title: NB4 leukemic cells, ARAC+RA, replicate 3


title: NB4 leukemic cells, MycA+RA, replicate 2

status: Public on Jan 05 2012

type: RNA

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: The labeled cRNA was hybridized to the Agilent Whole Human Genome 4x44k 60-mer oligo microarray (G4112F) according to the manufacturer's protocol. After hibridization, the microarrays were washed.

scan_protocol: Slides were scanned on an Agilent G2565BA microarray scanner at Green channel XDR Hi 100% and XDR Lo 100% green PMT and 5 um resolution.

data_processing: Intensity data was extracted using the Feature Extraction software (Agilent).

molecule: total RNA

organism: Homo sapiens

source_name: MycA+RA

label_protocol: 500 ng of total RNA was labeled using Agilent's QuickAmp Labeling Kit following manufacturer instructions. Briefly: mRNA was reverse transcribed in the presence of T7-oligo-dT primer to produce cDNA. cDNA was then in vitro transcribed with T7 RNA polymerase in the presence of Cy3-CTP to produce labeled cRNA.

growth_protocol: NB4 cells were cultured at 37C and 5% of CO2 in RPMI medium supplemented with 10% of fetal bovine serum.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit including DNAse I digestion to avoid potential contaminations of DNA  following the manufacturer's recommendations.

treatment_protocol: NB4 cells infected with MSCV-based retroviral vectors containing ER-tagged empty vector (CTL), MycA or MycD were seeded at a density of 0.5M/mL in RPMI medium containing 200nM of 4-OHT and 25uM of AraC if indicated. After 16 hours, 10 nM of RA or EtOH (vehicle) were added to the medium for 4 hours. Cells were then harvested and RNA was extracted.

tag: cell line

tag: cell type

value: leukemic


title: Atg5 deficient_IFNγ_replicate1

city: Saint Louis

first: Nicole

last: Maloney

state: MO

address: 660 South Euclid

department: Pathology/Immunology

country: USA

institute: Washington University in St Louis School of Medicine

description: Bone marrow derived macrophages

hyb_protocol: Following fragmentation, 12.5μg of cRNA were hybridized for 16 hr at 45°C on Mouse 430 2.0 Genome Array. Genechips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G06.

data_processing: Probe set summarization (CHP) files were derived from feature intensity (CEL) files using Affymetrix® Expression Console™ software (v.1.1). Default analysis settings were used for background adjustment and quantile normalization.

label: biotin

organism: Mus musculus

source_name: IFNγ treated Atg5 flox/flox + LysM cre macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2008, Affymetrix).

growth_protocol: Bone marrow derived macrophages were generated by isolating and culturing mouse marrows in media containing DMEM, FBS, horse serum, CMG14-12 (Takeshita et al., 2000), MEM nonessential amino acids, sodium pyruvate, L-glutamine.

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

treatment_protocol: Macrophages were incubated with media alone or 100U/ml IFNγ for 14 hrs before RNA was extracted

tag: genotype/variation

value: Atg5 flox/flox + LysM cre

tag: treatment

value: 100U/ml of IFN-gamma for 14 hrs


title: NB4 leukemic cells, MycA+RA, replicate 1


title: Atg5 deficient_IFNγ_replicate2

description: Bone marrow derived macrophages


title: NB4 leukemic cells, MycD+RA, replicate 3

source_name: MycD+RA


title: Transcriptional profiling of B.bifidum PRL2010 at different growth phases (late exponential phase)

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

country: Italy

institute: University of Parma

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of Labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20' at 95 °C Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20). - wash with PBST was solution (2X PBS, 0.1% Tween-20). - 2 washes with 2X PBS

scan_protocol: Scanning was performed on InnoScan 700 (Innopsys) scanner. Laser was set at 33% power and PMT at 650.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software and a quantile normalization of data was performed using Combimatrix Blist v0.6 software

organism: Bifidobacterium bifidum

source_name: B.bifidum grown anaerobically in the Man-Rogosa-Sharp (MRS)

label_protocol: Five µg of the same pool of total RNA were labeled using RNA Ampulse amplification and labeling kit with Cy5 for Combimatrix arrays (Kreatech Diagnostics, The Netherlands) according to manufacturer instructions.

growth_protocol: B. bifidum PRL2010 was grown anaerobically in the Man-Rogosa-Sharp (MRS) supplemented with 0.05% (w/v) L-cysteine hydrochloride and incubated at 37°C

extract_protocol: Total RNA was isolated using the macaloid acid method and then treated with DNase. Briefly, cell pellets were resuspended in 1 ml of QUIAZOL and placed in a tube containing 0.8 g of glass beads (diameter, 106 μm). The cells were lysed by shaking the mix on a BioSpec homogenizer at 4°C for 2 min (maximum setting). The mixture was then centrifuged at 12,000 rpm for 15 min, and the upper phase containing the RNA-containing sample was recovered. The RNA sample was further purified by phenol extraction and ethanol precipitation according to a previously described method (Sambrook et al., 1989).

tag: b.bifidum strain

tag: agent

value: control


title: NB4 leukemic cells, ARAC+RA, replicate 2

source_name: ARAC+RA


title: Transcriptional profiling of B.bifidum PRL2010 at different growth phases (early stationary phase)


title: NB4 leukemic cells, MycD+RA, replicate 4


title: Transcriptional profiling of B.bifidum PRL2010 at different growth phases (early exponential phase)


title: NB4 leukemic cells, MycD+RA, replicate 2


title: NB4 leukemic cells, RA, replicate 3

source_name: RA


title: Transcriptional profiling of B.bifidum PRL2010 at different growth phases (lag phase)

scan_protocol: Scanning was performed at InnoScan 700 (Inopsis). Laser was set at 33% power and PMT at 650.


