title: M58

city: Moscow

first: Maia

middle: J

last: Benner

state: Idaho

address: 875 Perimeter Drive

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Samples were hybridized on four 12-plex chips in conjunction with another zebrafish experiment and spread randomly across chips. An 18-hour hybridization was conducted at 42 degrees in a NimbleGen Hybridization System 4 chamber (NimbleGen, Madison, WI).

scan_protocol: The chips were washed and then scanned on a Roche MS200 scanner.

data_processing: The NimbleGen 12-plex zebrafish microarrays used in this study were designed based on the Sanger Zv7 zebrafish genome build. To improve the analysis of our microarray experiment, we created a custom NimbleGen Design File (NDF) that was based on the most current zebrafish genome build (Sanger Zv9), using a custom R script. Probe sequences from the NimbleGen microarray (113,549 probes) were aligned to Ensembl Zv9 transcripts (53,067) using the Sequence Search and Alignment by Hashing Algorithm (SSAHA2; parameters -kmer 13, -skip 2, -seeds 2, -score 12, -cmatch 9, -ckmer 6) [87]. Alignments were filtered based on the following conditions: (probe length – number of mismatches) ≤ 4, no gapped alignments, common strand per transcript (+/-), probes had only one matching gene, ≥ 3 probes per transcript, and only canonical transcripts (15,650 remaining transcripts). NimbleScan software (NimbleGen; Madison, WI) was used to align a chip-specific grid to control features and extract raw intensity data for each probe and each array. Chip images were then visually checked for each array and verified not to contain any significant spatial artifacts. Raw intensity data was then read into the R statistical computing environment and checked for quality. Further, chip intensity distributions, boxplots and hierarchical clusters were compared and checked for any unusual global patterns. Each array was then background corrected and normalized using the quantile normalization procedure and finally each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure. The median Polish procedure is a robust method for summarizing all probes contained within each probeset to a single expression value for each gene taking into account individual probe effects. Probesets with low levels of expression variation across all samples (Interquartile range: IQR < 0.5) were removed from further analysis, reducing the overall number of statistical tests to be performed (3,096 total genes).

organism: Danio rerio

source_name: Transgenic Mosaic 1 adult male zebrafish, midbrain, selenium supplemented

label_protocol: Double-stranded cDNAs were synthesized using Invitrogen's SuperScript cDNA Synthesis Kit with the standard protocol using random hexanucleotide primers (Invitrogen, Carlsbad, CA). cDNAs were fluorescently labeled with Cy3 using the standard NimbleGen Gene Expression Analysis protocol.

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

treatment_protocol: 1-year-old sexually mature adult male zebrafish from two populations (Pargana: P and Transgenic Mosaic 1: T) were fed either deficient (0.46ppmSe), control (1.7ppmSe), or supplemented Se diets (3.1ppmSe) as selenomethionine for 10 weeks.

tag: strain/background

value: Transgenic Mosaic 1

value: midbrain

value: 1 year (sexually mature adult)

tag: Sex

value: male

value: selenium-supplemented diet


title: Normal (H060417N)

status: Public on May 01 2014

type: RNA

city: Incheon

first: Farhan

last: Haq

address: 7-45, Songdo-dong, Yeonsu-gu

country: South Korea

institute: Gachon University

hyb_protocol: Samples passing these QC steps were next end-labeled with a biotinylated nucleoitde using Terminal Deoxynucleotidyl Transferase (TdT). The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).

scan_protocol: After hybridization was complete, the DNA sample was removed from each microarray and replaced with Array Holding Buffer. Arrays were then washed on the Fluidics Station 450 using AGCC software (Affymetrix GeneChip® Command Console, Version 3.2.2) This protocol includes 6 cycles of 5 mixes/cycle with low stringency Wash Buffer A (6X SSPE, 0.01% Tween-20) at 25℃ followed by 24 cycles of 5 mixes/cycle with high stringency Wash Buffer B (0.6X SSPE, 0.01% Tween-20) at 45℃. Binding of the biotinylated targets was detected by incubating the array for 10 min in a Streptavidin–Phycoerythrin (SAPE) solution at 25℃ followed by a post stain wash comprised of 6 cycles of 5 mixes/cycle with Wash Buffer A at 25℃. A second round of staining was then completed using a 10 min incubation in Anti-Streptavidin Antibody Stain Solution at 25℃ followed by a third stain for 10 min in SAPE solution at 25℃ and a final wash consisting of 10 cycles of 6 mixes/cycle with Wash Buffer A at 30℃, filling of the array with Array Holding Buffer, and a hold at 25℃.

data_processing: CNV analysis was performed using the Affymetrix Cytoscan HD platform (CEL files). CNV data were analysed with the Nexus Copy Number software (BioDiscovery, CA, ver. 6.1).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Liver

extract_protocol: Each DNA (250ng gDNA) aliquot was 96 well plate. Then, 24 of the samples on a plate were subjected to treatment with Nsp I restriction enzyme. After inactivation of the restriction enzyme, the sticky ends of the digested DNA were ligated to Nsp I adaptor/primers using T4 ligase. Aliquots from each ligated product were added to four separate plates for PCR amplification using a universal primer. The products of all four PCR reactions for each subject were combined and then purified with purification magnetic beads in 1.5ml microtube. The yield of each amplified DNA sample was assessed by UV spectrophotometry on a microplate reader. Any DNA showing lower than expected yield (≥ 3mg/ml) or an unusual size distribution was flagged and not processed further. Subsequently, each DNA was fragmented between 25 to 125 bp using partial DNase I digestion and the size distribution of the fragmented amplicons assessed by agarose gel electrophoresis (4% agarose in Tris-Acetate-EDTA buffer).

tag: tissue

value: liver


title: Weaned piglets' jejunum Replicate 2

city: Shanghai

first: Lihui

last: Zhu

state: Shanghai

address: 800 Dongchuang Road

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiaotong University

description:
Gene expression in 25d old weaned piglet's jejunum
Weaned-rep2

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Sus scrofa

source_name: Weaned piglets' jejunum

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit (Agilent technologies), following the manufacturer’s instructions. Cy3 was used to label the samples from the control sucking individuals and the weaned animals.

