE) software. Data were normalized using a combined rank consistency filtering with LOWESS intensity normalization. The gene expression values obtained from FE software were imported into GeneSpring 10.0.2 software (Agilent technologies) for preprocessing and data analysis.

organism: Nakaseomyces glabratus

label_protocol: Agilent one-color quick amp labeling kit protocol

growth_protocol: log-pase culture grown in YPD

extract_protocol: total RNA extraction using glass beads

tag: genotype

value: PDR1 with substitution L1081F

tag: isolate


title: HOP-62


title: M14


title: SK-MEL-2


title: strain DSY717; PDR1 with substitution L1081F DSY717_rep1


title: strain DSY717; PDR1 with substitution L1081F DSY717_rep2


title: strain DSY2317; wt PDR1 gene DSY2317_rep3

description: strain DSY2317; wt PDR1 gene


title: KNP Liver, biological rep 2

description: Gene expression profile


title: strain DSY2317; wt PDR1 gene DSY2317_rep2

description: strain DSY2317; wt PDR1 gene


title: MOLT-4


title: strain  SFY92; pdr1D SFY92_rep3

description: strain SFY92; pdr1D


title: muscle at T0, biological rep1

description: Gene expression data from leg muscle in normal

source_name: leg muscle of chicken in normal (in 28℃)


title: SR

value: SR


title: strain  SFY92; pdr1D SFY92_rep2

description: strain SFY92; pdr1D


title: strain  SFY92; pdr1D SFY92_rep1

description: strain SFY92; pdr1D


title: muscle at T0, biological rep3


title: strain DSY2317; wt PDR1 gene DSY2317_rep1

description: strain DSY2317; wt PDR1 gene


title: SK-N-AS_aCGH

description: aCGH analysis of untreated cell line

value: SK-N-AS

value: Human Genomic DNA:female Cat G1521,Promega, Madison, WI


title: muscle at T3, biological rep1


title: liver at T3, biological rep3

description: Gene expression data from liver in heat stress

source_name: liver of chicken in heat stress (in 40℃)

value: liver


title: STA-NB-1_aCGH

description: aCGH analysis of untreated cell line

value: Human Genomic DNA:male Cat G1471,Promega, Madison, WI


title: UACC-257


title: strain  SFY116; PDR1 with substitution P822L SFY116_rep3

value: PDR1 with substitution P822L


title: liver at T3, biological rep1


title: strain  SFY116; PDR1 with substitution P822L SFY116_rep2


title: liver at T0, biological rep2

description: Gene expression data from liver in normal

source_name: liver of chicken in normal (in 28℃)


title: liver at T3, biological rep2


title: Pt 6_Ballif et al._17q23.2

value: Female

value: Patient 6


title: Pt 7_Ballif et al._17q23.2

value: Patient 7

value: phenotypically normal female


title: liver at T0, biological rep3


title: Pt 4_Traylor et al._20q13.33

data_processing: Agilent Feature Extraction software v9.5.3.1 and Agilent CGH Analytics software v3.5.14 and displayed using oligonucleoted aCGH analysis softare Genoglyphix

source_name: Genomic DNA, extracted from blood

extract_protocol: Genomic DNA was extracted from lymphoblastoid from lymphoblastoid cell lines, peripheral blood, or cultured tissues of the subjects and phenotypically normal male and female references using M48 following the manufacture's instructions.

value: Male

tag: subject

value: Patient 4

value: control


title: Pt 2_Ballif et al._17q23.2

value: Patient 2


title: Pt 3_Ballif et al._17q23.2

value: Patient 3

value: phenotypically normal male


title: liver at T0, biological rep1


title: HL-60(TB)


title: muscle at T0, biological rep2

value: leg muscle


title: Pt 5_Traylor et al._20q13.33

value: Patient 5


title: strain  SFY115; PDR1 with substitution L280F SFY115_rep3

value: PDR1 with substitution L280F

tag: strain


title: brain at T3, biological rep3

description: Gene expression data from brain in heat stress

source_name: brain of chicken in heat stress (in 40℃)

value: cerebral cortex


title: DU-145


title: Pt 6_Traylor et al._20q13.33

tag: gender


title: Pt 3_Traylor et al._20q13.33


title: strain  SFY115; PDR1 with substitution L280F SFY115_rep2


title: SK-OV-3


title: strain  SFY115; PDR1 with substitution L280F SFY115_rep1


title: strain  SFY116; PDR1 with substitution P822L SFY116_rep1


title: brain at T3, biological rep2


title: KM12


title: Pt 2_Traylor et al._20q13.33


title: Pt 1_Ballif et al._17q23.2

value: Patient 1


title: strain  SFY111; PDR1 with substitution Y584C SFY111_rep3

value: PDR1 with substitution Y584C


title: brain at T0, biological rep3

description: Gene expression data from brain in normal

source_name: brain of chicken in normal (in 28℃)


title: strain  SFY111; PDR1 with substitution Y584C SFY111_rep2


title: OVCAR-8


title: HT29


title: HCT-116


title: HCT-15


title: MDA-MB-435


title: strain  SFY111; PDR1 with substitution Y584C SFY111_rep1


title: brain at T0, biological rep1


title: GerminatedUrediniospores_replicate2

city: Cambridge

first: Christina

middle: A

last: Cuomo

state: MA

address: 7 Cambridge Center

institute: Broad Institute

description: Fresh urediniospores were germinated for 24 hr as described by Liu et al (1993. Mol Plant-Microbe Inter 6:84)

hyb_protocol: Hybridization was performed by Roche NimbleGen, following their standard operating protocol.  See www.nimblegen.com

scan_protocol: Scanning was performed by Roche NimbleGen, following their standard operating protocol.  See www.nimblegen.com

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization, and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

organism: Puccinia graminis f. sp. tritici

source_name: Puccinia graminis f. sp. tritici germinated urediniospores

label_protocol: Labelling was performed by Roche NimbleGen, following their standard operating protocol.  See www.nimblegen.com

extract_protocol: Total RNA was extracted using a hot (60C) Trizol (Invitrogen Corp, Carlsbad, CA) method followed by Rneasy Midi kit (Qiagen, Valencia, CA) a modification of the method described by Caldo et al, 2004.

value: CDL 75-36-700-3 race SCCL

tag: developmental stage of fungus

value: 24hr germinated urediniospores


title: InfectedWheat_replicate2

description: 7-day-old wheat seedlings (cultivar McNair 701) were inoculated as described by Liu et al (1993. Mol Plant-Microbe Inter 6:84) and grown in a Conviron growth chamber for 8 days with 16h light periods at 20 C and 8h dark periods at 16C. Wheat and barley seedlings were place in a random block array within the same growth chamber.

source_name: Puccinia graminis f. sp. tritici infected wheat

tag: infected host

value: 7-day-old wheat seedlings


title: Jurkat

city: Vancouver

first: Youwen

address: 835 W 10th Ave

country: Canada

institute: University of British Columbia

description: T cell leukemia cell line Jurkat

hyb_protocol: Hybridizations were performed on Whole Human Genome Oligo microarrays (G4112F, Agilent Technologies, Canada), comprising 41,059 60-nt oligonucleotide probes, most represented as single spots.

scan_protocol: Agilent microarray slides will be scanned using the Agilent DNA Microarray Scanner and quantified using Agilent’s Feature Extraction software.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) and GeneSpring GX software was used for background subtraction and LOWESS normalization.

source_name: Leukemia cell line Jurkat

label_protocol: 500ng RNA were reverse-transcribed into cDNA and linearly amplified by in vitro transcription in the presence of fluorescent-labeled CTP using the Low RNA Input Linear Amplification Kit, PLUS, Two-Color from Agilent following the manufacturer’s instructions. Each microarray was hybridized with 825ng of each amplified cDNA labelled with Cy5 or Cy3 at a specific activity between 8 and 15 pmol/µg.

growth_protocol: Sezary cells and control CD4+ cells were directly isolated from patients' PBMC using RosetteSep CD4+ enrichment kit.  Cell lines were cultured in RPMI 1640 medium with 10% fetal bovine serum, 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 10-4 M beta-mercaptoethanol in 37℃ with 5% CO2.

extract_protocol: Total RNA were extracted and purified by Trizol reagent then cleaned us using Qiagen RNAeasy kit.