title: NB4 leukemic cells, MycD+RA, replicate 1


title: NB4 leukemic cells, RA, replicate 4


title: NB4 leukemic cells, RA, replicate 1


title: polII_rep2

type: genomic

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: polII ChIP-chip K652 cells, rep2

hyb_protocol: see manufacturer's web site www.nimblegen.com

scan_protocol: Scanning perfomed by NimbleGen using NimbleScan

data_processing: Tukey biweight-scaled log2 ratio GFF files were created by NimbleGen.  Replicates were combined into single GFF files by computing average value for each probe across replicates (e.g., log2(mean((value1^2, value2^2, value3^2))) ) then re-scaling all new values by Tukey bi-weight.  Resulting GFF files were used with ACME package for R as described in paper. The matrixdata file was  created by merging all GFF files and NimbleGen .ndf file

molecule: genomic DNA

source_name: polII ChIP DNA

value: adult erythroid cells

tag: chip antibody

value: polII

source_name: Input DNA, K562 cells

value: none, input DNA


title: NLI_rep2

description: NLI ChIP-chip K562 cells, rep2

source_name: NLI ChIP DNA

label_protocol: see manufacturer's web site www.nimblegen.com

value: NLI


title: headkidney_lineK_day3_rep2

city: Liege

first: Leonor

last: Palmeira

address: Bd Colonster 20

department: Faculty of Veterinary Medicine

country: Belgium

institute: University of Liege

hyb_protocol: Hybridization was carried out for 17 h at 65°C. After 17 h, the glass slides were washed with GE Wash Buffer for 1 min at RT and subsequently with GE Wash Buffer 2 for 1 min at 37°C using the Low Input Quick Amp Labeling Kit (Agilent Technologies, USA).

scan_protocol: After washing the glass slides were dried and scanned immediately using the Gene Pix 4000B scanner (Axon Instruments, USA) and the Gene Prix Pro 6.1 software. The data was extracted using the Agilent Feature Extraction software.

data_processing: The data was analyzed in R using the 'limma' package from the Bioconductor project. The single-channel arrays were first background corrected with the normexp method and an offset of 50 and then normalized with a quantile normalization.

organism: Cyprinus carpio

source_name: Head kidney from infected carps (CyHV-3) at day 3 p.i.

label_protocol: Labelling was performed using Cy3 dye according to the Low Input Quick Amp Labeling Kit Protocol (Agilent Technologies, USA).

growth_protocol: Fish from each group were grown in aquaria with UV treated recirculating water and bio-filters. The total capacity of the system was 3 m3 and the water temperature was maintained at 21±1°C. Daily feeding with commercial carp pellets (Aller Aqua, Poland) was applied at 5-3% body weight per day.

extract_protocol: The total RNA was isolated from head kidney samples using the RNeasy Mini Kit (Qiagen, Japan) according to the manufacturer’s instruction.

treatment_protocol: Before sampling, fish were anaesthetised by the use of Propiscin (5ml/L).

tag: line

value: K

tag: weight

value: around 120gr

tag: tissue

value: Head kidney


title: headkidney_lineK_day3_rep1


title: 12-D21-IFNgamma

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Gene expression data from HNECs treated with IFNgamma

hyb_protocol: Following fragmentation and labeling, 3ug of DNA were hybridized for 17 hr at 45C on Huge gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and Gene Level-RMA sketch  as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

extract_protocol: Absolutely RNA® Microprep Kit  extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HNECs were treated with 100 ng/mL IFNgamma for 6 h

tag: sample type

value: Differentiated HNECs cultured in ALI between D15-D21

value: HNECs


title: headkidney_lineR3_day3_rep4


title: headkidney_lineK_day3_rep4


title: headkidney_lineR3_day0_rep1

source_name: Head kidney from non-infected carps (CyHV-3) at day 0.


title: headkidney_lineK_day0_rep4


title: NB4 leukemic cells, empty vector, replicate 1

source_name: empty vector


title: headkidney_lineR3_day0_rep3


title: headkidney_lineR3_day3_rep3


title: headkidney_lineR3_day0_rep4


title: NB4 leukemic cells, empty vector, replicate 4


title: headkidney_lineR3_day3_rep1


title: NB4 leukemic cells, RA, replicate 2


title: headkidney_lineR3_day0_rep2


title: headkidney_lineK_day3_rep3


title: headkidney_lineR3_day3_rep2


title: HUVEC donor 4_CD34-positive fraction

city: Amsterdam

first: Ingeborg

last: Klaassen

address: Meibergdreef 15

department: Ophthalmology

country: Netherlands

institute: AMC

hyb_protocol: Samples were hybridized to Affymetrix HT HG-133+PM 24 Array Plate GeneChips using the Affymetrix standard hybridization protocol.

scan_protocol: Array Plates were scanned using a Gene Titan System.

data_processing: Data was normalized using the RMA method included in the Affy R Bioconductor package.

source_name: HUVEC_CD34-positive fraction

label_protocol: Samples were labeled using the Affymetrix GeneChip 3’ IVT Express kit.

growth_protocol: Primary HUVECs were isolated from umbilical veins by collagenase digestion and routinely grown in M199 basal medium supplemented with 10% human serum, 10% fetal bovine serum and 1% penicillin-streptomycin-glutamine.

treatment_protocol: Primary HUVEC cells were cultured up untill passage 3, isolated and then FACS-sorted by CD34 and divided in CD34-positive and CD34-negative fractions.

tag: donor id

value: donor 4

value: cultured HUVEC cells

tag: passage

value: passage 3


title: polII_rep1

description: polII ChIP-chip K562 cells, rep1

extract_protocol: see manufacturer's web site www.nimblegen.com


title: NB4 leukemic cells, empty vector, replicate 3


title: HUVEC donor 3_CD34-negative fraction

source_name: HUVEC_CD34-negative fraction

value: donor 3


title: HUVEC donor 4_CD34-negative fraction


title: NB4 leukemic cells, empty vector, replicate 2

value: leukemic


title: GATA1_rep2

description: GATA-1 ChIP-chip K562 cells, rep2

source_name: GATA-1 ChIP DNA


title: HUVEC donor 3_CD34-positive fraction


title: GATA1_rep1

description: GATA-1 ChIP-chip K562 cells, rep1


title: HUVEC donor 2_CD34-negative fraction

value: donor 2


title: NLI_rep1

description: NLI ChIP-chip K562 cells, rep1


title: HUVEC donor 2_CD34-positive fraction


title: headkidney_lineK_day0_rep3


title: headkidney_lineK_day0_rep2


title: headkidney_lineK_day0_rep1


title: HUVEC donor 1_CD34-positive fraction

value: donor 1


title: MKN7_EB_No2

status: Public on Jan 04 2012

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

description: Gastric cancer cell line MKN7 infected with recombinant EBV, and cloned, and cultured for 18 weeks.

hyb_protocol: 10 micrograms of fragmented cRNA were hybridised (45degree CelsiusC, 16 hours). Hybridization was controled by use of the GeneChip Eukaryotic Hybridization Control Kit (Affymetrix). Washing and staining was performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v4.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: Genechip analysis was performed using the Affymetrix GeneChip Operating Software v1.3. Signal value was calculated using MAS5 algorithm with target intensity=100.