growth_protocol: A total of fourty 21-d old pigs (Duroc × Landrace) from 4 litters (10 piglets per litter) were assigned randomly to control (suckling) and weaning groups on the basis of their litter origins (n = 20/ group). Piglets in control group continued to be nursed by sows, whereas piglets in weaning group were weaned and moved from the farrowing pens to nursery pens without mixing any litters (5 piglets per pen), and had ad libitum access to the basal diet and water with 14.48 MJ/kg DE and 20.50% CP (N × 6.25).

extract_protocol: Total RNA of jejunum tissues was extracted following the Trizol Reagent instructions (Invitrogen), and checked for a RNA integrity number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies).Qualified total RNA was further purified by RNeasy mini kit (Qiagen) and RNase-Free DNase Set (Qiagen). Only those samples that had an OD260/OD280 ratio of approximately 2.0 and showed no degradation (RNA integrity number ≥ 7.0) were used to generate labeled targets.

treatment_protocol: At 25 d of age, 1 piglet closed to the average weight was randomly chosen from each litter, resulting in 4 piglets per treatment. Animals were then anesthetized by intramuscular injection of sodium pentobarbital (50 mg/kg BW) and then euthanized. Jejunal samples, approximately 2 cm in length, were resected from the middle portion of the jejunum, washed in PBS, and frozen in liquid N2 and stored at - 80°C before used for the isolation of total RNA.

value: jejunum

tag: age

value: day 25

tag: protocol

value: weaned


title: HeLa cells 5

city: Paris

first: Suk Min

last: JANG

address: 25 rue du Dr-Roux

department: Biologie Development

country: France

institute: Institut Pasteur

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HeLa_DYRK1A depletion

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) with 100 U/ml penicillin-streptomycin and incubated at 37°C with 7% CO2.

extract_protocol: RNA was extracted using the High Pure RNA Isolation Kit (Roche REF 11 828 665 001).

treatment_protocol: siRNA were transfected into HeLa cells at a final concentration of 50 nM using DharmaFECT1 (T-2001). Cells were harvested three days after transfection.

tag: cell line

value: HeLa

tag: cell type

value: Cervical cancer cells

tag: transfected with

value: siRNA against DYRK1A

tag: genotype/variation

value: depletion of DYRK1A


title: 48h_A_X1(1)

city: Evanston

first: Christian

middle: Paul

last: Petersen

state: IL

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

country: USA

institute: Northwestern University

description: Gene expression in neoblasts after 48h head regeneration

hyb_protocol: Hybridizations were performed according to manufacturerer's protocol

scan_protocol: Scan was performed according to manufacturer's protocol

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Schmidtea mediterranea

source_name: X1 neoblasts, anterior-facing wounds, 48h regeneration, replicate 1

label_protocol: WTA2 whole genome amplification (Sigma) followed by Kreatech labeling with Cy5

growth_protocol: Asexual planarians, strain CIW4 Schmidtea mediterranea, were cultured at 19 degrees in 1x planarian water after amputation of heads and tails.

extract_protocol: RNA was extracted in trizol followed by purification of the aqueous phase using RNAeasy kits. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

treatment_protocol: Tissues ~200 microns from amputation sites were diced and mascerated in 1xCMF (calcium-magnesium free media) with collagenase, labeled with Hoechst dye and propidium iodide, and FACS sorted as the population of G2/S/M cells of high DNA content

tag: strain

value: neoblasts

tag: regeneration type

value: head


title: Tumor (H060362T)

label_protocol: The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).

tag: tumor size

tag: microvascular invasion

value: No

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: M54

tag: strain/background

tag: treatment


title: 0h_A_X1(1)

description: Gene expression in neoblasts after 0h head regeneration

source_name: X1 neoblasts, anterior-facing wounds, 0h regeneration, replicate 1


title: Normal (H060362N)

tag: tissue


title: Normal (H060303N)


title: Tumor (H060272T)

value: Yes


title: LTED

type: genomic

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

hyb_protocol: Purified DNA was amplified and hybridized to Affymetrix promoter tiling array 1.0 by the core facility at EMBL, Heidelberg, Germany.

scan_protocol: standard Affymetrix protocol

data_processing:
data were processed by Model-based Analysis of Tiling-arrays (MAT) software.
control CEL files (MCF7_0hr_1-4) were used for both Samples and are available on the Series record.
bar files are generated by Model-based Analysis of Tiling-arrays (MAT) software.

molecule: genomic DNA

source_name: MCF7 LTED cells MBD pull down

label_protocol: Genomic DNA (20μg in 200μl) was then sonicated to an average size of approximately 300bp (1min at maximum power, interval 0.2 using a CosmoBio Bioruptor). Sonicated DNA (5μg) was then incubated with 5μg of GST–MBD fusion protein [20] or GST alone in a final volume of 200μl pull-down buffer. Reactions were incubated for 2h at 4°C with constant rotation. DNA–protein complexes were then captured by the addition of 100μl of 50% slurry of glutathione agarose beads, with a further incubation at 4°C for 1h. Beads were washed four times with 500μl of pull-down buffer. Bound GST or GST–MBD–DNA complexes were eluted with 10mM glutathione in pull-down buffer. This eluate was purified using a Qiaquick PCR Purification Kit (Qiagen).

growth_protocol: C4-12 cells were routinely maintained in αMEM (Invitrogen Life Technologies) without phenol red supplemented with 5% charcoal/dextran-treated fetal bovine serum (Hyclone), 2 mM glutamine, 100 IU/ml penicillin, 100 μg/ml streptomycin, 10 mM HEPES (Gibco) and 10 μg/ml Insulin. LTED cells were maintained in Improved MEM that was supplemented with 5% charcoal-dextran treated fetal bovine serum (HyClone), 2mM glutamine, 100 IU/ml penicillin, and 100 μg/ml streptomycin. The cells were cultured at 37°C with 5% CO2 in the air.

extract_protocol: Genomic DNA from ~2×106 cells was prepared from cells lysed in guanidine thiocyanate buffer (3.6M guanidine thiocyanate, 0.05% SDS, 50mM Tris, pH 8), the lysate was extracted with phenol/chloroform and then precipitated twice with ethanol.