value: CD3+ T lymphocytes

tag: disease

value: Acute T cell leukemia

source_name: Normal control donor 9

value: Non-Sezary skin inflammation (Psoriasis)

value: CD4+ T lymphocyte


title: InfectedBarley_replicate3

description: 7-day-old barley seedlings (cultivar Hypana) were inoculated as described by Liu et al (1993. Mol Plant-Microbe Inter 6:84) and grown in a Conviron growth chamber for 8 days with 16h light periods at 20 C and 8h dark periods at 16C. Wheat and barley seedlings were place in a random block array within the same growth chamber.

source_name: Puccinia graminis f. sp. tritici infected barley

value: 7-day-old barley seedlings


title: InfectedBarley_replicate2


title: strain  SFY109; PDR1 with substitution E1083Q SFY109_rep3

value: PDR1 with substitution E1083Q


title: strain  SFY109; PDR1 with substitution E1083Q SFY109_rep2


title: strain  SFY109; PDR1 with substitution E1083Q SFY109_rep1


title: InfectedBarley_replicate1


title: GerminatedUrediniospores_replicate1


title: EKVX

tag: cell line

value: EKVX


title: brain at T3, biological rep1

tag: tissue


title: strain  SFY105; PDR1 with substitution T588A SFY105_rep3

value: PDR1 with substitution T588A


title: InfectedWheat_replicate1


title: GerminatedUrediniospores_replicate3


title: Hut78

description: CTCL cell line Hut78

source_name: Sezary cell line Hut78 cell

tag: cell type

value: CD4+ cutaneous T lymphocytes

value: Sezary syndrom

source_name: Normal control donor 7

value: Healthy Normal (Rosacea)


title: InfectedWheat_replicate3


title: Urediniospores_replicate3

description: Urediniospores were collected from wheat seedling leaves (Liu et al., 1993. Mol Plant-Microbe Inter 6:84) and stored at 4C and 30% RH for 1-3 days before RNA extraction.

source_name: Puccinia graminis f. sp. tritici urediniospores

value: uredinospores


title: Sezary cell replicate 6

description: Biological replicate 6 of 6. Sezary cells from patient with Sezary syndrom.

source_name: Sezary patient 11

value: CD4+CD7- T lymphocytes

source_name: Normal control donor 6


title: NCI-H460

source_name: Cell line


title: brain at T0, biological rep2

value: cerebral cortex


title: SF-268


title: A549/ATCC


title: Sezary cell replicate 3

description: Biological replicate 3 of 6. Sezary cells from patient with Sezary syndrom.

source_name: Sezary patient 7

source_name: Normal control donor 3


title: NCI-H322M


title: NCI-H522


title: strain  SFY103; PDR1 with substitution D1082G SFY103_rep2

value: PDR1 with substitution D1082G


title: LOX IMVI

value: LOX IMVI


title: Sezary cell replicate 4

description: Biological replicate 4 of 6. Sezary cells from patient with Sezary syndrom.

source_name: Sezary patient 9

source_name: Normal control donor 4


title: strain  SFY103; PDR1 with substitution D1082G SFY103_rep3


title: strain  SFY105; PDR1 with substitution T588A SFY105_rep1


title: strain  SFY103; PDR1 with substitution D1082G SFY103_rep1


title: Sezary cell replicate 5

description: Biological replicate 5 of 6. Sezary cells from patient with Sezary syndrom.

source_name: Sezary patient 10

source_name: Normal control donor 5


title: Urediniospores_replicate2

value: CDL 75-36-700-3 race SCCL


title: Pt 4_Ballif et al._17q23.2

source_name: test genomic DNA, extracted from blood

value: Female

tag: test

value: Patient 4

source_name: control genomic DNA, extracted from blood

tag: reference

value: phenotypically normal female


title: MCF7


title: Urediniospores_replicate1


title: strain  SFY101; PDR1 with substitution R376W SFY101_rep2

value: PDR1 with substitution R376W


title: strain  SFY101; PDR1 with substitution R376W SFY101_rep1


title: Sezary cell replicate 1

description: Biological replicate 1 of 6. Sezary cells from patient with Sezary syndrom.

source_name: Sezary patient 1

source_name: Normal control donor 1

value: Healthy Normal

value: CD4+ T lymphocyte


title: Sezary cell replicate 2

description: Biological replicate 2 of 6. Sezary cells from patient with Sezary syndrom.

source_name: Sezary patient 4

source_name: Normal control donor 2


title: HS 578T

value: HS 578T


title: BT-549


title: strain  SFY114; wt PDR1 gene SFY114_rep2

description: strain SFY114; wt PDR1 gene


title: strain  SFY114; wt PDR1 gene SFY114_rep3

description: strain SFY114; wt PDR1 gene


title: MALME-3M


title: strain  SFY114; wt PDR1 gene SFY114_rep1

description: strain SFY114; wt PDR1 gene


title: NCI/ADR-RES

value: NCI/ADR-RES


title: MDA-MB-231/ATCC


title: Hut102

description: Hut102 cell line originally isolated from mycosis fungoides patient

source_name: Sezary cell line Hut102 cell

value: CD4+ cutaneous T lymphocytes

value: Lymphoma;mycosis fungoides

source_name: Normal control donor 8

value: Non-Sezary skin inflammation (Psoriasis)


title: Allelic status: HCC1937

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

description:
Data obtained from caBIG (https://cabig.nci.nih.gov)
HCC1937

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Analyzed using dChip with the reference genotypes of sixty individuals obtained from the dChip website

label: standard Affymetrix protocol

source_name: DNA from breast cancer cell line

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

treatment_protocol: standard Affymetrix protocol

tag: catalog number

value: ATCC# CRL-2336


title: NCI-H226

tag: barcode


title: BY41_rep3

source_name: Clinical isolate

tag: phenotype

value: azole-resistant, repiratory-deficient


title: SNB-19

source_name: Cell line

tag: sample tag


title: BY41_rep2


title: strain  SFY105; PDR1 with substitution T588A SFY105_rep2

tag: genotype

value: PDR1 with substitution T588A


title: OVCAR-4


title: strain  SFY101; PDR1 with substitution R376W SFY101_rep3


title: bcballif_20q13 Patient 1nsp

city: Melbourne

first: Damien

last: Bruno

address: Flemington Road

department: Cytogenetics

country: Australia

institute: Murdoch Childrens Research Institute

description: Hybridized to 250K_Nsp

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing:
Copy Number Analyser for GeneChip (CNAG) version 3.0(1) was used for all analyses. Inter-sample normalisation of log2 intensity data (a measure of the signal intensity at a given locus) was performed using a ?reference set? of 80 clinical samples analysed in-house within a one year period. CNVs were detected by visual inspection of the normalised log2 intensity plots as well as numerical analysis of the SNP log2 intensity ratios. The CNAG v3.0 output was exported to Microsoft Excel, which was then filtered for clusters of SNPs fulfilling the criteria described above. As the distribution of SNP targets within the genome on the 250K/Nsp array is not uniform, no lower threshold for the length of a region of copy number gain or loss was used in the selection of CNVs for analysis. The recognition of CNVs was also aided by the automatic Hidden Markov Model (HMM) inferences of DNA copy number in CNAG v3.0. CNV breakpoints were determined by inspecting the log2 intensity ratios of SNP probes within and flanking detected regions of gain or loss.
An internal "reference set", consisting of data generated from 80 clinical samples, was used for the analysis of Patient 1. The reference samples have not been de-identified and thus we cannot submite them at this time.
1. Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, Ogawa S. A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005;65:6071-9.

source_name: blood, bcballif_20q13 Patient 1

label_protocol: According to Affymetrix protocol

extract_protocol: Genomic DNA was isolated from peripheral blood samples using Nucleon? BACC2 DNA extraction kits (GE Healthcare, Wisconsin, USA). DNA concentrations were measured with a NanoDrop spectrophotometer (ND-1000 V.3.1.2).  Samples (250ng) were run on 250K Nsp arrays (Affymetrix, California, USA) using the manufacturer's protocol.

value: Patient 1

value: male


title: ACHN

value: ACHN


title: BPY40_rep2

tag: isolate


title: 786-0


title: BPY40_rep1


title: SK-MEL-28


title: BPY40_rep3


title: BY41_rep1


title: Cervus elaphus uninfected sample 2

city: Ciudad Real

first: Ruth

middle: Cecilia

last: Galindo

state: Ciudad Real

address: Ronda de Toledo s/n

department: Animal Health

country: Spain

institute: Instituto de Investigacion en Recursos Cinegéticos

description: Cervus elaphus uninfected sample

hyb_protocol: GeneChip® HT IVT Labeling Kit (Affymetrix)

scan_protocol: Microarray Analysis Suite 5.0

data_processing: RMA normalization and statistical analyses were done using the free statistical language R and the libraries developed by the Bioconductor Project (www.bioconductor.org).