source_name: MKN7 infected with recombinant EBV

label_protocol: In vitro transcription was performed on 1 microgram of cDNA using the Enzo BioArray High Yield RNA transcript labelling kit (Enzo Diagnostics). The cRNA was cleaned using RNAeasy clean-up columns (Qiagen). The cRNA was fragmented by heating in 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc.

extract_protocol: Total RNAs were extracted using TRIzol (Invitrogen, Carlsbad, CA). 3 micrograms of total RNA was reverse transcribed using the SuperScript III system for cDNA synthesis (Invitrogen) according to the protocol recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Invitrogen). Double-stranded cDNA was cleaned by phenol:chloroform extraction and the aqueous phase removed by centrifugation through Phase-lock Gel (Eppendorf).

value: gastric cancer


title: control_100pct_2

description: Infinium methylation assay of control_100%_2

hyb_protocol: Bisulphite-converted (EZ DNA methylation kit) DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

scan_protocol: BeadChips were coated and imaged on an Illumina BeadArray Reader.

data_processing: Images were processed with BeadStudio software and background-subtracted beta values were calculated.

label: Cy5, Cy3

source_name: methylation control sample

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted using QIAamp DNA Micro Kit (QIAGEN, Hilden, Germany). For methylation control samples, genomic DNA of human peripheral lymphocyte was amplified by GenomiPhi v2 DNA amplification kit (GE Healthcare Lifescience, Piscataway, NJ), and used as unmethylated (0%) control. GenomiPhi-amplified DNA was methylated by SssI methylase (New England Biolabs, Beverly, MA) and used as fully methylated (100%) control. By mixing the 0% and 100% control samples, partially methylated control samples (25%, 50%, and 75%) were generated.

treatment_protocol: For bisulfite conversion of genomic DNA, we used 500 ng of genomic DNA and followed the manufacturer's protocol for Zymo EZ DNA methylation kit (Zymo Research). The bisulfite-converted DNA was eluted from column in 10uL of elution buffer. For the Infiniium Methylation Assay, 4 uL of bisulfite-converted DNA was used in the whole-genome amplification (WGA) reaction, following the Infinium Methylation Assay amplification and BeadArray protocols.

value: methylation control sample


title: HUVEC donor 1_CD34-negative fraction


title: control_50pct_1

description: Infinium methylation assay of control_50%_1


title: MKN7_EB_No3


title: control_75pct_1

description: Infinium methylation assay of control_75%_1


title: control_100pct_1

description: Infinium methylation assay of control_100%_1


title: MKN7_EB_minus

description: Mock gastric cancer cell line MKN7 cultured for the same period of 18 weeks without EBV infection.

source_name: MKN7 without EBV infection


title: control_50pct_2

description: Infinium methylation assay of control_50%_2


title: 4-pre

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: diaphargm muscle, first biopsy was taken as the diaphragm was exposed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station F-450.

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data were analyzed with dChip using perfect-match only analysis settings and global scaling as normalization method.

label_protocol: 200ng total RNA was labeled using GeneChip® 3' IVT Express Kit according to manufacturer's instructions

growth_protocol: All patients underwent a scheduled cardiothoracic surgery. Hypothermic CPB (temperatures of 18-24°C) with a retro-grade blood cardioplegia was used in all patients. Hypothermic circulatory arrest was performed. Mean arterial pressure of 50-80 mmHg and blood flows of 2.4-2.8 • min-1 • m-2 were maintained during CPB. The hematocrit was maintained at >20% during CPB.

extract_protocol: RNA was extracted using Qiagen RNeasy Fibrous Tissue Mini Kit according to manufacturer's instructions.

treatment_protocol: Two full-thickness biopsy specimens (approximately 6 mm diameter) were taken from the antero-lateral aspect of the right and left diaphragm near the costal margin during surgery. The first biopsy was obtained immediately after exposing the diaphragm; the second biopsy was obtained as late in surgery as possible. Each specimen was stabilized by using RNAlater® solution (Ambion Inc. Austin, TX, USA) and then transferred to liquid nitrogen and stored at -80°C until for microarray analysis.

tag: age

tag: gender

value: Male

tag: body weight

tag: height


title: control_75pct_2

description: Infinium methylation assay of control_75%_2


title: control_25pct_1

description: Infinium methylation assay of control_25%_1


title: control_25pct_2

description: Infinium methylation assay of control_25%_2


title: 6-post

description: Cardio-pulmonary bypass time was 255 mins

source_name: diaphargm muscle, second biopsy was taken as late in the surgery (in-between 7 hours 15 mins)


title: 3-post

description: Cardio-pulmonary bypass time was 266 mins

source_name: diaphargm muscle, second biopsy was taken as late in the surgery (in-between 2 hours 30 mins)

value: 87 kg


title: 1-post

description: Cardio-pulmonary bypass time was 243 mins

source_name: diaphargm muscle, second biopsy was taken as late in the surgery (in-between 4 hours 15 mins)


title: 3-pre

source_name: diaphargm muscle, first biopsy was taken as the diaphragm was exposed


title: 6-pre


title: 1-pre


title: 4-post

description: Cardio-pulmonary bypass time was 159 mins

source_name: diaphargm muscle, second biopsy was taken as late in the surgery (in-between 4 hours 30 mins)


title: MKN7_EB_No1

tag: cell line


title: 5-post

description: Cardio-pulmonary bypass time was 166 mins

source_name: diaphargm muscle, second biopsy was taken as late in the surgery (in-between 5 hours 45 mins)


title: areaX_singer_bird14

city: Los Angeles

first: Austin

middle: T

last: Hilliard

state: CA

address: 610 Charles E Young Dr East

institute: UCLA

description: Gene expression in area X of adult male zebra finch after 2hr of singing