value: MCF7 LTED

source_name: control MCF7 cells MBD pull down


title: HeLa cells 4


title: HeLa cells 3

value: non-targeting siRNA (siNT)

value: control


title: C412

source_name: MCF7 C4-12 cells MBD pull down


title: Normal (H060264N)


title: M127

source_name: Transgenic Mosaic 1 adult male zebrafish, midbrain, selenium deficient

value: Transgenic Mosaic 1

value: midbrain

tag: age

value: 1 year (sexually mature adult)

tag: Sex

value: male

value: selenium-deficient diet


title: M3

value: selenium-supplemented diet


title: Normal (H060272N)

value: liver


title: Tumor (H060264T)


title: M122


title: HeLa cells 2

tag: cell line

value: HeLa

value: Cervical cancer cells


title: Tumor (H060236T)


title: Tumor (H060617T)


title: Tumor (H060303T)


title: Normal (H060236N)


title: M110

source_name: Pargana adult male zebrafish, midbrain, selenium supplemented

value: Pargana


title: M99

source_name: Transgenic Mosaic 1 adult male zebrafish, midbrain, control

value: control diet


title: HeLa cells 1

tag: cell type


title: M104


title: M63


title: M81


title: Tumor (H060228T)


title: M101


title: M51


title: Normal (H060203N)


title: Normal (H060228N)


title: Effects of swimming on rainbow trout white muscle, Cy5-labeled reference

city: Barcelona

first: Josep

middle: V

last: Planas

address: Av. Diagonal 643

department: Fisiologia i Immunologia (Biologia)

country: Spain

institute: Universitat de Barcelona

hyb_protocol: We used a dye swap experimental design and each sample was hybridized to two microarrays. For the first slide, cDNA from resting and swimming fish was labeled with Cy5 and Cy3 respectively, and for the second array dye assignment was reversed. A total of four slides were used in this study. The slides were pretreated with 1% BSA (fraction V), 5 × SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) at room temperature and hybridized overnight at 60°C in a cocktail containing 1.3 × Denhardt, 3 × SSC, 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA. All chemicals were from Sigma-Aldrich (Madrid, Spain). After hybridization, slides were washed at room temperature in 0.5 × SSC and 0.1% SDS for 15 min, 0.5 × SSC and 0.01% SDS for 15 min, and twice in 0.06 × SSC for 2 and 1 min, respectively.

scan_protocol: Scanning was performed with ScanArray 5000 (GSI Lumonics) and images were processed with GenePix Pro 5.0 (Axon).

data_processing: The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of median background from median signal intensities, the expression ratios (ER) were calculated. Locally weighted non-linear regression (Lowess) normalization was performed, first for the whole slide and then for twelve rows and four columns per slide. The differential expression was assessed by the difference of the mean log2 ER from zero between the slides with reverse labeling (6 spot replicates per gene on each slide, Student's t-test, p < 0.01).

organism: Oncorhynchus mykiss

source_name: Resters

label_protocol: Total RNA from red and white skeletal muscle samples of individual rainbow trout from each group (resting fish, n=8; swimming fish, n=8) was extracted as described before, pooled and labelled with Cy3-dUTP and Cy5-dUTP (GE Healthcare, Barcelona, Spain) using SuperScript III reverse transcriptase (Invitrogen). The cDNA synthesis reaction was performed at 50°C for 2 h in a 20 μl reaction volume, followed with RNA degradation with 0.2 M NaOH at 37°C for 15 min and alkaline neutralization with 0.6 M Hepes. Labeled cDNA was purified with Microcon YM30 (Millipore, Madrid, Spain).

growth_protocol: Juvenile rainbow trout were held in 1000 liter tanks with fresh water in a semi-closed system (10% of water renovation daily) with physical and biological filters, ozone skimmers and continuous aeration at 15oC and a 12 h light–12 h dark photoperiod. Fish with an average weight of 60 g were randomly distributed into four 200 liter circular tanks at a density of 4 kg/m3. Of these four tanks, two were kept in standard rearing conditions, with a water flow of 350 liters/h and vertical water inflow and held the control fish (resting group). The other two tanks (swimming group) were kept in a circular, uniformly distributed flow of 700 liters/h, induced by the perpendicular water entrance at the surface and a submerged water pump at the bottom of the tank, isolated from the free-living area. The shape of the tank prevented the fish from entering a central area of lower velocity, thus guaranteeing similar swimming velocities throughout the experiment. Consequently, water volume and fish density were the same as in the resting group. This design and water flow resulted in a uniformly distributed swimming velocity of 1.3 BL/s, measured with a low-speed mechanical flow meter (General Oceanics, Inc., Miami, FL, USA). All fish were kept in the same semi-closed circuit, guaranteeing that physico-chemical water parameters were the same for both groups

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. The quantity of the isolated RNA was tested spectrophotometrically, while its quality was tested by electrophoresis in agarose gel (1% W/V). Afterwards, cDNA was synthesized from 5 μg DNase-treated (RQ1 DNase, Promega, Barcelona, Spain) total RNA in a 20 μl reaction, using SuperScript III Transcriptase (Invitrogen) and a mix of oligo(dT) (Promega) and random primers (Promega) according to the manufacturer’s protocols. The RNA was stored at -80ºC until use.

treatment_protocol: Fish from the swimming and the resting groups were fed twice daily to apparent satiety with a diet rich in digestible carbohydrates for 30 days. After 30 days, eight fish from the sustained swimming group and eight fish from the resting group were anesthetized and subsequently euthanized by sectioning the spinal cord. Red and white muscle tissues were dissected from regions established previously. Samples were frozen in liquid nitrogen and stored at -80°C for analyses.

value: White muscle

source_name: Swimmers


title: Tumor (H060203T)

value: No


title: Effects of swimming on rainbow trout red muscle, Cy5-labeled reference

value: Red muscle


title: Effects of swimming on rainbow trout white muscle, Cy3-labeled reference


title: Effects of swimming on rainbow trout red muscle, Cy3-labeled reference


title: Tumor (H060115T)

value: Yes


title: M120

source_name: Pargana adult male zebrafish, midbrain, selenium deficient


title: GFP+EpCAM+ cells

city: Melbourne

first: Ed

last: Stanley

state: Victoria

address: Flemington Road

department: Cell Biology

country: Australia

institute: Murdoch Childrens Research Institute

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was analyzed using GenomeStudio Gene Expression Module v1.5.4 (Illumina) using average normalization across all samples, with additional analysis performed using GeneSpring GX software (Agilent Technologies).

source_name: FACS purifed

label_protocol: RNA samples were amplified, labeled and hybridized to the Human HT-12 v3.0 BeadChip (Illumina) at the Australian Genome Research Facility.