organism: Cervus elaphus

source_name: Spleen cells

label_protocol: Standard affimetryx labeling protocol

extract_protocol: Tri reagent, and Qiagen purification kit.

tag: infection

value: none, uninfected sample free of Anaplasma ovis and Mycobacterium complex (PCR and cultured tested)


title: Cervus elaphus naturally infected with Mycobacterium complex sample 1

description: Cervus elaphus infected with Mycobacerium complex.

value: Mycobacterium complex


title: Cervus elaphus uninfected sample 1

description: Cervus elaphus uninfected sample


title: UACC-62


title: TK-10


title: Cervus elaphus naturally infected with Anaplasma ovis sample 2

description: Naturally Anaplasma ovis infected deer Cervus elaphus. (Spain)

value: Anaplasma ovis (Spain)


title: RPMI-8226


title: Cervus elaphus naturally infected with Anaplasma ovis sample 1


title: Cervus elaphus naturally infected with Anaplasma ovis sample 3


title: Tumour_1step_5dpi III

description: FB1∆fox1/FB2∆fox1 crossings were used to infect 7 day old early golden bantam maize plants.  FB1fox1/FB2∆fox1 crossings were compared to FB1/FB2 wild-type crossings to identify fox1 dependent genes in planta.

hyb_protocol: Affymetrix EukGE-2V4 on GeneChip Fluidics Station 400

scan_protocol: Affymetrix GSC3000

organism: Mycosarcoma maydis

source_name: Tumor material from maize leaves 5 days post FB1/FB2 mixed infection at 28°C

label_protocol: Target preparation was performed according to the standard Affymetrix protocol using the Enzo BioArray RNA transcript labeling kit, except for a reaction temperature of 50 °C for first strand cDNA synthesis.

growth_protocol:
U. maydis strains were grown at 28°C in YEPS (Tsukuda et al., 1988) medium as pre-culture for plant infections. Plant infections were performed as described by (Brachmann et al., 2001).
- Brachmann, A., Weinzierl, G., Kämper, J., and Kahmann, R. (2001) Mol Microbiol 42(4): 1047-63.
- Tsukuda, T., Carelton, S., Fotheringham, S., and Holloman, W.K. (1988). Mol Cell Biol 8: 3703-09.

extract_protocol: Total RNA was extracted using the TRIZOL-reagent (Invitrogen) according to the manufacturer's instructions. RNA samples were further column purified using (Qiagen RNeasy) and the quality checked using a Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent).

treatment_protocol: U. maydis FB1/FB2 infected maize plants (Early Golden Bantam) were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Maize plants were kept at 28 °C (light) and 20 °(dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period and directly frozen in liquid nitrogen for RNA-extraction.

value: tumor material from maize leaves

tag: strain


title: blood of the 3rd GK rat

city: Shanghai

first: Zhi-Qiang

last: Ye

address: No. 320 of Yueyang Road

institute: Shanghai Institutes for Biological Sciences

description: The genomic DNA taken from GK rat as test samples (Cy5) while pooled genomic DNA from Wistar rats as the referrence (Cy3). In dye-swap design (the 2nd raw data file), GK DNA dyed by Cy3 while Wistar DNA dyed by Cy5.

hyb_protocol: Standard protocol of Agilent. Hybridization in an Agilent's Rat Genome CGH Microarray Kit 244A (P/N G4435A)

scan_protocol: High resolution Agilent Scanner (G2505B, US80803205)

data_processing: Agilent's Feature Extraction software was used to generate the raw intensities. Bioconductor packages including MANOR, snapCGH, limma, and DNACopy were used to process the data. Dye-swap pairs were merged.

organism: Rattus norvegicus

source_name: Blood from pericardium

label_protocol: Standard protocol of Agilent. 2 μg of genomic DNA from test (GK rats) and 2 μg of genomic DNA from common reference (Wistar rats) were digested by AluI/RsaI and random primer-labeled, incorporating Cy5 (red) and Cy3 (green) fluorescent dyes, respectively.

growth_protocol: The rats were fed until the age of 8 weeks.

extract_protocol: DNeasy Blood & Tissue Kit (Qiagen, P/N 69504)

treatment_protocol: The rats were anesthetized by formalin. The blood was taken from the pericardiums, and was anticoagulated.

value: Goto-Kakizak

tag: gender

value: Wistar


title: blood of the 2nd GK rat


title: UO-31


title: Tumour_1step_5dpi II


title: OVCAR-5


title: SN12C


title: blood of the 1st GK rat


title: Tumour_1step_5dpi I


title: Cervus elaphus naturally infected with Mycobacterium complex sample 2


title: SF-539


title: Patient_61 at remission

city: Catania

first: Vincenza

last: Barresi

address: V.le A Doria, 6

institute: University of Catania

description: AML62R exp14

hyb_protocol: Biotin-labeled fragments were hybridized to a Genechip Affymetrix SNP 6.0 arrays at 50°C for 16-18 hours in a GeneChip® Hybridization Oven 640 (Affymetrix, Inc.). Washing and staining with streptavidin-phycoerthrin was performed in a GeneChip® Fluidics Station 450 (Affymetrix, Inc.).

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix, Inc.) and raw data processing was performed using the  “GeneChip Operating Software”.

data_processing: Data processing was performed by the software "Genotyping Console v3.0.1 ". The following algorithms were used: 1) SNP 6.0 Birdseed v2 algorithm for genotyping, 2) BRLMM-P-Plus algorithm and Hidden Markov Model with regional GC correction for copy number analysis, 3) the LOH algorithm (CN5).

source_name: R bone marrow

label_protocol: Amplification and labeling were performed according to the protocol supplied by the Affymetrix for  SNP 6.0 arrays. 500 ng of gDNA was digested with NspI and StyI restriction enzymes, ligated to respectively NspI and StyI adaptors, amplified by PCR using a single primer. PCR products were purified and the amplicons were quantified using a NanoDrop spectrophotometer. 40-70 µg of purified amplicons were fragmented and biotin end-labeled

extract_protocol: Genomic DNA (gDNA) was extracted from bone marrow cells at the diagnosis (Dx samples; blasts >90%) and at the first complete remission phase (R samples; <5% blasts at morphological evaluation) using the QIAamp DNA Blood Mini Kit according to the manufacturer’s instructions. The concentration and the quality of the DNA were determined using  NanoDrop spectrophotometer.

value: bone marrow

tag: leukemia type

value: Normal Karyotype-Acute Myeloid Leukemia

tag: disease stage

value: remission


title: Patient_57 at diagnosis

description: AML57Dx exp14

source_name: Dx bone marrow

value: diagnosis


title: Patient_65 at diagnosis

description: AML65Dx exp14


title: Tumour_1step_dfox1_5dpi II

source_name: Tumor material from maize leaves 5 days post FB1∆fox1/FB2∆fox1 mixed infection at 28°C

treatment_protocol: U. maydis FB1∆fox1/FB2∆fox1 infected maize plants (Early Golden Bantam) were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Maize plants were kept at 28 °C (light) and 20 °(dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period and directly frozen in liquid nitrogen for RNA-extraction.

value: FB1∆fox1 (a1,b1) and FB2∆fox1 (a2,b2)


title: Patient_59 at diagnosis

description: AML59Dx exp14


title: Patient_5 at diagnosis

description: AML5Dx exp4


title: Patient_45 at diagnosis

description: AML45Dx exp11


title: Patient_55 at remission

description: AML56R exp14


title: Patient_61 at diagnosis

description: AML61Dx exp14


title: Patient_43 at remission

description: AML44R exp10


title: Tumour_1step_dfox1_5dpi I


title: SNB-75


title: U251


title: Tumour_1step_dfox1_5dpi III


title: SC_UT_120min

city: Peoria

first: Z Lewis

last: Liu

state: IL

address: 1815 N University

institute: USDA-ARS

description: No biological replicate. No HMF treated, harvested at 120min.

hyb_protocol: Hybridization was performed based on Hegde et al (2000) with modifications using HS 4800 Hybridization station.