hyb_protocol: Cy3-labeled cRNA (1.65 ng) from each sample was hybridized to Agilent Custom Zebra Finch microarrays using the manufacturer's established procedures for the analysis of Eukaryotic RNA.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan_MicronsPerPixel: 5x5, Dye channel set to Green).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent, protocol GE1-v5_95 and Grid: 019785_D_F_20080327) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. All subsequent pre-processing and analysis was done in the R software environment (www.r-project.org). R functions written by ATH for array pre-processing are available at www.ibp.ucla.edu/research/white/code.html. Area X and VSP samples were pre-processed separately, but identically, as follows. Control probes were removed and probes with raw fluorescence values >3 standard deviations (SD) away from the mean of measurements across all samples for that probe were removed. Then, samples were hierarchically clustered on the basis of inter-array correlations to identify array outliers. For area X, all arrays fell within 2SD of the mean IAC (0.977), and were retained for a total n=26 (18 singing birds and 8 non-singers). One VSP sample (1V) was >3SD from the mean VSP IAC (0.974) and was removed, leaving total n=25 (18 singing birds and 7 non-singers). Arrays were quantile normalized, and a preliminary area X gene co-expression network was built using all 42,921 probes to assess overall connectivity. From this network, the 20,000 probes with the highest connectivity were retained for the main analysis. Also, 104 probes for genes of interest that were not among the 20,000 most connected were re-inserted, thus a total of 20,104 probes were used in the final network construction. These genes of interest included autism associated genes such as CNTNAP2, Parkinson's disease related genes including PARK2, PARK7, and SNCA, and genes for dopamine receptors, e.g. DRD2 and DRD5.
*NOTE: A principal components analysis of gene expression data from all samples in this study revealed that the area X and VSP samples segregated cleanly into 2 distinct groups, except for the samples from bird 21 where the area X sample (21X) grouped with all of the other VSP samples, and the VSP sample (21V) grouped with all of the other area X samples. Average linkage hierarchical clustering (based on inter-array correlations) re-iterated this finding, suggesting that the samples from bird 21 may have been mislabeled, thus they were excluded from further analysis.

organism: Taeniopygia guttata

source_name: bilateral area X, 2hr, singer

label_protocol: 200 ng of total RNA was converted into labeled cRNA with nucleotides coupled to Cy3 using the Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer's protocol.

extract_protocol: Area X and VSP tissue punches were removed from RNAlater and processed separately for each bird (27 birds; 54 samples) using an optimized version of the Qiagen RNeasy Micro Kit protocol for purification of total RNA from animal and human tissues. Modifications were: substitution of QIAzol lysis reagent for beta-mercaptoethanol, and additional washes in the RW1 and RPE buffers. Tissue punches were homogenized in QIAzol with a handheld homogenizer (Kontes, Fisher Scientific, Pittsburgh, PA), incubated with chloroform, centrifuged, and the aqueous supernatant retrieved for further processing. Following purification, 1 ul of each eluted sample was analyzed for RNA purity and quantity using a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE), and quality using an Agilent Bioanalyzer (Santa Clara, CA).

treatment_protocol: After undergoing the behavioral protocol, birds were decapitated, and brains rapidly extracted and frozen, then stored at ␣80°C until use. Tissue punches of area X and VSP were obtained at the same plane of section and histologically validated for anatomical precision. Area X and VSP punches were stored separately in RNAlater (Qiagen, Valencia, CA) at -20°C until RNA isolation.

tag: sample id

value: male

tag: age (days)

tag: number of motifs sung

tag: mean pitch

tag: mean frequency modulation

tag: mean wiener entropy

tag: mean pitch goodness


title: control_0pct_2

description: Infinium methylation assay of control_0%_2

tag: cell type


title: VSP_singer_bird20

description: Gene expression in VSP of adult male zebra finch after 2hr of singing

source_name: bilateral VSP, 2hr, singer


title: 5-pre


title: areaX_singer_bird26


title: AGS_EB_No3

description: Infinium methylation assay of AGS_EB#3

source_name: Gastric cancer cell line, rEBV infection(+)

value: AGS

value: Gastric cancer cell line


title: control_0pct_1

description: Infinium methylation assay of control_0%_1


title: AGS_EB_No1

description: Infinium methylation assay of AGS_EB#1


title: VSP_singer_bird14


title: areaX_singer_bird20


title: AGS_EB_No2

description: Infinium methylation assay of AGS_EB#2


title: GH4C1 cells expressing POU1F1(R271W), Biological rep.3

city: Marseille

first: Jean-Louis

last: Franc

address: Bd J. Moulin

institute: CNRS

description: Gene expression data from cells expressing POU1F1(R271W)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on an Affymetrix microarray Rat 230 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

organism: Rattus norvegicus

source_name: GH4C1 cells expressing POU1F1(R271W)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from1 ug total RNA.

growth_protocol: GH4C1 somatolactotrope pituitary cells were grown in Ham’s F10 medium supplemented with 15% horse serum and 2.5% fetal calf serum

extract_protocol: total RNA was isolated with a nucleospin RNA II kit (Macherey-Nagel)

treatment_protocol: For the transduction experiments, GH4C1 cell cultures plated in 12-well plates (10 x 104 cells/well) were supplemented with lentiviral particles containing medium in the presence of 2 µg/ml polybrene at a multiplicity of infection (MOI) of 5. After a 16-h incubation period, the cells were washed and grown in regular medium for 4 days.

value: GH4C1 cells (somatolactorope cells)


title: GH4C1 cells expressing POU1F1(R271W), Biological rep.1


title: AGS_EB_minus

description: Infinium methylation assay of AGS_EB(-)

source_name: Gastric cancer cell line, rEBV infection(-)


title: VSP_singer_bird26


title: areaX_singer_bird6


title: VSP_singer_bird6


title: GH4C1 cells expressing POU1F1(R271W), Biological rep.2


title: GH4C1 cells, Biological rep.2

description: Gene expression data from control cells

source_name: GH4C1 cells control


title: GH4C1 cells, Biological rep.3

description: Gene expression data from control cells


title: MKN7_EB_No2

description: Infinium methylation assay ofMKN7_EB#2


title: VSP_singer_bird11


title: areaX_singer_bird11


title: MKN7_EB_No1

description: Infinium methylation assay ofMKN7_EB#1


title: Re04 vs Re05-979

city: College Park

first: Monica

last: Pava-Ripoll

address: 4112 Plant Sciencies Bldg

department: Entomology

institute: University of Maryland

description:
Biological replicate 3 out of 3.
Platform GPL8193

hyb_protocol: Hybridization of 5 mg labeled cDNA to Metarhizium robertsii arrays was conducted following the recommendations of the array manufacturer. Gamma amino propyl II-coated glass slides (Corning Incorporated, Corning, N.Y.) were used.

scan_protocol: Hybridized slides were scanned at the University of Maryland Biotechnology Institute (http://www.umbi.umd.edu/carb/core-facilities/microarray-services/facility.php) using the Axon 4200 microarray scanner (Molecular Devices).

data_processing: To obtain differential signal expressions, the TIFF images generated (2 image files per hybridized slide) were analyzed using the Spotfinder program (http://www.pfgrc.tigr.org/tools.shtml.  Data was then normalized using LOWESS (LOcally WEighted Scatterplot Smoothing) technique with MIDAS software (http://www.pfgrc.tigr.org/tools.shtml. MIDAS output files project included standard deviation regularization, low intensity filter and in-slide replicate analysis.