growth_protocol: Human embryonic stem cells harbouring GFP sequences inserted into the FOXN1 locus were differentiated according to the protocol described by Soh et al, 2014. Briefly, cells were initially differentiated in BPEL Medium [Ng et al.,3(5):768, 2008, Nature Protocols], supplemented with 150 ng ml-1 human Activin A. On day 5, Activin A-containing BPEL Medium was replaced with BPEL Medium alone. On day 7, EBs were transferred to 96-well flat-bottom adherent plates (BD Falcon) in BEL Medium (Ng et al., 2008) (BPEL lacking PVA). BEL Medium supplemented with 40 ng ml-1 human Keratinocyte Growth Factor (KGF; R&D Systems) was used to replenish the cultures on days 14, 21, 28 and 35.

extract_protocol: Total RNA was prepared using High Pure RNA Isolation Kit (Roche), according to manufacturer’s instructions.

treatment_protocol: At differentiation day 30, cells were isolated by FACS on the basis of FOXN1-GFP and EpCAM expression. This procedure generated three populations: GFP+EpCAM+, GFP-EpCAM+, GFP-EpCAM-

value: Human Embryonic Stem Cells

tag: time point

value: Differentiation Day 30

tag: cell subtype

value: FACS sorted GFP+ EpCAM+ cells


title: Normal (H060115N)


title: Tumor (H060098T)


title: GFP-EpCAM- cells

value: FACS sorted GFP- EpCAM- cells


title: GFP-EpCAM+ cells

value: FACS sorted GFP- EpCAM+ cells


title: E coli 150 mM EMIMCl 60 min 2

city: Emeryville

first: Marijke

last: Frederix

state: CA

address: 5885 Hollis Street

institute: JBEI

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: Escherichia coli DH1

source_name: mid-log phase

label_protocol: Labeling was performed as described in Ouellet et al, 2009, BMC Biotechnology)

growth_protocol: E. coli DH1 was grown to mid-log phase (O.D.600nm 0.6) at 37°C in M9 minimal medium in 250 mL shaken flasks)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis on an agarose gel and concentrations were measured using Nanodrop (Thermo Fischer Scientific, USA).

treatment_protocol: Mid-exponential cultures were treated with either 150 mM [C2mim]Cl or nothing and left to grow for 30 / 60 minutes.

tag: strain

value: 150 mM EMIMCl 60 min


title: E coli 150 mM EMIMCl 60 min 3


title: Normal (H060098N)


title: M9

value: midbrain

value: 1 year (sexually mature adult)

value: male

value: selenium-deficient diet


title: M140

source_name: Pargana adult male zebrafish, midbrain, control


title: E coli 150 mM EMIMCl 60 min 1


title: E coli 150 mM EMIMCl 30 min 1

value: 150 mM EMIMCl 30 min


title: E coli 150 mM EMIMCl 30 min 2


title: M131

value: Pargana


title: Tumor (H060030T)

source_name: Liver

value: liver


title: M85

value: control diet


title: Blood female Saint Joseph Bay, FL SJB 2006_X27

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

country: Italy

institute: University of Ferrara

description: Gene expression wild dolphin blood

hyb_protocol: 500ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custom Tursiops truncatus Microarray (Agilent) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately with a wash in acetonitrile (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software A8.5.3 (Agilent) using default parameters (protocol GE1) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Tursiops truncatus

source_name: Peripheral Blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Amplification  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA from blood samples from wild dolphins was extracted using the RNAeasy Kit according to the manufacturer (Qiagen, Valencia, CA). RNA was quantified using a NanoDrop ND-1000 (Wilmington, DE), qualified on an Agilent 2100 Bioanalyzer (Foster City, CA) and stored at −80°C until needed for gene expression profiling.

treatment_protocol: Blood samples were collected from wild dolphins in PAXgene™ Blood tubes (Qiagen, Valencia, CA, USA), mixed immediately to stabilize the RNA, and stored according to the manufacturer’s instructions.

value: whole blood

tag: gender

value: female

tag: location

value: Saint Joseph Bay, FL


title: Normal (H060030N)


title: Tumor (H060018T)

tag: tumor size

tag: microvascular invasion

value: No


title: E coli 150 mM EMIMCl 30 min 3


title: Normal (H060018N)


title: Tumor (H050604T)

tag: early recurrence

tag: edmondson-steiner histological grade


title: Normal (H050604N)


title: Tumor (H050603T)

value: Yes

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: E coli 60 min 2

tag: treatment

value: no EMIMCl 60 min


title: Normal (H050603N)

tag: tissue


title: E coli 60 min 3


title: Tumor (H050572T)


title: E coli 30 min 3

value: no EMIMCl 30 min


title: E coli 60 min 1


title: E. coli 30 min 2


title: Normal (H050572N)


title: Blood male Saint Joseph Bay, FL SJB 2006_X24

description: Gene expression wild dolphin blood


title: Blood female Saint Joseph Bay, FL SJB 2006_X21

description: Gene expression wild dolphin blood


title: Blood male Saint Joseph Bay, FL SJB 2006_X18

description: Gene expression wild dolphin blood


title: Tumor (H050566T)


title: Blood male Saint Joseph Bay, FL SJB 2006_X20

description: Gene expression wild dolphin blood


title: Blood female Saint Joseph Bay, FL SJB 2005_X01

description: Gene expression wild dolphin blood


title: Normal (H050566N)


title: Blood female Saint Joseph Bay, FL SJB 2006_X15

description: Gene expression wild dolphin blood


title: Blood male Saint Joseph Bay, FL SJB 2005_X009

description: Gene expression wild dolphin blood


title: E. coli 30 min 1


title: Reprogrammed Parthenogenetic cell #41

city: Jerusalem

first: Jonathan

last: Nissenbaum

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: reprogrammed from teratoma cell

hyb_protocol: Standard Illumina protocol for DNA methylation.

scan_protocol: Standard Illumina protocol for DNA methylation using the Bead Array Scanner.

data_processing: Illumina's Genome studio software.

label: Cy5 and Cy3

source_name: Reprogrammed Parthenogenetic cell

label_protocol: Cy5 and Cy3 and procedure according to vendor's protocols

growth_protocol: Cell were grown according to standard protocols. Upon 80-100% confluence of colonies in plates, DNA has been extracted and treated according to the appropriate protocols for methylation assays.

extract_protocol: 500 ng of genomic DNA from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation) according to the manufacturer's recommendations. After bisulfite conversion, each sample was whole genome amplified and enzymatically fragmented, and about 200 ng DNA was applied to BeadChips (Illumina).