scan_protocol: scanned on a genePix 4000b scanner. A pre-scan control mini-array was used to adjust PMT Gain against Cy3 and Cy5 channels and the ratios of signal intensities between Cy3 and Cy5 were balanced to 1.0 using the calibration control as described by Liu and Slininger (2007). Each spot was individually examined and adjusted or flagged if necessary.

data_processing:
All test samples (ch1) were compared to the same reference. Raw data file for the reference are available as a supplementary file on the Series record.
Median of foreground signal intensity subtracted by background for each dye channel was used for analysis. Raw data for each slide were normalized based on spike-in control gene CAB. GeneSpring GX 10.0 (Agilent software) was used. expression values less than 100 in 7 of 16 samples were filtered out from probesets, then a 2-way ANOVA analysis (p≤ 0.05) was performed. Genes showing statistically significant differential expressions with a minimum of 2-fold changes were selected for Principal Component Analysis and clustering analysis by Hierarchical and Self Organizing Maps.

organism: Saccharomyces cerevisiae

source_name: Yeast RNA, HMF untreated, 120min

label_protocol: Fifteen μg of total RNA was used for each sample labeling reaction in a total volume of 30 μl. RNA probe together with incorporated RNA controls was labeled using an indirect dUTP Cy3 or Cy5 dye as described by Liu and Slininger (2007).

growth_protocol: The yeast was maintained and cultured on a synthetic complete (SC) medium.Culture inocula were prepared using freshly grown cells harvested at logarithmic growth phase after incubation with agitation of 250 rpm at 30˚C for 16 h. Cells were incubated on SC medium in a fleaker fermentation system at 30˚C with agitation.

extract_protocol: Total RNA was extracted by hot phenol method and further purified using RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: HMF was added into the culture at a final concentration of 30 mM 6 h after the inoculation. Cultures grown under the same conditions without the HMF treatment served as a control.

source_name: Yeast RNA, HMF untreated, 0min


title: CAKI-1


title: RXF 393

value: RXF 393


title: Patient_29 at diagnosis

description: AML29Dx exp9


title: wild_9

first: Charlotte

middle: N.

last: Henrichsen

address: Quartier Sorge

department: Center for Integrative Genomics

institute: University of Lausanne

hyb_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.

data_processing: qspline normalised log ratios

organism: Mus musculus domesticus

source_name: Wild mouse, France, Male, liver

extract_protocol: Genomic DNA was prepared from liver using a chloroform-based extraction protocol.

value: Wild mouse

tag: country

value: France

value: Male

value: liver

source_name: C57BL/6J, Male, liver


title: SC_UT_60min_rep1

description: Biological replicate 1 of 2. No HMF treated, harvested at 60min.

source_name: Yeast RNA, HMF untreated, 60min


title: Patient_43 at diagnosis

description: AML43Dx exp10


title: IGROV1

tag: cell line


title: Patient_53 at diagnosis

description: AML53Dx exp12

tag: tissue


title: Patient_49 at diagnosis

description: AML49Dx exp12


title: Patient_25 at remission

description: AML26R exp9


title: Patient_63 at diagnosis

description: AML63Dx exp14


title: SC_UT_30min_rep2

description: Biological replicate 2 of 2. No HMF treated, harvested at 30min.

source_name: Yeast RNA, HMF untreated, 30min


title: Patient_55 at diagnosis

description: AML55DX exp 14


title: SF-295


title: Patient_25 at diagnosis

description: AML25Dx exp9


title: wild_8

scan_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.

source_name: Wild mouse, Denmark, Male, liver

value: Denmark


title: PC-3


title: Patient_23 at remission

description: AML24R exp8


title: SC_UT_60min_rep2

description: Biological replicate 2 of 2. No HMF treated, harvested at 60min.


title: Patient_29 at remission

description: AML30R exp9


title: HCC-2998


title: SC_UT_10min_rep1

description: Biological replicate 1 of 2. No HMF treated, harvested at 10min.

source_name: Yeast RNA, HMF untreated, 10min


title: Patient_21 at remission

description: AML22R exp8


title: SC_UT_30min_rep1

description: Biological replicate 1 of 2. No HMF treated, harvested at 30min.


title: wild_7

label_protocol: Labelling, hybridisation, scanning and data extraction was performed by Nimblegen, Inc.


title: SC_UT_10min_rep2

description: Biological replicate 2 of 2. No HMF treated, harvested at 10min.


title: wild_5

source_name: Wild mouse, Tahiti (French Polynesia), Male, liver

value: Tahiti (French Polynesia)


title: CCRF-CEM

source_name: Cell line

value: CCRF-CEM


title: wild_6

source_name: Wild mouse, Tunisia, Male, liver

value: Tunisia


title: SC_T_120min

description: No biological replicate. HMF (30mM) treated, harvested at 120min.

source_name: Yeast RNA, HMF treated, 120min


title: HGF WT Mouse Tumor (20wks)

city: Pittsburgh

first: Jill

last: Siegfried

address: The Hillman Cancer Center, UPCI Research Pavilion Suite 2.18, 5117 Centre Avenue

institute: University of Pittsburgh

description: Positive and negative controls are included within the array. Final images were saved in either .tiff or .jpg, and uploaded for further analysis as described below.

hyb_protocol: Hybridization was completed following the GEArray® protocol (SABiosciences) for HybTube. In brief: prehybridization was carried out 60°C for 2 hours followed by an overnight hybridization with labeled cDNA probe (4μg). On the second day two 15 minute washes at 60°C were completed before blocking and detection of spot signal. http://www.sabiosciences.com/support_manual.php

scan_protocol: X-ray film, exposed to the chemiluminescent array, was scanned on a flatbed scanner to obtain a digital image.

data_processing: Data analysis was conducted using online with GEArray Expression Analysis Suite at www.SuperArray.com. Absolute and comparison analyses were conducted using the following settings: average density, clover off, and no background correction. Data in the Value column are presented as relative induction of each gene normalized to the housekeeping gene GAPDH.

source_name: isolated tumors from lung

label_protocol:
cDNA template was reverse-transcribed from total RNA followed by amplification and biotin-16-labeling using the Oligo GEArray TrueLabeling-AMP™ 2.0 Kit (SABiosciences) according to the manufacturers protocol. Resulting cDNA was further purified using cRNA clean-up kit (SABiosciences) following the manufacturers procedure.
http://www.sabiosciences.com/support_manual.php

extract_protocol:
Total RNA was isolated from whole lung tissue in TRIzol (Invitrogen) following the manufacturers instructions. RNA was resuspended in RNase-free water and further purified using the RT² qPCR-Grade RNA Isolation Kit (SABiosciences) by following the manufacturers protocol.
http://www.sabiosciences.com/support_manual.php

treatment_protocol: Twice weekly nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) injections over 2 weeks

value: Male/Female (equal numbers)

tag: age

value: 20 weeks

value: Isolated tumors from lung tissue


title: Patient_23 at diagnosis

description: AML23Dx exp8

value: bone marrow


title: Weaver salmon onne_ad_2006_0672_gill_II001_005_Perkin, Pre Spawning mortality

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

hyb_protocol: Each fish examined in the array experiments was run on a single slide against a reference control that was a pool of all of the fish used in the experiment.  Microarray data were expressed in terms of normalized (background corrected) log2 ratios between each fish and the reference control.  All slides were processed on Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland). All steps from washing, hybridization, denaturation, and slide drying were carried out automatically.

scan_protocol: Fluorescent images were scanned using a Perkin Elmer ScanArray Express (Perkin Elmer, Boston, MA), adjusting the PMT gain for optimized visualization of each image.  The images were quantified using Imagene (BioDiscovery, El Segundo, CA, www.biodiscovery.com).

data_processing: Data were prepared using GeneSight (BioDiscovery, Inc.). Local background correction was used and spots with flags 1-7 were considered missing (representing spots with poor signals or other quality issues). Intensity values of less than 20 were set to 20. Missing values were replaced with the mean of the probe intensity across all arrays in the series. LOESS Normalization was carried out using a smoothing parameter of 0.2 and degree of fit 1.