organism: Metarhizium robertsii

source_name: Fungal mycellium, Field recovered, Re04

label_protocol: Total RNA was amplified using the Ovation RNA Amplification system (NuGen, Inc.)Total RNA was immediately extracted from the samples using the Qiagen RNeasy Mini kit, according to manufacturer's instructions.

growth_protocol: Fungal Mycellium grown for 30 h at 27C in Saboreaud dextrose broth (SDB)

extract_protocol: Total RNA was immediately extracted from the samples using the Qiagen RNeasy Mini kit and treated with DNase I, according to manufacturer's instructions.

treatment_protocol: Hybridization using Loop design where every time point is compared to the next one (Time0h-Rep1/Time1h-Rep1).

tag: strain

value: ARSEF 2575

tag: tissue

value: Fungal Mycellium grown for 30 h at 27C

value: field recovered Re04

source_name: Fungal mycellium, Field recovered, Re05

value: field recovered Re05


title: Re05 vs Control-962

description:
Biological replicate 2 out of 3.
Platform GPL8193

tag: sample type

source_name: Fungal mycellium, lab grown strain

value: lab grown


title: Re05 vs Control-963


title: Re05 vs Control-961

description:
Biological replicate 1 out of 3.
Platform GPL8193


title: MKN7_EB_No3

description: Infinium methylation assay ofMKN7_EB#3


title: Re04 vs Re05-919


title: VSP_singer_bird25


title: GH4C1 cells, Biological rep.1

description: Gene expression data from control cells


title: Re02 vs Re03-968

source_name: Fungal mycellium, Field recovered, Re02

value: field recovered Re02

source_name: Fungal mycellium, Field recovered, Re03

value: field recovered Re03


title: Re02 vs Re03-924


title: Re03 vs Re04-964


title: areaX_singer_bird25


title: VSP_singer_bird16


title: KT

description: Infinium methylation assay of KT

source_name: Gastric cancer xenograft, EBV(+)

value: Gastric cancer xenograft


title: Re03 vs Re04-971


title: Re03 vs Re04-965


title: Re02 vs Re03-918


title: Re04 vs Re05-912


title: Re01 vs Re02-967

source_name: Fungal mycellium, Field recovered, Re01

value: field recovered Re01


title: SNU719

description: Infinium methylation assay of SNU719

source_name: Gastric cancer cell line, EBV(+)


title: Re01 vs Re02-923


title: AGS_p

description: Infinium methylation assay of AGS_p

source_name: Gastric cancer cell line, EBV(-)


title: Re01 vs Re02-925


title: MKN7_EB_minus

description: Infinium methylation assay of MKN7_EB(-)


title: Control vs Re01-915-966

description:
Biological replicates 1 and 2 out of 3.
Platform GPL8193


title: Control vs Control-980

description:
Biological replicate 5 out of 5. Lab grown Metarhizium robertsii ARSEF 2575-GFP.
Platform GPL8193


title: areaX_singer_bird16


title: areaX_singer_bird19


title: VSP_singer_bird22


title: Control vs Re01-914


title: Control vs Control-905-906

description:
Biological replicates 1 and 2 out of 5. Lab grown Metarhizium robertsii ARSEF 2575-GFP.
Platform GPL8193


title: VSP_singer_bird19


title: GC290T

description: Infinium methylation assay of GC290T

source_name: Gastric cancer tissue, EBV(+)

value: Gastric cancer tissue


title: Control vs Control-913-960

description:
Biological replicates 3 and 4 out of 5. Lab grown Metarhizium robertsii ARSEF 2575-GFP.
Platform GPL8193


title: MKN7_p

description: Infinium methylation assay of MKN7_p


title: areaX_singer_bird22


title: VSP_singer_bird12


title: DOX, rep3

city: Nashville

first: Justin

middle: M

last: Balko

state: TN

address: 777 Preston Research Building

department: Medicine

institute: Vanderbilt University

description: gene expression data from organoids treated with DOX

hyb_protocol: Affy-169 : 300.0 ng at 45 degree_C during 17 hours

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

data_processing: Data were processed using RMA normalization in R using the affy package and the justRMA function

source_name: ErbB3 DOX-KO

growth_protocol: The mammary glands of  ErbB3 DOX-KO mice were harvested under sterile conditions, minced, and digested in 1 mg/ml collagenase/0.3 mg/ml hyaluronidase (Stem Cell Technologies, Vancouver, Canada). Organoids were processed according to protocol provided by Stem Cell Technologies, resuspended in growth factor-reduced Matrigel (BD Life Sciences) and plated in 8-well chamber slides.

treatment_protocol: Mammary epithelial organoids harvested from age-matched female mice were plated in growth factor-reduced Matrigel ± 5 µM DOX, cultured for 14 d

value: FVB

tag: genotype/variation

value: ErbB3 DOX-KO

value: Mammary epithelial organoids

tag: treatment

value: DOX


title: GC277T

description: Infinium methylation assay of GC277T


title: GC287T

description: Infinium methylation assay of GC287T


title: GC195T

description: Infinium methylation assay of GC195T

source_name: Gastric cancer tissue, EBV(-)


title: VSP_non-singer_bird7

description: Gene expression in VSP of adult male zebra finch after 2hr of no singing

source_name: bilateral VSP, 2hr, non-singer

tag: gender

value: male


title: GC280T

description: Infinium methylation assay of GC280T


title: areaX_singer_bird12

source_name: bilateral area X, 2hr, singer


title: control, rep2

description: gene expression data from organoids not treated with DOX

value: control


title: areaX_non-singer_bird7

description: Gene expression in area X of adult male zebra finch after 2hr of no singing

source_name: bilateral area X, 2hr, non-singer


title: DOX, rep2


title: DOX, rep1


title: GC45T

description: Infinium methylation assay of GC45T


title: control, rep1


title: control, rep3


title: GC254T

description: Infinium methylation assay of GC254T


title: areaX_singer_bird24

description: Gene expression in area X of adult male zebra finch after 2hr of singing


title: GC11T

description: Infinium methylation assay of GC11T


title: GC131T

description: Infinium methylation assay of GC131T


title: Yy1_siRNA_rep1

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

department: Experimental Oncology

institute: European Institute of Oncology

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix cat #900720) is used  to prepare the Hybridization Cocktail. The kit contains mix for target  dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled  control oligo B2 and bioB, bioC, bioD and Cre controls (Affymetrix cat  #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM,  respectively. These control oligos serve as positive controls for  hybridization. Biotin-labeled sense targets were diluted in hybridization  buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes.  Hybridization cocktails were incubated at 45 °C for 5 minutes and centrifuged  at maximum speed for 1 minute prior to loading into the GeneChip® array  cartridge.  Hybridizations were performed for 16 h at 45 °C in a rotisserie oven at 60  RPM. Upon hybridization, GeneChip cartridges were washed and stained with  GeneChip Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station  450 following the FS450_0007 standard protocol. The cartridge is then loaded  into the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip arrays are scanned using default parameters. Affymetrix GeneChip  Command Console software (AGCC) was used to acquire GeneChip images and  generate .DAT and .CEL files.

data_processing: Data were RMA normalized and expression changes determined as fold difference between the average signals of Yy1 vs Ctrl datasets. P-values were determined by ANOVA [The fold-change data is provided as a Series supplementary file].