treatment_protocol: Standard Illumina Protocol

tag: sample id

value: SAMPLE 13

value: reprogrammed parthenogenetic cell

tag: source of cell

value: Reprogrammed from SAMPLE 10


title: Blood male Saint Joseph Bay, FL SJB 2005_X006_b

description: Gene expression wild dolphin blood


title: Parthenogenetic cell #1

description: ovarian teratoma - non normal

source_name: female ovarian teratoma

value: SAMPLE 9

value: parthenogenetic cell

value: Ovarian teratoma


title: Tumor (H050510T)


title: Normal (H050510N)


title: Blood female Saint Joseph Bay, FL SJB 2005_X09

description: Gene expression wild dolphin blood


title: Blood male Sarasota, FL SAR 2010_260

description: Gene expression wild dolphin blood

value: male

value: Sarasota, FL


title: Blood male Saint Joseph Bay, FL SJB 2005_X006_a

description: Gene expression wild dolphin blood


title: Parthenogenetic cell #2

description: ovarian teratoma - non normal

value: SAMPLE 10


title: Reprogrammed Parthenogenetic cell #20

description: reprogrammed from teratoma cell

value: SAMPLE 11

value: Reprogrammed from SAMPLE 9


title: Reprogrammed Human fibroblast #29

description: reprogrammed from normal somatic cell

source_name: Reprogrammed Human fibroblast

value: SAMPLE 8

value: reprogrammed fibroblast

value: Reprogrammed from SAMPLE 6


title: Blood female Sarasota, FL SAR 2010_231

description: Gene expression wild dolphin blood

value: whole blood

value: female


title: Reprogrammed Parthenogenetic cell #36

description: reprogrammed from teratoma cell

value: SAMPLE 12


title: Blood female Sarasota, FL SAR 2010_258

description: Gene expression wild dolphin blood


title: Tumor (H050493T)

value: liver

value: No


title: Normal (H050493N)


title: Tumor (H050452T)


title: Normal (H050452N)


title: Tumor (H050420T)

value: Yes


title: Blood female Sarasota, FL SAR 2010_229

description: Gene expression wild dolphin blood


title: Reprogrammed Human fibroblast #28

description: reprogrammed from normal somatic cell

value: SAMPLE 7


title: Reprogrammed beta cell 1

description: reprogrammed from normal somatic cell

source_name: Reprogrammed beta cell

value: SAMPLE 4

value: reprogrammed beta cell

value: Reprogrammed from SAMPLE 2


title: Human fibroblast

description: somatic cell

source_name: human fibroblasts

value: SAMPLE 6

value: fibroblast

value: Foreskin


title: Reprogrammed beta cell 2

description: reprogrammed from normal somatic cell

value: SAMPLE 5

value: Reprogrammed from SAMPLE 3


title: Normal (H050420N)


title: Blood female Sarasota, FL SAR 2010_225

description: Gene expression wild dolphin blood

value: Sarasota, FL


title: Tumor (H050350T)


title: Beta cell from human islet 2

description: normal somatic cell

source_name: human islets

value: SAMPLE 3

value: Beta cell

value: Pancreatic islet


title: Tumor (H050401T)


title: Blood female Sarasota, FL SAR 2010_211

description: Gene expression wild dolphin blood

value: whole blood

value: female


title: Blood female Sarasota, FL SAR 2010_227

description: Gene expression wild dolphin blood


title: Blood female Sarasota, FL SAR 2010_151

description: Gene expression wild dolphin blood


title: Beta cell from human islet 1

description: normal somatic cell

value: SAMPLE 2


title: Normal (H050401N)

value: liver


title: Human embryonic stem cell H9

description: normal

source_name: Embryonic stem cells

value: SAMPLE 1

value: embryonic stem cell (H9)

value: ICM


title: Tumor (H050329T)

value: Yes

value: No


title: Normal (H050350N)


title: J9 8 days 2

city: Saint Louis

first: Anmaar

last: Abdul-Nabi

state: Missouri

address: 660 South Euclid Avenue.  PO box 8118

department: Pathology and Immunology

institute: Washington University in Saint louis

hyb_protocol: Affymetrix Hybridization protocol

scan_protocol: arrays were scanned in the Affymetrix Genearray 2500 scanner to generate flourescent images, as described in Affymetrix GeneChip protocol.

data_processing:
Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA)
intensity where obtained after processing with the justRMA() function from the affy package in R

source_name: CD34+ cells_J9 8 days

label_protocol: amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

growth_protocol: GFP-sorted cells were collected and snap-frozen 6 h after nucleofection, or 3 and 8 days after retroviral transduction.

extract_protocol: Total RNA isolated using the RNeasy mini kit (Qiagen) was submitted to the Siteman Cancer Center Laboratory for Clinical Genomics. Target was prepared using linear amplification protocol for the 6 h time point and standard protocol for the 3 and 8 day time points and hybridized to Affymetrix HG-U133 Plus 2.0 GeneChip arrays according to manufacturer's instructions.

treatment_protocol: Preactivated primary human CD34+ cells were nucleofected with pTracer-CMV/Bsd constructs expressing the fusion proteins or empty vector as described Takeda A, Goolsby C, Yaseen NR (2006) Cancer Res 66: 6628–6637.). Cells were cultured at 2x10^5/mL in complete cytokine medium (Takeda A, Goolsby C, Yaseen NR (2006) Cancer Res 66: 6628–6637.) for 3.5 h. GFP+ cells were sorted using MoFlo sorter and cultured at 105/mL in complete cytokine medium for 2.5 h before RNA isolation.

value: primary human CD34+ cells

tag: transduced/nucleofected with

tag: culture time (hrs)


title: J9 3 days 2

source_name: CD34+ cells_J9 3 days

tag: cell type


title: J9 3 days 1


title: J9 8 days 1


title: Blood female Beaufort, NC BEA 2006_443

description: Gene expression wild dolphin blood

value: Beaufort, NC


title: Tumor (H050313T)


title: Normal (H050313N)


title: Blood male Sarasota, FL SAR 2010_20T

description: Gene expression wild dolphin blood

value: male


title: Blood male Sarasota, FL SAR 2010_54S

description: Gene expression wild dolphin blood


title: Tumor (H050267T)


title: Normal (H050329N)


title: Blood female Sarasota, FL SAR 2010_113

description: Gene expression wild dolphin blood


title: Blood female Brunswick, GA GEO 2009_Z17

description: Gene expression wild dolphin blood

value: Brunswick, GA


title: Normal (H050267N)


title: J9 6 hours 2

source_name: CD34+ cells_J9 6 hrs


title: Tumor (H050250T)


title: Normal (H050250N)


title: J9 6 hours 1


title: NPTr_H1N1&S.suis (MGK 153)

city: Mississauga

first: Claude

last: Lachance

state: Ontario

address: 1329 Meyerside Drive

country: Canada

institute: Bio-Rad

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were normalized with VSN method using Flexarray 1.6.2

label: Cyanine 3

label_protocol: cDNA was labelled with Cyanine 3 Labeling Master Mix according to Manufacturer's protocol.