label: Alexa 555

organism: Oncorhynchus nerka

source_name: gill

label_protocol: 500 nanograms to 5 micrograms of total RNA was amplified 1x using a MessageAmp(TM) II-96 kit (Ambion, TX, USA), performed manually according to manufacturers instructions.  Five micrograms of aRNA was reverse transcribed into cDNA and labelled with Alexa dyes using the Invitrogen Indirect Labelling Kit, with modifications from the manufacturer's instructions.  Briefly, the cDNA was purified using Zymo-25 Clean-Up columns (Zymo Research, Orange, CA) and eluted using the 2X coupling buffer, supplied by Invitrogen.  During dye labelling, samples were processed individually by first adding DMSO, then cDNA to the Alexa dye tube and incubating for 1h at room temperature.  All individual (experimental) samples were fluorescently tagged with Alexa 555 and references were labelled with Alexa 647.  Samples and references were cleaned up by adding 50 microliters of DNA binding buffer (Zymo) to each Alexa tube and then combining the sample and references for each slide into Zymo-25 Clean-Up columns.  The unbound portion of the labelled cDNA was removed by centrifugation at 13,000 rpm/min. The labelled cDNA was washed three times with DNA wash buffer (Zymo) and eluted in 9 microliters of 1X TE buffer.  Two microlitres of poly dA was added to the targets, which were then denatured for 10 min at 80C, followed by the addition of 125 microliters of pre-warmed SlideHybe3 buffer (Ambion, TX, USA) before loading into the hybridization chamber in Tecan-HS4800 Pro Hybridization Station (Tecan Trading AG, Switzerland)

extract_protocol: Field collected samples were initially stored in a charged liquid nitrogen cryo-shipper and transferred to -80C upon arrival to the lab. Total RNA was purified from individual fish gill using Magmax(TM)-96 for Microarrays Kits (Ambion Inc, Austin, TX, USA) with a Biomek FXP (Beckman-Coulter, Mississauga, ON, Canada) automated liquid-handling instrument.  Two gill filaments per fish were homogenized with stainless steel beads in TRI-reagent (Ambion Inc, Austin, TX, USA) on a MM301 mixer mill (Retsch Inc., Newtown, PA, USA).  One hundred micro liter aliquots of homogenates were pipetted into 96 well plates and extractions were carried out according to the manufacturer's instructions using the No-Spin Procedure on the Biomek FXP.  In the final step, RNA was eluted with RNAase-, DNAase-free water and RNA yield was determined by measuring the A260 of the eluate. Purity was assessed by measuring the A260/A280 ratio of the eluate. Solutions of RNA were stored at -80C until use for cDNA synthesis or quantitative RT-PCR.

value: gill

tag: alternative identifier

tag: run

value: Late run

tag: sex

value: F

tag: fate

value: Pre Spawning mortality

tag: stock

value: Weaver

label: Alexa 647

source_name: gill from all samples in the series

value: Pooled RNA reference


title: HGF TG Mouse Tumor (20wks)

tag: genome/variation

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways


title: HGF WT Mouse Whole Lung #2 (20wks)

source_name: whole lung

value: Whole Lung


title: Patient_19 at diagnosis

description: AML19Dx exp8

source_name: Dx bone marrow

value: Normal Karyotype-Acute Myeloid Leukemia

value: diagnosis


title: SC_T_60min_rep2

description: Biological replicate 2 of 2. HMF (30mM) treated, harvested at 60min.

source_name: Yeast RNA, HMF treated, 60min


title: Patient_19 at remission

description: AML20R exp8

source_name: R bone marrow

value: remission


title: Weaver salmon onne_ad_2006_0665_gill_II001_168_Tecan, Spawned

value: Spawned

tag: reference


title: Weaver salmon onne_ad_2006_0663_gill_II001_162_Tecan, Spawned


title: Weaver salmon onne_ad_2006_0666_gill_II001_067_Perkin, Spawned


title: HGF WT Mouse Whole Lung #1 (20wks)


title: wild_20

source_name: Wild mouse, Corsica (France), Male, liver

value: Wild mouse

value: Corsica (France)

value: Male

value: liver


title: SC_T_30min_rep2

description: Biological replicate 2 of 2. HMF (30mM) treated, harvested at 30min.

source_name: Yeast RNA, HMF treated, 30min

source_name: Yeast RNA, HMF untreated, 0min


title: wild_4

source_name: Wild mouse, Switzerland, Female, liver

value: Switzerland

value: Female

source_name: C57BL/6J, Male, liver


title: Weaver salmon onne_ad_2006_0640_gill_II001_167_Tecan, Pre Spawning mortality

value: gill

value: Late run


title: SC_T_60min_rep1

description: Biological replicate 1 of 2. HMF (30mM) treated, harvested at 60min.


title: HGF TG Mouse Whole Lung #2 (20wks)

value: Male/Female (equal numbers)

value: 20 weeks


title: Weaver salmon onne_ad_2006_0659_gill_II001_066_Tecan, Pre Spawning mortality

value: F

value: Pre Spawning mortality

value: Weaver

value: Pooled RNA reference


title: HGF TG Mouse Whole Lung #1 (20wks)

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways

value: Whole Lung


title: SC_T_30min_rep1

description: Biological replicate 1 of 2. HMF (30mM) treated, harvested at 30min.


title: SC_T_10min_rep2

description: Biological replicate 2 of 2. HMF (30mM) treated, harvested at 10min.

source_name: Yeast RNA, HMF treated, 10min


title: wild_3


title: Patient_17 at remission

description: AML18R exp7

value: bone marrow

value: Normal Karyotype-Acute Myeloid Leukemia

value: remission


title: wild_21

source_name: Wild mouse, France, Female, liver

value: Wild mouse

value: France

value: Male


title: Weaver salmon onne_ad_2006_0633_gill_II001_019_Perkin, Pre Spawning mortality


title: SC_T_10min_rep1

description: Biological replicate 1 of 2. HMF (30mM) treated, harvested at 10min.


title: HGF WT Mouse Tumor (40wks)

value: 40 weeks

value: Isolated tumors from lung tissue


title: HGF TG Mouse Tumor (40wks)


title: wild_2

source_name: Wild mouse, Switzerland, Male, liver

value: Switzerland

value: liver


title: B3K_T2

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

description: Renal tumor, technical replicate 2

hyb_protocol: standard Affy protocol

scan_protocol: standard Affy protocol

data_processing: GCRMA processed data utilizing custom CDF-files for Ensembl genes (R package hs133phsensg).

source_name: kidney

label_protocol: standard Affy protocol

extract_protocol: Trizol

value: tumor


title: HGF WT Mouse Whole Lung #3 (40wks)

value: Male/Female (equal numbers)


title: HGF WT Mouse Whole Lung #4 (40wks)


title: B3K_T3

description: Renal tumor, technical replicate 3


title: Patient_11 at remission

description: AML12R exp8


title: Weaver salmon onne_ad_2006_0613_gill_II001_018_Tecan, Pre Spawning mortality

value: gill

value: Late run

value: F

value: Pre Spawning mortality


title: Weaver salmon onne_ad_2006_0636_gill_II001_181_Tecan, Spawned

value: Spawned

value: Weaver

value: Pooled RNA reference


title: Patient_11 at diagnosis

description: AML11Dx exp11

value: bone marrow

value: Normal Karyotype-Acute Myeloid Leukemia

value: diagnosis


title: wild_19

source_name: Wild mouse, Israel, Male, liver

value: Wild mouse

value: Israel

value: Male


title: Patient_17 at diagnosis

description: AML17Dx exp7


title: B3K_T1

description: Renal tumor, technical replicate 1


title: Patient_21 at diagnosis

description: AML21Dx exp8


title: wild_17

source_name: Wild mouse, Italy, Male, liver

value: Italy


title: B3K_N2

description: Normal kideny, techincal replicate 2

value: normal


title: wild_16

source_name: Wild mouse, Spain, Male, liver

value: Spain

value: liver


title: Weaver salmon onne_ad_2006_0399_gill_II001_175_Tecan, Pre Spawning mortality

source_name: gill

value: gill

source_name: gill from all samples in the series


title: B3K_N3

description: Normal kideny, techincal replicate 3


title: HGF TG Mouse Whole Lung #2 (40wks)

source_name: whole lung

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways

value: Male/Female (equal numbers)

value: 40 weeks

value: Whole Lung


title: Weaver salmon onne_ad_2006_0626_gill_II001_004_Tecan, Pre Spawning mortality