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of totRNA.  Double stranded cDNA synthesis and related cRNA amplification was performed  with Ambion® WT Expression Kit (Ambion, Austin, TX). cRNA was reverse  transcribed to cDNA fragmented and terminal labeled with Affymetrix GeneChip®  WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA). All steps of the  protocol were performed according to manufacturer’s specifications. Efficacy  of fragmentation procedure was checked on Agilent Bioanalyzer 2100.

growth_protocol: ES cell lines were grown on 0.1% gelatinaized tissue culture dishes in DMEM in presence of  15% Serum and Leukemia inhibitory factor.

extract_protocol: Total RNA was extracted in TRIzol (invitrogen) and cleaned -up with RNAesy Quiagen purification kit.

value: embryonic stem cells

value: transfected with yy1-specific siRNA


title: CTRL_siRNA_rep1

value: transfected with scrampled-control siRNA


title: Tet1-KD ES cells siRNA #1 48hr, rep2

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

hyb_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hours. 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to Affymetrix 430 2.0 array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

data_processing: Data was processed by performing background correction, quantile normalization, and calculation of expression set summaries using the Robust Multichip Average (RMA) protocol (Irizarry et al. (2003); Biostatistics 4: pages 249-264) as implemented in the affy packge from Bioconductor (http://www.bioconductor.org). Gene-specific probesets were constructed using the Entrez Gene – centric custom CDF, version 13 (Dai et al. (2005); Nucl Acids Res 33: e175).  Log-scale data was further normalized by 1) setting the per-sample median to 6.5 and 2) subtracting the per-gene median.

source_name: E14Tg2a Embryonic Stem Cells

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen)

tag: transfection

value: Tet1 siRNA #1


title: Yy1_siRNA_rep2


title: CTRL_siRNA_rep2


title: VSP_non-singer_bird15


title: VSP_singer_bird24

source_name: bilateral VSP, 2hr, singer


title: Tet1-KD ES cells siRNA #1 48hr, rep1


title: GC250T

description: Infinium methylation assay of GC250T


title: areaX_non-singer_bird15


title: VSP_singer_bird9


title: Tet1-KD ES cells siRNA #2 96hr, rep2

value: Tet1 siRNA #2


title: GC219T

description: Infinium methylation assay of GC219T


title: GC214T

description: Infinium methylation assay of GC214T


title: Tet1-KD ES cells siRNA #1 96hr, rep2


title: Control ES cells 96hr, rep1

value: control siRNA


title: Control ES cells 96hr, rep2


title: areaX_singer_bird9


title: Tet1-KD ES cells siRNA #1 96hr, rep1


title: Tet1-KD ES cells siRNA #2 96hr, rep1


title: VSP_non-singer_bird4


title: VSP_non-singer_bird1

description:
Gene expression in VSP of adult male zebra finch after 2hr of no singing

This sample (V1) not included in final analysis (see Data processing for further explanation)


title: areaX_non-singer_bird4


title: GC177T

description: Infinium methylation assay of GC177T


title: VSP_non-singer_bird18


title: GC153T

description: Infinium methylation assay of GC153T


title: areaX_singer_bird3


title: VSP_singer_bird3

description: Gene expression in VSP of adult male zebra finch after 2hr of singing


title: GC194T

description: Infinium methylation assay of GC194T


title: areaX_non-singer_bird18


title: GC203T

description: Infinium methylation assay of GC203T


title: GC141T

description: Infinium methylation assay of GC141T


title: areaX_non-singer_bird1


title: GC122T

description: Infinium methylation assay of GC122T


title: GC136T

description: Infinium methylation assay of GC136T


title: areaX_singer_bird5


title: GC151T

description: Infinium methylation assay of GC151T


title: areaX_non-singer_bird21

description:
Gene expression in area X of adult male zebra finch after 2hr of no singing

This sample (X21) not included in final analysis (see Data processing for further explanation)


title: VSP_non-singer_bird21

description:
Gene expression in VSP of adult male zebra finch after 2hr of no singing

This sample (V21) not included in final analysis (see Data processing for further explanation)


title: GC24T

description: Infinium methylation assay of GC24T


title: VSP_singer_bird17


title: GC64T

description: Infinium methylation assay of GC64T


title: GC121T

description: Infinium methylation assay of GC121T


title: GC140T

description: Infinium methylation assay of GC140T


title: GC18T

description: Infinium methylation assay of GC18T


title: GC264T

description: Infinium methylation assay of GC264T


title: GC3T

description: Infinium methylation assay of GC3T


title: GC12T

description: Infinium methylation assay of GC12T


title: GC216T

description: Infinium methylation assay of GC216T


title: GC8T

description: Infinium methylation assay of GC8T


title: GC217T

description: Infinium methylation assay of GC217T


title: GC209T

description: Infinium methylation assay of GC209T


title: areaX_singer_bird2


title: areaX_non-singer_bird23


title: GC226T

description: Infinium methylation assay of GC226T


title: areaX_singer_bird17


title: VSP_singer_bird2


title: VSP_singer_bird13


title: areaX_singer_bird8


title: VSP_non-singer_bird27


title: GC215T

description: Infinium methylation assay of GC215T


title: areaX_non-singer_bird10


title: GC65T

description: Infinium methylation assay of GC65T


title: VSP_non-singer_bird23


title: GC270T

description: Infinium methylation assay of GC270T


title: VSP_non-singer_bird10


title: VSP_singer_bird8


title: GC17T

description: Infinium methylation assay of GC17T


title: areaX_non-singer_bird27


title: GC200T

description: Infinium methylation assay of GC200T


title: TßRII-cKO Total skin keratinocytes set #2

city: New York

first: Naoki

last: Oshimori

state: New York

address: 1230 York Avenue

institute: The Rockefeller University/HHMI

description: Gene expression data from total skin keratinocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G Scanner.