extract_protocol: Total RNA was extracted from NPTr cells using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: NPTr cells were pre-infected 12 h with H1N1 at a MOI of 1. Where appropriate, NPTr cells were then infected with S. suis strain 31533 for 12 h at a MOI of 10

tag: cell line

value: NPTr cells

tag: infection

value: Influenza virus strain H1N1 & Streptococcus suis strain 31533


title: Tumor (H050227T)


title: PML 3 days 2

source_name: CD34+ cells_PML 3 days

value: PML-RARA


title: NPTr_H1N1&S.suis (MGK 156)


title: PML 6 hours 2

source_name: CD34+ cells_PML 6 hrs


title: NPTr_H1N1&S.suis (MGK 155)


title: PML 8 days 2

source_name: CD34+ cells_PML 8 days


title: NPTr_H1N1 (MGK 152)

value: Influenza virus strain H1N1


title: NPTr_H1N1&S.suis (MGK 154)


title: NPTr_H1N1 (MGK 151)


title: Normal (H050227N)


title: PML 6 hours 1


title: NPTr_H1N1 (MGK 150)


title: PML 8 days 1


title: Tumor (H050226T)


title: NPTr_S.suis (MGK 148)

value: Streptococcus suis strain 31533


title: Normal (H050226N)


title: PML 3 days 1


title: Tumor (H050154T)


title: Normal (H050154N)


title: AML1-ETO 8 days 2

source_name: CD34+ cells_AML1-ETO 8 days


title: AML1-ETO 3 days 2

source_name: CD34+ cells_AML1-ETO 3 days


title: NPTr_S.suis (MGK 147)


title: AML1-ETO 8 days 1


title: Tumor (H050150T)

source_name: Liver


title: Normal (H050150N)


title: NPTr_S.suis (MGK 145)


title: NPTr_mock-infected (MGK 144)

value: Mock-infected


title: NPTr_mock-infected (MGK 142)


title: AML1-ETO 6 hours 2

source_name: CD34+ cells_AML1-ETO 6 hrs


title: NPTr_H1N1 (MGK 149)


title: AML1-ETO 3 days 1


title: liver tissue of HIRI mouse

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Mus musculus

source_name: mosue liver of IRI

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Liver

tag: Sex

value: Male


title: AML1-ETO 6 hours 1


title: TBT repl 3 vs Reference

city: Antwerp

first: Anna

last: Pereira-Fernandes

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

description: Sample 30

hyb_protocol: 825 ng of both Cy3 and Cy5 labelled cRNA were co-hybridized on a 44K Whole Rat Genome Oligo Microarray (G4131F, Agilent) for 17h at 60°C in a continuous rotation Agilent hybridization oven. Slides were subsequently washed with Agilent wash buffers and acetonitrile and finally submersed in stabilization and drying solution (Agilent Technologies, Diegem, Belgium) to prevent ozone-induced Cy5-degradation.

scan_protocol: Arrays were scanned at 532 and 635 nm using a Genetix Personal 4100A confocal scanner (Axon Instruments, Union City, CA, USA) at a resolution of 5 µm. The photomultiplier tube voltage (PMT) was adjusted for each slide for the separate wavelengths to obtain an overall red/green ratio of one.

data_processing: The images were analyzed using the Genepix Pro software 4.1 (Axon Instruments) for spot identification and for quantification of the fluorescent signal intensities. Statistical analysis of microarray data was performed with the R package limma. Briefly, spots for which red or green FG < BG + 2SD on all arrays were deleted before analysis (FG: medium foreground intensity; BG: average local background intensity calculated over the full microarray; SD: standard deviation of local background intensities). After background correction (backgroundCorrect, method “normexp”, offset = 50) of the median intensity data, loess normalization (normalizeWithinArrays) was applied. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. Exposure versus control contrasts were fitted to the linear models and considered significant if p<0.05 and ǀlog2FCǀ>0.75 (log2 fold change).

source_name: Reference

label_protocol: Low Input Quick Amplification Labeling Kit (LIQA, Agilent, Diegem, Belgium), according to the protocol of the manufacturers. Briefly, starting from 200 ng of total RNA, poly-A RNA was reverse transcribed using a poly dT-T7 primer. The resulting cDNA was used for one round of amplification by T7 in vitro transcription reaction in the presence of Cyanine 3-CTP or Cyanine 5-CTP. The amplified and labelled RNA samples were purified separately on an RNeasy purification column (Qiagen).

growth_protocol: 3T3-L1 murine cell line (ATCC CRL-173) were cultured in 75 cm2 Nunc cell culture flasks in standard growth medium (DMEM high glucose, Gibco BRL, 31885-023) supplemented with 10% heat inactivated Newborn Calf serum, 100 U/mL Penicillin, 100 µg/mL Streptomycin (Life Technologies) and 1 mM sodium pyruvate  and phenol red as pH indicator. Cells were grown in a 37°C incubator under a 5% CO2 atmosphere and cultures were routinely verified as mycoplasma free with the PCR-based VenorTM GeM Mycoplasma Detection kit (Sigma-Aldrich, Bornem, Belgium). At 70-90% confluence, cells were detached with 0.25% tryspin/EDTA during 3 min (37°C). The  trypsin was neutralized with growth medium and cells were split, with a maximum of 12 passages. Every 2-3 days, medium was refreshed.