value: Late run

value: F

value: Pre Spawning mortality

value: Weaver


title: Weaver salmon onne_ad_2006_0607_gill_II001_006_Perkin, Spawned

value: Spawned

value: Pooled RNA reference


title: Weaver salmon onne_ad_2006_0391_gill_II001_150_Tecan, Spawned


title: B3K_N1

description: Normal kideny, techincal replicate 1


title: wild_15

value: Wild mouse

value: Israel


title: Patient_9 at diagnosis

description: AML9Dx exp5

source_name: Dx bone marrow

value: bone marrow

value: Normal Karyotype-Acute Myeloid Leukemia

value: diagnosis


title: wild_18

source_name: Wild mouse, Algeria, Male, liver

value: Algeria

value: Male

value: liver


title: HGF TG Mouse Whole Lung #4 (40wks)

value: heterozygous with high copy number for HGF under control of Clara cell promoter, over-expresses human HGF in small airways

value: Male/Female (equal numbers)


title: HGF TG Mouse Whole Lung #1 (40wks)

value: 40 weeks

value: Whole Lung


title: HGF WT Mouse Whole Lung #2 (40wks)


title: HGF WT Mouse Whole Lung #1 (40wks)


title: Weaver salmon onne_ad_2006_0387_gill_II001_014_Tecan, Spawned

value: gill

value: Late run

value: F


title: Weaver salmon onne_ad_2006_0386_gill_II001_149_Perkin, Spawned

value: Spawned

value: Weaver


title: HGF TG Mouse Whole Lung #3 (40wks)


title: Cd3B

city: Boston

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

description: Biological replicate 6 of 6

hyb_protocol: Agilent Technologies Quick Amp Two Color Labeling protocol and Agilent microarray hybridization chamber user guide (G2534-90001)

scan_protocol: Axon GenePix 4000B scanner

data_processing: local background subtraction, alpha-outlier-generating model (see Loguinov et al. (2004) Genome Biol. 5(3), R18.)

organism: Daphnia magna

source_name: Cd exposed replicate 6

label_protocol: Agilent Technologies Quick Amp Two Color Labeling kit with Two Color RNA Spike-in kit using 1.5 micrograms of total RNA

growth_protocol: Daphnia magna were cultured at the US EPA culture facility in Cincinnati OH in Moderately Hard Reconstituted water at 25 degrees C.  They were fed 3 times weekly a combination of Pseudokirchneriella subcapitata and alfalfa extract.

extract_protocol: Standard TriReagent protocol from Molecular Research Center, treated with DNAse I using DNAfree kit from Ambion.

treatment_protocol: 10-d old females were exposed to 18 micrograms/L Cadmium sulfate for 24-hrs.

tag: agent

value: Cd

value: 10 days

tag: culture media

value: Moderately hard reconstituted water

value: whole organism

source_name: unexposed replicate 6


title: Weaver salmon onne_ad_2006_0385_gill_II001_161_Perkin, Spawned

value: Pooled RNA reference


title: Cd2B

description: Biological replicate 4 of 6

source_name: Cd exposed replicate 4

source_name: unexposed replicate 4


title: Cd2A

description: Biological replicate 3 of 6

source_name: unexposed replicate 3

source_name: Cd exposed replicate 3


title: Weaver salmon onne_ad_2006_0383_gill_II001_160_Perkin, Pre Spawning mortality

value: Pre Spawning mortality


title: Weaver salmon onne_ad_2006_0617_gill_II001_021_Perkin, Spawned


title: Cd1B

description: Biological replicate 2 of 6

source_name: Cd exposed replicate 2

source_name: unexposed replicate 2


title: wild_11

source_name: Wild mouse, Switzerland, Female, liver

tag: strain

value: Wild mouse

value: Switzerland

value: Female

source_name: C57BL/6J, Male, liver

value: Male


title: Weaver salmon onne_ad_2006_0379_gill_II001_148_Perkin, Pre Spawning mortality


title: wild_12

tag: gender

value: liver


title: Cd1A

description: Biological replicate 1 of 6

source_name: unexposed replicate 1

source_name: Cd exposed replicate 1


title: Cd3A

description: Biological replicate 5 of 6

source_name: unexposed replicate 5

source_name: Cd exposed replicate 5


title: Weaver salmon onne_ad_2006_0376_gill_II001_166_Tecan, Pre Spawning mortality

source_name: gill

source_name: gill from all samples in the series


title: wild_10


title: Weaver salmon onne_ad_2006_0363_gill_II001_176_Tecan, Spawned


title: TNNT2sp zebrafish replicate 4

city: Charlestown

first: Jason

last: Becker

address: 13th St, Building 149

department: CVRC

institute: Massachusetts General Hospital

description: Biological replicate 4 of 4

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software

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

organism: Danio rerio

source_name: Whole embryo TNNT2sp morphants

label_protocol: 5 µg of total RNA from each sample was labeled using the Agilent Low RNA Input Kit (T7 promoter primer, Cy3 or Cy5 dyes)

extract_protocol: Groups of 30 control or TNNT2sp morphant embryos were collected at 96hpf and RNA extracted with Trizol (Invitrogen). RNA was further processed with RNeasy purification columns (Qiagen)

treatment_protocol: Embryos were injected with a control or TNNT2sp morpholino at the 1-4cell stage. They were then allowed to develop at 28 degrees Celsius for 96hrs.

value: whole embryo

tag: developmental stage

source_name: Whole embryo control morphants


title: wild_13

source_name: Wild mouse, Morocco, Male, liver

value: Morocco


title: wild_14

source_name: Wild mouse, Georgia, Male, liver

value: Georgia


title: wild_1

source_name: Wild mouse, Switzerland, Male, liver


title: Weaver salmon onne_ad_2006_0356_gill_II001_180_Tecan, Spawned

value: gill

value: Late run

value: F


title: TNNT2sp zebrafish replicate 3

description: Biological replicate 3 of 4


title: Weaver salmon onne_ad_2006_0345_gill_II001_065_Tecan, Pre Spawning mortality

value: Weaver


title: Patient_9 at remission

description: AML10R exp8

source_name: R bone marrow

value: bone marrow

tag: leukemia type

value: Normal Karyotype-Acute Myeloid Leukemia

tag: disease stage

value: remission


title: TNNT2sp zebrafish replicate 2

description: Biological replicate 2 of 4


title: CD3/CD28mAb-treated Jurkat cells

city: Xi'an

first: An-Gang

last: Yang

address: No.17,Changle West Road

institute: Fourth Military Medical University

description: Jurkat cells treated with CD3/CD28mAb.

hyb_protocol: Labeled miRNAs were incubated with hybridization solution at 95°C for 3-5 min and then loaded onto the array. Array was hybridized overnight (16-18 h) at 60°C.

scan_protocol: Array was scanned using a Genepix 4000B microarray scanner (Molecular Devices).

data_processing:
The scanned array images were annotated and analyzed using the Spotfire 8.0 software.

The raw data for this Sample is in the "635"-labeled columns of the "GSM575159.txt" file.

source_name: Jurkat cells, CD3/CD28mAb

label_protocol: 5 µg of total RNA mixed with 8 µl of 2.5×labeling buffer, 2 µl of Spike-in miRNA kit, 2 µl of Hy3 or Hy5 fluorescent label and 2 µl of Labeling enzyme incubated in the dark at 0-4°C for 1 h, then incubated at 60°C for 15 min.

growth_protocol: Jurkat cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol reagent.

treatment_protocol: Treated cells were exposed to 10μg/mL of Anti-CD3 (HIT3a, BD PharMingen) and 5μg/mL of Anti-CD28 (CD28.2, BD PharMingen) antibody for 24 h.

tag: cell line

value: Jurkat

tag: cell type

value: T lymphocyte derived from acute T cell leukemia


title: Untreated Jurkat cells

description: Untreated Jurkat cells.

data_processing:
The scanned array images were annotated and analyzed using the Spotfire 8.0 software.