data_processing: The data were analyzed with MAS5.0 method using Gene Pattern analysis settings and median scaling as normalization method.

source_name: Mouse back skins

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: HG and bulge HFSCs and Rosa26YFP+ total skin keratinocytes were FACS-purifed from the back skins of indicated ages of mice

treatment_protocol: No treatment

value: Female

tag: age

value: mixed C57BL/6 and CD1

value: TßRII-cKO

tag: sorting markers

value: Rosa26-YFP, P-cadherin, CD34

value: total skin keratinocytes


title: GC225T

description: Infinium methylation assay of GC225T

value: Gastric cancer tissue


title: GC87T

description: Infinium methylation assay of GC87T


title: GC97T

description: Infinium methylation assay of GC97T


title: GC125T

description: Infinium methylation assay of GC125T


title: TßRII-cKO Hair Germ set #2

description: Gene expression data from aberrantly quiescent HG HFSCs in TßRII-cKO mice


title: TßRII-cKO Total skin keratinocytes set #1


title: TßRII-cKO Bugle set #2

description: Gene expression data from aberrantly quiescent bulge HFSCs in TßRII-cKO mice


title: TßRII-Het Total skin keratinocytes set #2

value: TßRII-Het


title: GC82T

description: Infinium methylation assay of GC82T


title: TßRII-Het Hair Germ set #2

description: Gene expression data from activated HG HFSCs

value: activated HG HFSCs


title: TßRII-cKO Hair Germ set #1

description: Gene expression data from quiescent HG HFSCs

value: quiescent HG HFSCs


title: GC94T

description: Infinium methylation assay of GC94T


title: GC52T

description: Infinium methylation assay of GC52T


title: TßRII-Het Total skin keratinocytes set #1


title: TßRII-Het Bugle set #2

description: Gene expression data from activated bulge HFSCs

value: activated bulge HFSCs


title: GC256T

description: Infinium methylation assay of GC256T


title: TßRII-Het Hair Germ set #1


title: GC75T

description: Infinium methylation assay of GC75T


title: GC063T

description: Infinium methylation assay of GC063T


title: GC191T

description: Infinium methylation assay of GC191T


title: TßRII-cKO Bugle set #1

description: Gene expression data from quiescent bulge HFSCs

value: quiescent bulge HFSCs


title: GC092T

description: Infinium methylation assay of GC092T


title: GC123T

description: Infinium methylation assay of GC123T


title: TßRII-Het Bugle set #1


title: NGM_No1

description: Infinium methylation assay of NGM#1

source_name: Normal gastric mucosa, purchased genomic DNA

value: Normal gastric mucosa


title: GC39T

description: Infinium methylation assay of GC39T


title: GC159T

description: Infinium methylation assay of GC159T


title: PBC_No2

description: Infinium methylation assay of PBC#2

source_name: Peripheral blood cell, purchased genomic DNA

value: Peripheral blood cell


title: NGM_No2

description: Infinium methylation assay of NGM#2


title: Serum sample 870

status: Public on Jan 03 2012

type: protein

city: Perugia

first: tania

last: dottorini

address: via del Giochetto

department: Dept. Exp.Medicine and Bichem. Sci.

institute: University of Perugia

description: no additional information

hyb_protocol: Printed slides were blocked with PBS containing 2% BSA for 1 h at room temperature. Slides were then incubated with serum samples (100 µl) for 60 minutes at 37°C. To reveal bound IgE, the slides were incubated with a secondary mouse monoclonal antibody directed against human IgE (0.14 µg/ml - 100µl) for 45 minutes at 37°C, followed by an incubation with anti-mouse IgG HRP conjugated antibody (1.6 µg/mL - 100µl) for 45 minutes at 37°C and finally incubated with tyramide-Alexa 555 (TSA™ Kit #42 *with HRP—streptavidin and Alexa Fluor® 555 tyramide* *50-150 slides*) (Invitrogen) diluted 1:200 (100µl), for 15 minutes at 37°C. Slides were dried at 37°C before measuring the fluorescence signal.

scan_protocol: The processed slides were scanned using a fluorescence-detecting scanner ScanArray™ Gx and the images were generated with the ScanArray™ software provided by Perkin Elmer Life Sciences Inc. All the slides were scanned under identical settings: 90 % laser power and 60 % photomultiplier gain.

data_processing: Quantification of bound IgE: The fluorescence signal was acquired using ProScanArray Express™ version 3.0 software. PMC reading values of individual spots were corrected against the internal negative control to identify signals above background. Duplicate measurements of individual allergens were utilized. The signal collected from the allergens was interpolated with an external calibration curve to obtain the IU/ml value (see supplementary file GSE20020_IU_ml values.txt on the GSE20020 record), and translated into a Class Score by plotting the data in a standard reactivity scale (see Sample data tables). Class Score values: CLASS 0 (less than 0.35 IU/ml); CLASS 1 (0.35-0.7 IU/ml); CLASS 2 (0.71-3.5 IU/ml); CLASS 3 (3.51-17.5 IU/ml); CLASS 4 (17.51-50 IU/ml); CLASS 5 (50.01-100 IU/ml).

label: Alexa 555

molecule: protein

source_name: Human sera

label_protocol: TSA™ Kit #42 *with HRP—streptavidin and Alexa Fluor® 555 tyramide* *50-150 slides* (Invitrogen)

extract_protocol: At the recruitment sessions, each subject was interviewed, disease status was ascertained by physical examination, permission was asked to access personal health records, and blood samples were collected

tag: fluid

value: Human serum

value: F

tag: clinical status

value: asthmatic

tag: eczema

value: positive

tag: conjunctivitis

tag: rhinitis


title: Serum sample 869

description: no additional information

value: non-asthmatic

value: negative


title: Serum sample 868

description: no additional information

value: M


title: Serum sample 861

description: no additional information


title: Serum sample 862

description: no additional information


title: Serum sample 871

description: no additional information

value: undefined diagnosis


title: Serum sample 872

description: no additional information


title: PBC_No1

description: Infinium methylation assay of PBC#1


title: Serum sample 860

description: no additional information


title: Serum sample 866

description: no additional information


title: Serum sample 863

description: no additional information


title: Serum sample 865

description: no additional information


title: Serum sample 864

description: no additional information


title: Serum sample 867

description: no additional information


title: Serum sample 857

description: no additional information


title: Serum sample 855

description: no additional information


title: Serum sample 858

description: no additional information


title: Serum sample 852

description: no additional information


title: Serum sample 854

description: no additional information


title: areaX_singer_bird13

tag: sample id

value: male

tag: age (days)