extract_protocol: Total RNA extracted using the Qiagen RNeasy mini kit

treatment_protocol: Cells were seeded in 6- well plates at a density of 200,000 cells/well and grown until confluence. Standard medium of 2 days post-confluent cells was replaced by mature medium containing 10% Heat Inactivated Foetal Bovine Serum (FBS, Life Technologies) instead of Newborn Calf Serum and the test compound were added for 10 days, changing the medium every 2-3 days. A solvent control (0.1% DMSO) was included in each experiment. As positive control, 2 days post-confluent cells were stimulated for 48h in mature medium containing a MDI hormonal cocktail (0.5 mM isobutyl methylxanthine, 0.25 µM dexamethasone and 10 µg/mL insulin) and another 8 days in mature medium containing only insulin (10 µg/mL) and changed every 3 days. After exposure, cells were harvested for RNA extraction at day10.

tag: reference composition

value: a mixture of equal aliquots from control and exposed samples

source_name: TBT

tag: agent

value: TBT


title: NPTr_S.suis (MGK 146)


title: Blood female Sarasota, FL SAR 2010_223

description: Gene expression wild dolphin blood

source_name: Peripheral Blood

value: whole blood

tag: gender

value: female

tag: location

value: Sarasota, FL


title: liver tissue of control

source_name: mouse liver of control


title: MLL 8 days 2

source_name: CD34+ cells_MLL 8 days

value: primary human CD34+ cells


title: array4 53_48/53

city: Hannover

first: Kürsad

last: Turgay

address: Schneiderberg 50

department: Institut für Mikrobiologie

country: Germany

institute: Leibniz Universität Hannover

description: Thermotolerance in B. subtilis

hyb_protocol: The respective cDNA's labelled with Alexa 555 or Alexa 647 were combined, concentrated and with SlideHyb Glass Array Hybridisation Buffer # 1 (Ambion) with the help of a lifter slip (22x40, IMPLEN GmbH) in a Micro-Array Hybrid Chamber (Amlab) in a water bath o/n at 55°C hybridized with an oligonucleotide Microaaray prepared and spotted on a glassslide by the Center of Applied Genomics (ICPH, UMDNJ, Newark). The array was subsequently washed with 55°C warm buffer 1 (2xSSC, 0.5%SDS), buffer 2 (0.5xSSC, 0.5%SDS)  buffer 3 (0.5 SSC, 0.03% SDS) and further washed with buffer 4 (0.2xSSC), buffer 5 (0.1xSSC) and buffer 6 (0.1xSSC) at RT

scan_protocol: The hybridzed slides were scanned with a Genepix 4100 (Molecular Devices) Laserscanner using auto PMT

data_processing: The data was analyzed with Genepix Pro 6.1 (Axon), the dye swap and further analysis was performed with Acuity (Axon) and Excel.

label: Alexa 555, Alexa 647

organism: Bacillus subtilis

source_name: exponential LB 15 min 53°C

label_protocol: The cDNA synthesis purification and labeling was performed with Superscript SuperScript Plus Indirect cDNA Labeling Kit using random hexamer primers and Alexa Fluor R555 & 647 dyes (Invitrogen)

growth_protocol: B. subtilis cells were grown at 37°C  in 200 ml LB at 300 rpm to an OD of 0.6.

extract_protocol: The total RNA was prepared using FastRNA ProBlue Kit (Qbiogene, CA) using a Retsch Mixer Mill. The total RNA was DNAseI  treated and purified using Phenol/Chloroform/Isoamyl extraction and EtOH precipitation.

treatment_protocol: The cultures were divided in four 50 ml cultures, which were (1) shaken another 15 min at 37°C and harvested, (2) shaken for 15 min at 37° and shifted to shake for another 15 min at 53°C and harvested, (3) shaken and incubated for another 15 min at 48°C and harvested, or (4) shaken for 15 min at 48° and shifted to shake for another 15 min at 53°C and harvested.The cells were harvested by centrifugation and the pellets frozen in liquid nitrogen.

tag: strain

value: exponential LB 15 min 53°C

label: Alexa 647, Alexa 555

source_name: exponential LB 15 min 48°C and 15 min 53°C


title: TBT repl 2 vs Reference

description: Sample 29


title: MLL 3 days 2

source_name: CD34+ cells_MLL 3 days


title: NPTr_mock-infected (MGK 141)


title: MLL 8 days 1


title: array3 48_53

description: Thermotolerance in B. subtilis

source_name: exponential LB 15 min 48°C

value: exponential LB 15 min 48°C


title: MLL 3 days 1


title: TBT repl 1 vs Reference

description: Sample 28


title: NPTr_mock-infected (MGK 143)


title: array2 37_53

description: Thermotolerance in B. subtilis

source_name: exponential LB 15 min 37°C

value: exponential LB 15 min 37°C


title: MLL 6 hours 2

source_name: CD34+ cells_MLL 6 hrs


title: array1 48_48/53

description: Thermotolerance in B. subtilis

value: exponential LB 15 min 48°C and 15 min 53°C


title: PP repl 3 vs Reference

description: Sample 27

source_name: PP

value: PP


title: PP repl 2 vs Reference

description: Sample 26


title: MLL 6 hours 1


title: control 8 days 1

source_name: CD34+ cells_control 8 days

value: empty retroviral vector (control)


title: control 3 days 1

source_name: CD34+ cells_control 3 days


title: Dendritic-cells_rep4

city: Jouy en Josas

first: pierre

last: Sibille

address: domaine de Vilvert, bât 440

department: Virologie et Immunologie Moléculaires

institute: INRA

hyb_protocol: Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 12 to 50 ng of total RNA. Following fragmentation, labeled cRNA were hybridized on Agilent “SurePrint G3 Chicken Custom Gene Expression 8x60K Microarray” (Design ID 038072), for 17 hrs, at 65°C under 10 rpm.

scan_protocol: slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 µm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol

data_processing: Raw gene expression data were background corrected using the normexp method and quantile normalized with the limma package through Bioconductor in the R statistical environment (version 2.15.0). Independent biological triplicates (B cells) and quadruplicates (cDC, MP and T cells) were performed by using cells isolated from 4 different animals. Quality control of the expression data was assessed by boxplots of raw expression data, density plots of normalized data, scatter plots and calculation of the Pearson's correlation coefficients between arrays, using the Ringo package.

organism: Gallus gallus

source_name: Dendritic-cells

label_protocol: RNA labeling was performed using the one-color Low Input Quick Amp Labeling kit (Agilent Technologies) following the manufacturer’s recommendations. Each RNA sample (50 ng) was amplified and cyanin 3 (Cy3) -labelled, and subsequently the complementary RNA (cRNA) was checked for quality on Nanodrop and Agilent 2100 Bioanalyzer.