The raw data for this Sample is in the "532"-labeled columns of the "GSM575158.txt" file.

source_name: Jurkat cells, untreated

value: control


title: Interm Hypoxia 4

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

institute: JHU

description: replicate 4

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalised using RMA (Bioconductor affy package) protocol and analyzed using Significance Analysis of Microarray (SAM) software.

source_name: Interm Hypoxia

label_protocol: Total RNA (5 µg) from each sample was converted into double-stranded cDNA using SuperScript Choice system (Invitrogen, Carlsbad, CA).  Each double-stranded cDNA was subsequently used as a template to make biotin-labeled cRNA using the BioArray HighYield RNA Transcript Kit (Enzo Life Sci., Inc., Farmingdale, NY) and 15 µg of fragmented, biotin-labeled murine lung cRNA from each sample was hybridized to the Affymetrix GeneChip® Mouse Genome 430A 2.0 Array

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

tag: age

value: 6-8 wk-old

value: male

tag: tissue

value: whole lung


title: Interm Hypoxia 5

description: replicate 5


title: Interm Hypoxia 3

description: replicate 3


title: Spret/Ei_2

organism: Mus spretus

source_name: Spret/Ei, Male, liver

value: Spret/Ei

value: Male

value: liver


title: TNNT2sp zebrafish replicate 1

description: Biological replicate 1 of 4

value: whole embryo


title: Interm Hypoxia 1

description: replicate 1


title: Spret/Ei_3

source_name: C57BL/6J, Male, liver


title: Interm Hypoxia 2

description: replicate 2


title: SJL/J_2

source_name: SJL/J, Male, liver

value: SJL/J


title: Normoxia 5

description: replicate 5

source_name: Normoxia


title: Embryonic stem cell sample 1

city: St. Catharines

first: Ping

last: Liang

state: Ontario

address: 500 Glenridge Ave

department: Department of Biological Sciences

institute: Brock University

hyb_protocol: Hybridization performed according to standard procedures by Nimblegen

scan_protocol: Scanning performed according to standard procedures by Nimblegen using NimbleScan.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.  VALUE is the P score. To calculate the P score, the ratio of the input signals for input DNA and the MeDIP DNA from the same sample that were co-hybridized to the array is first computed and scaled to center the ratio data around zero.  Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. A fixed-length window (750bp) is then placed around each consecutive probe and the one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether the probes are drawn from a significantly more positive distribution of intensity log-ratios than those in the rest of the array. The resulting score for each probe, called P score, is the -log10 p-value from the windowed KS test around that probe. The identification of methylation peaks is done by searching for at least 2 consecutive probes above a P score of 2. Peaks within 500bp of each other are merged.

source_name: Cy3, total input sonicated DNA

label_protocol: Labeling performed according to standard procedures by Nimblegen

extract_protocol: Total genomic DNA was extracted using Qiagen DNeasy kit (Qiagen) according to the manufacture's instruction.  DNA was  sonicated to give fragments between 200bp and 1000bp.

value: ES cells

source_name: Cy5, methylated DNA enriched by MeDIP

extract_protocol: Sonicated total genomic DNA was digested with MseI (TTAA) (New England Biolabs) to produce small fragments (200 - 1,000bp) while keeping CpG islands  intact. Fragmented DNA was heat denatured to produce single-stranded DNA, and a portion of the denatured DNA stored as control (input) DNA.  Monoclonal mouse anti 5-methyl cytidine (Eurogentec, Reference ID: BI-MECY-0500; batch#: 080128) was used to  immunoprecipitate methylated DNA fragments. The immune complexes were captured with Protein A agarose beads (Invitrogen). Complexes were washed to remove nonspecifically bound material. MeDIP DNA was obtained by elution of bound complexes and ethanol precipitation.


title: SJL/J_3


title: Normoxia 4

description: replicate 4


title: adult testis sample2

value: testis

value: adult


title: Normoxia 3

description: replicate 3


title: SJL/J_1


title: PL/J_1

source_name: PL/J, Male, liver

value: PL/J


title: Control-148

city: Houston

first: April

last: Hall

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: The nanodrop fluorospectrometer was used to measure DNA concentrantion and Dye incorporation inorder to pair subjects with controls according to the following criteria: pmoles of dye were required to be within 3 units and DNA concentration within 100ng/uL. For each hybridization, the labeled experimental and reference DNAs were boiled for 3 minuted and incubated at 37°C for 30-90 minutes with human Cot-1 DNA (Invitrogen, Carlsbad, CA), blocking agent and hybridization buffer (Agilent Technologies, Santa Clara, CA).  The samples were then added to an array, which was placed inside a microarray hybridization chamber (Agilent Technologies, Santa Clara, CA), and allowed to hybridize at 65°C for 35-68 hours in a rotating hybridization oven (Agilent Technologies, Santa Clara, CA).  Following hybridization, slides were washed following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Agilent G2565 DNA Microarray Scanner (Agilent Technologies, Santa Clara, CA) with 3 um resolution.

data_processing: scanned images were quantified using the Agilent Feature Extraction (FE) software (version 10.7.3.1, Agilent Technologies)

source_name: lymphobast cell lines

label_protocol: The digested DNA was labeled with Bioprime Array CGH Genomic Labeling System following the manufacturer’s recommended protocol with minor additions (Invitrogen, Carlsbad, CA). Following the addition of random primers to the digested DNA, the mixture was boiled for 5 minutes then cooled on ice for 5 minutes. Cyanine 5-dCTP (for the experimental sample), cyanine 3-dCTP (for the reference sample) (PerkinElmer, Boston, MA), dCTP nucleotide mix, and exo-Klenow fragment (40 units/µL) were added and the reaction was incubated at 37°C for 2 hours then incubated at 65°C for10 minutes to inactivate the enzyme.  The labeled product was purified from unincorporated nucleotides using Millipore columns or plate (Millipore, Billerica, MA, USA)

extract_protocol: DNA was isolated from lymphoblastoid cell lines by Rutgers University by desalting using the Autopure LS robotic workstation with Autopure reagents (Qiagen, Inc., Valencia, CA)

value: lymphoblast cell line

tag: disease state

tag: id (rutgers)

tag: nimh identifier

value: M

source_name: blood

tag: sample type

value: blood


title: LP/J_3

source_name: LP/J, Male, liver

value: LP/J


title: PL/J_3


title: Control-152

value: control

tag: sex


title: PL/J_2


title: Control-149


title: adult liver sample2


title: LP/J_1


title: Normoxia 2

description: replicate 2

value: 6-8 wk-old


title: LP/J_2


title: Normoxia 1

description: replicate 1

value: male


title: Control-147


title: Control-145


title: Control-144


title: adult liver  sample1


title: DBA/2J_3

source_name: DBA/2J, Male, liver


title: Embryonic stem cell sample 2


title: BMDM_MOUSE_LPS_REP2

city: DUNDEE

first: Claire

last: Monk

address: James Black Centre, University of Dundee, Dow Street

country: United Kingdom

institute: University of Dundee

hyb_protocol: The hybridization conditions are 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide, 34 °C, and overnight.

scan_protocol: AxoHybridization images are collected using a laser scanner (GenePix 4000B, Molecular Device). Scan resolution is set at 10 µ and PTM is set between 350 to 700 V.

data_processing: The values from each probe location targeting a sequence (5 locations per target) were averaged. The data processing software used was ArrayPro, and data subjected to background adjustment and Global normalization.

source_name: BMDM_RNA_Control 2

label_protocol: Small RNAs (< 300 nt) are 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag is then ligated to the poly(A) tail for later fluorescent dye staining

growth_protocol: Bone marrow derived macrophages were isolated from C57Bl/6 mice and cultured in DMEM, 10% heat inactivated FBS, 2mM L-glutamine, 100 units/ml, 0.25 ug/ml amphotericin, 100 units/ml penicillin G, 100 ug/ml streptomycin, 5 ng/ml rCSF. Cells were maintained

extract_protocol: RNA from Bone marrow derives macrophages was isolated using the microRNeasy mini kits (Qiagen) in line with the manufacturer’s protocol.

treatment_protocol: Bone marrow derived macrophages were plated onto tissue culture plates with fresh media 24 h before treatment. Cells were left unstimulated or were treated with either 100 ng/ml LPS or 10^6 cells/ml heat killed Candida albicans

tag: reference

value: unstimulated control 2

source_name: BMDM RNA LPS 16h 2

value: LPS 16h 2


title: Control-150


title: DBA/2J_1

city: Lausanne

value: Male


title: adult heart sample2

value: heart


title: adult heart sample1


title: BMDM_MOUSE_LPS_REP1

source_name: BMDM_RNA_Control 1

value: unstimulated control 1

source_name: BMDM RNA LPS 16h 1

tag: agent

value: LPS 16h 1


title: Cast/Ei_3

source_name: Cast/Ei, Male, liver

value: Cast/Ei

value: liver


title: BMDM_MOUSE_CA_REP3

source_name: BMDM_RNA_Control 3

value: unstimulated control 3

source_name: BMDM RNA Candida 16h 3

value: Candida 16h 3


title: adult brain sample2

value: brain

value: adult


title: DBA/2J_2

source_name: C57BL/6J, Male, liver


title: Cast/Ei_2


title: BMDM_MOUSE_CA_REP2

source_name: BMDM RNA Candida 16h 2

value: Candida 16h 2


title: Cast/Ei_1


title: BMDM_MOUSE_CA_REP1

source_name: BMDM RNA Candida 16h 1

value: Candida 16h 1


title: adult brain  sample1

source_name: Cy3, total input sonicated DNA


title: C57BL/6J_5


title: 1nM T3 and 4OHPCB106 treat 2

city: Shizuoka

first: Akinori

last: Ishihara

country: Japan

institute: Shizuoka University

hyb_protocol: Samples were hybridized to Xenopus laevis chips (Agilent, Santa Clara, CA) according to manufacturer's protocol.