tag: number of motifs sung

tag: mean pitch

tag: mean frequency modulation

tag: mean wiener entropy


title: Serum sample 851

description: no additional information


title: Serum sample 850

description: no additional information


title: Serum sample 849

description: no additional information


title: Serum sample 848

description: no additional information


title: Serum sample 856

description: no additional information


title: Serum sample 847

description: no additional information


title: Serum sample 846

description: no additional information


title: Serum sample 845

description: no additional information


title: Serum sample 853

description: no additional information


title: Serum sample 840

description: no additional information


title: Serum sample 841

description: no additional information


title: Serum sample 842

description: no additional information


title: Serum sample 838

description: no additional information


title: Serum sample 844

description: no additional information


title: Serum sample 843

description: no additional information


title: Serum sample 839

description: no additional information


title: Serum sample 836

description: no additional information


title: Serum sample 859

description: no additional information


title: Serum sample 834

description: no additional information


title: Serum sample 835

description: no additional information


title: Serum sample 832

description: no additional information


title: Serum sample 833

description: no additional information


title: Serum sample 828

description: no additional information


title: Serum sample 831

description: no additional information


title: Serum sample 837

description: no additional information


title: Serum sample 827

description: no additional information


title: Serum sample 824

description: no additional information


title: Serum sample 823

description: no additional information


title: Serum sample 825

description: no additional information


title: Serum sample 822

description: no additional information


title: Serum sample 819

description: no additional information


title: Serum sample 821

description: no additional information


title: Serum sample 829

description: no additional information


title: Serum sample 818

description: no additional information


title: Serum sample 820

description: no additional information


title: Serum sample 816

description: no additional information


title: Serum sample 830

description: no additional information


title: Serum sample 814

description: no additional information


title: Serum sample 817

description: no additional information


title: Serum sample 815

description: no additional information


title: Serum sample 813

description: no additional information


title: Serum sample 811

description: no additional information


title: Serum sample 826

description: no additional information


title: Serum sample 812

description: no additional information


title: GC192T

description: Infinium methylation assay of GC192T

tag: cell type

value: Gastric cancer tissue


title: Serum sample 810

description: no additional information


title: Serum sample 809

description: no additional information


title: Serum sample 805

description: no additional information


title: Serum sample 806

description: no additional information


title: Serum sample 803

description: no additional information


title: Serum sample 804

description: no additional information


title: Serum sample 793

description: no additional information


title: Serum sample 795

description: no additional information


title: Serum sample 794

description: no additional information


title: Serum sample 798

description: no additional information


title: Serum sample 796

description: no additional information


title: Serum sample 797

description: no additional information


title: Serum sample 799

description: no additional information


title: Serum sample 800

description: no additional information


title: Serum sample 801

description: no additional information


title: Serum sample 802

description: no additional information


title: Serum sample 808

description: no additional information


title: Serum sample 786

description: no additional information


title: Serum sample 785

description: no additional information


title: Serum sample 783

description: no additional information


title: Serum sample 784

description: no additional information


title: Serum sample 782

description: no additional information


title: Serum sample 807

description: no additional information


title: Serum sample 781

description: no additional information


title: Serum sample 791

description: no additional information


title: Serum sample 790

description: no additional information


title: Serum sample 787

description: no additional information


title: Serum sample 788

description: no additional information


title: Serum sample 789

description: no additional information


title: Serum sample 792

description: no additional information


title: Serum sample 780

description: no additional information


title: Serum sample 772

description: no additional information


title: Serum sample 771

description: no additional information


title: Serum sample 773

description: no additional information


title: Serum sample 775

description: no additional information


title: Serum sample 770

description: no additional information


title: Serum sample 768

description: no additional information


title: Serum sample 778

description: no additional information


title: Serum sample 777

description: no additional information


title: Serum sample 779

description: no additional information


title: Serum sample 769

description: no additional information


title: Serum sample 774

description: no additional information


title: Serum sample 767

description: no additional information


title: Serum sample 765

description: no additional information


title: Serum sample 764

description: no additional information


title: Serum sample 759

description: no additional information


title: Serum sample 763

description: no additional information


title: Serum sample 776

description: no additional information


title: Serum sample 760

description: no additional information


title: Serum sample 761

description: no additional information


title: Serum sample 766

description: no additional information


title: Serum sample 762

description: no additional information


title: Serum sample 758

description: no additional information


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description: no additional information


title: Serum sample 187

description: no additional information


title: Serum sample 181

description: no additional information


title: Serum sample 180

description: no additional information


title: Serum sample 190

description: no additional information


title: Serum sample 185

description: no additional information


title: Serum sample 177

description: no additional information


title: Serum sample 175

description: no additional information


title: Serum sample 173

description: no additional information


title: Serum sample 176

description: no additional information


title: Serum sample 183

description: no additional information


title: Serum sample 182

description: no additional information


title: Serum sample 171

description: no additional information


title: Serum sample 172

description: no additional information


title: Serum sample 170

description: no additional information


title: Serum sample 168

description: no additional information


title: Serum sample 167

description: no additional information


title: Serum sample 169

description: no additional information


title: Serum sample 174

description: no additional information


title: Serum sample 162

description: no additional information


title: Serum sample 165

description: no additional information


title: Serum sample 161

description: no additional information


title: Serum sample 164

description: no additional information


title: Serum sample 163

description: no additional information


title: Serum sample 166

description: no additional information


title: Serum sample 282

description: no additional information


title: Serum sample 160

description: no additional information


title: Serum sample 159

description: no additional information


title: Serum sample 151

description: no additional information


title: Serum sample 157

description: no additional information


title: Serum sample 155

description: no additional information


title: Serum sample 153

description: no additional information


title: Serum sample 152

description: no additional information


title: Serum sample 150

description: no additional information


title: Serum sample 156

description: no additional information


title: Serum sample 149

description: no additional information


title: Serum sample 148

description: no additional information


title: Serum sample 147

description: no additional information


title: Serum sample 146

description: no additional information


title: Serum sample 158

description: no additional information


title: Serum sample 143

description: no additional information


title: Serum sample 142

description: no additional information


title: Serum sample 154

description: no additional information


title: Serum sample 144

description: no additional information


title: Serum sample 138

description: no additional information


title: Serum sample 145

description: no additional information


title: Serum sample 140

description: no additional information


title: Serum sample 141

description: no additional information


title: Serum sample 139

description: no additional information


title: Serum sample 136

description: no additional information