scan_protocol: Hybridized chips were scanned using GenePix 4000B scanning equipment.

data_processing: Agilent Feature Extraction Software (version 9.5.3.1) was used for data extraction from scanner generated TIFF files. Global normalization settings were used with Subio platform with basic plug-in. See http://www.subio.jp/ for details. Briefly, the data that exhibited low raw signal were cut off by 1.0. The values were log transformed and were processed to global normalization with 75 percentile value. Finally, centering was performed with mean value.

organism: Xenopus laevis

source_name: T3 and 4OHPCB106 treat

label_protocol: Probes were labeled with Cy3 using Quick Amp Labeling Kit (Agilent, Santa Clara, CA). Input is 400 ng RNA.

growth_protocol: Tadpoles were reared in dechlorinated tap water and transferred to FETAX buffer during experiment.

extract_protocol: RNA was extracted using SV total RNA Isolation System (Promega, Madison, WI) per the procedure supplied by the manufacturer.

treatment_protocol: Tadpoles were treated with DMSO vehicle, 1 nM T3 alone, or 1nM T3 and 500 nM hydroxylated PCBs for 4 days.

value: Premetamorphic tadpole

value: T3 and 4OHPCB106


title: Spret/Ei_1

source_name: Spret/Ei, Male, liver

value: Spret/Ei

organism: Mus musculus


title: Control-131

organism: Homo sapiens

source_name: lymphobast cell lines

value: lymphoblast cell line

value: control

value: M

value: blood


title: new born liver sample2

value: newborn

source_name: Cy5, methylated DNA enriched by MeDIP


title: Control-132

source_name: blood


title: Control-126


title: C57BL/6J_1

value: Male


title: Control-130


title: 1nM T3 and 4OHPCB106 treat 3


title: C57BL/6J_2


title: new born liver  sample1


title: new born testis sample2

value: testis


title: C57BL/6J_4

value: liver


title: 1nM T3 and 4OHPCB106 treat 1


title: C57BL/6J_3


title: Control-143


title: 1nM T3 and 4OHPCB159 treat 3

source_name: T3 and 4OHPCB159 treat

value: T3 and 4OHPCB159


title: new born testis  sample1


title: Control-125


title: new born heart sample2

value: heart


title: Control-124


title: 1nM T3 and 4OHPCB159 treat 2

value: brain


title: new born heart  sample1


title: 1nM T3 and 4OHPCB159 treat 1


title: 1nM T3 treat 6

source_name: T3 treat


title: Control-119


title: 1nM T3 treat 5


title: Control-122


title: E15 testis sample1


title: Control-117


title: C3HeB/FeJ_2

source_name: C3HeB/FeJ, Male, liver


title: C3HeJ_2

source_name: C3HeJ, Male, liver


title: Control-116


title: C3HeJ_1


title: C3HeB/FeJ_3


title: Control-114


title: E15 testis sample2


title: adult testis  sample1

value: adult


title: C3HeB/FeJ_1


title: Control-123


title: E15 liver sample1


title: new born brain sample2


title: E15 liver sample2


title: new born brain sample1


title: Ffujikuroi_vel1_120h_rep2

first: Daren

middle: W.

last: Brown

address: 1815 N. University St.

department: Bacterial Foodborn Pathogens and Mycology Research

description: Ffvel1 mutant

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

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

organism: Fusarium fujikuroi

source_name: Fusarium fujikuroi IMI58289 delta vel1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Fusarium fujikuroi wild type IMI58289 and Ffvel1 mutant strains were grown in liquid ICI (Imperial Chemical Industries Ltd., UK) media containing 6 mM glutamine (10 % ICI medium).

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany).

tag: genotype variation

value: Ffvel1 mutant

tag: growth time

value: 72 hrs


title: Control vs ATRX

hyb_protocol: Cy3- and Cy5-labelled were denatured and hybridized competitively to the microarray slides.  Upon overnight incubation, the slides were washed successively in 1X SSC/0.1% SDS, 1X SSC and 0.2X  SSC for 2 min each, then rinsed in 0.5 X SSC and spin-dried.

scan_protocol: The two fluorescent intensities (Cy3 and Cy5) were measured simultaneously.

data_processing: The results were analyzed with the GEMTOOLS Analysis Software (Incyte Genomics)

source_name: blood mononuclear cells, controls

label_protocol: Total RNA from Controls was converted in Cy3-labeled cDNA  and total RNA from ATRX patients was converted  in Cy5-labeled cDNA

extract_protocol: Total RNA was extracted as described by Chomczynski and Sacchi. The quantity and purity of RNA were confirmed by spectrophotometry and agarose gel electrophoresis.

value: normal

value: blood mononuclear cells

tag: gender

value: male

value: pool of 42 males

source_name: blood mononuclear cells, ATRX

value: ATRX

value: pool of 3 males


title: 1nM T3 treat 2

tag: developmental stage

value: Premetamorphic tadpole


title: 1nM T3 treat 1


title: DMSO treat 4

source_name: DMSO vehicle

value: control


title: 1nM T3 treat 3


title: 1nM T3 treat 4


title: BALB/cByJ_2

source_name: BALB/cByJ, Male, liver

tag: strain

value: BALB/cByJ

value: Male

source_name: C57BL/6J, Male, liver


title: BALB/cByJ_1

value: liver


title: DMSO treat 5


title: yAPSp4b - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Experimental and reference probes were combined and hybridized to custom Agilent 44K whole mouse genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2565BA (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to normalize the Agilent array data using Agilent's default protocol (essentially LOWESS dye normalization on background subtracted signal values). Spots of poor quality or average intensity levels <300 were removed from further analysis.

source_name: MGS

label_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following Agilent suggested protocols.

extract_protocol: Reference RNA was purified using Trizol (Life Technologies, Rockville, MD) following the manufacturer’s protocol. The RNA was then further purified by RNeasy maxi kit (Qiagen Inc, Valencia, CA) and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: Swiss-Webster

value: Adult

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

tag: amplification

value: one round aRNA

growth_protocol: Young (4 month-old) and old (20-24 monthold) C57BL/6 male mice were obtained from the National Institutes of Aging (NIA) Rodent Colony at Harlan Sprague Dawley (Chicago, IL) and maintained in a barrier facility and cared for in accordance with approved IACUC protocols. Following shipment, mice were acclimated to a common temperature, day-night cycle, and diet for at least 12 days to minimize environmental differences. Mice from each age group were randomized for the day and time of sacrifice. Following halothane anesthesia, mice were sacrificed by cervical dislocation. Prostates were rapidly excised, immersed in OCT embedding compound (Miles Diagnostics, Elkhart, Ind., USA) and snap-frozen in liquid nitrogen and stored at -80º C.

extract_protocol: Approximately 10,000 cells were laser-capture microdissected using the Veritas LCM system (Arcturus Mountain View, CA). Total RNA from LCM experimental samples were isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl UTP incorporation into the second round aRNA using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: 4 month-old

value: pool of anterior lobe prostate stroma laser capture microdissected from three mice

value: two round aRNA


title: BALB/cByJ_4

extract_protocol: Genomic DNA was prepared from liver using a chloroform-based extraction protocol.


title: Ffujikuroi_vel1_120h_rep1

description: Ffvel1 mutant

value: Ffvel1 mutant

value: 72 hrs


title: C3HeJ_3


title: Control-98

value: lymphoblast cell line

value: M

value: blood


title: Control-97


title: E15 heart sample1

source_name: Cy3, total input sonicated DNA

value: heart