extract_protocol: When insufficient total RNA amounts for hydridization was obtained (< 50 ng), the RNA from the sorted subsets of distinct spleen pools were mixed

treatment_protocol: Spleen from 4 different exsanguinated chicken were used for cell isolation. Spleens were crushed on stainless steel mesh, and cell suspension was digested with DNAse / Collagenase D before 1.077 histopaque gradient centrifugation. Four populations were separated according to cell surface staining : B and T cells were respectively labeled with 2 µg/ml phycoerythrin (PE)-conjugated anti Bu-1 AV20 monoclonal antibody (mAb) and PE-conjugated anti chicken CD3 CT-3 mAb respectively; macrophage population (MP) was sorted after labelling with 2 µg/ml PE-conjugated KUL01 mAb ; for cDC candidate cell sorting, splenocytes were first stained with the 8F2 hybridoma cell supernatant directed to the putative chicken CD11c, followed by 50 µg/ml Alexa647-conjugated goat anti-mouse Fab (Jackson Immuno Research), and subsequently reacted with a cocktail of FITC -conjugated mAb anti chicken MHC-II, PE -conjugated KUL01, anti Bu-1, and anti CD3 mAbs. Putative cDCs were sorted as 8F2+, MHC-II+, KUL01-, BU-1-, CD3- cells. Hybridizations were performed at the Platform Biopuces et Séquençage (IGBMC, 67400 Illkirch, France, http://www.igbmc.fr/grandesstructures/cbi/).

value: spleen

value: spleen mononuclear cells

tag: cell subtype

value: putative conventional Dendritic cells

tag: fluorescence sorted cell population

value: CD3- Bu-1-, KUL01-, MHCII+, 8F2+(putative CD11c)


title: PP repl 1 vs Reference

description: Sample 25


title: BBP repl 3 vs Reference

description: Sample 24

source_name: BBP

value: BBP


title: BBP repl 2 vs Reference

description: Sample 23

value: a mixture of equal aliquots from control and exposed samples


title: Uc283+a overexpression variant 1 - GAC11

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

hyb_protocol: The labeled targets of first-strand biotin-cDNA are used to hybridize miRNA arrays in 6 X SSPE/30% formamide at 25oC for 18 h.

scan_protocol: Hybridization signals were detected by biotin binding of a streptavidin-Alexa647 conjugate on an Axon Scanner 4000B (Axon Instruments, Union City, CA). The images were quantified by GENEPIX 6.0 software (Axon Instruments, Union City, CA).

data_processing:
Data was processed in R (3.0.1) using functions of LIMMA library
The raw intensity for each probe is the median feature pixel intensity with the median background subtracted.  Setting an offset 1 ensures that there will be no negative values after log-transforming data.  Data was quantile normalized followed by log2 transform.  Signals from probes measuring same genes were averaged.    Data was quantile normalized followed by log2 transform.  Signals from probes measuring same genes were averaged.

label: Biotin

source_name: Transiently transfected HCT-116

label_protocol: We labeled 4 microgram of total RNA of each testing sample by reverse transcription with a 5'-biotin end-labeled random octomer oligo primer

extract_protocol: Total RNA was isolated from all cancer cell lines by Trizol extraction according to the manufacturer's instructions (Invitrogen) and treated  with Turbo DNA-free (Ambion).

value: cancer cell line

tag: transfection

value: Uc283+a overexpression variant 1


title: Uc283+a overexpression variant 2 - GAC13

value: Uc283+a overexpression variant 2


title: Uc283+a overexpression variant 1 - GAC12


title: control 3 days 2


title: control 6 hours 2

source_name: CD34+ cells_control 6 hrs

value: empty pTracer-CMV/Bsd vector (control)


title: Uc283+a overexpression variant 2 - GAC14


title: BJ fibroblast cell line - MYC transfected

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

hyb_protocol: According to manufacturer's instructions

data_processing: MAS5.0 method was used to process the data.

growth_protocol: BJ cell lines were cultured in Dulbecco’s modified minimal essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT, USA).

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

treatment_protocol: BJ human fibroblast cells were introduced wild type MYOD1, MYOD1 L122R, MYC, and GFP by retroviral infection. For retrovirus production, the pcx4 and pBabe vectors system were used.  Retroviruses were obtained by using 293T cells as packaging cells, and were infected into BJ cell lines and selected with 500 μg/ml Zeocin (Invitrogen, Carlsbad, CA, USA) for 1 week.

value: BJ fibroblast

value: MYC transfected


title: BPA repl 2 vs Reference

description: Sample 20

source_name: Reference

source_name: BPA

value: BPA


title: control 6 hours 1

value: primary human CD34+ cells


title: BBP repl 1 vs Reference

description: Sample 22


title: BPA repl 3 vs Reference

description: Sample 21


title: BPA repl 1 vs Reference

description: Sample 19


title: BJ fibroblast cell line - MYOD1 L122R mutant transfected

scan_protocol: According to manufacturer's instructions

value: MYOD1 L122R mutant transfected


title: 532138_A10

city: MEXICO, D.F.

first: JORGE

last: FERNANDEZ-RETANA

address: AV. SAN FERNANDO No22 COL SECCION XVI

department: INVESTIGACION BASICA

country: Mexico

institute: INSTITUTO NACIONAL DE CANCEROLOGIA

description: SAMPLE 87

hyb_protocol: Hybridization was performed by NimbleGen Systems (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. After standard washes, arrays were scanned.

scan_protocol: Scanning was performed byNimblegen MS200 microarray scanner. Nimblegen Roche, Mannheim, Germany, following their standard operating protocol. Scanned images were gridded by using the NimbleScan v2.6 Software (Nimblegen Roche, Mannheim, Germany).

source_name: Cervical tissue

label_protocol: Labeling was performed by NimbleGen Systems One Color Llabeling kit (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. (Nimblegen Roche, Mannheim, Germany).

growth_protocol: Biopsies were frozen in liquid nitrogen until nucleic acid extractionThe population under study included 89 patients prospectively enrolled into the National Cancer Institute of Mexico. All patients included signed informed consent; the protocol was approved by institutional ethics and scientific committees. Immediately after surgical excision, tumor biopsies were analyzed for pathological confirmation and frozen in liquid nitrogen until nucleic acid extraction.

extract_protocol: Total RNA was extracted using the MagNAPure Compact Instrument following manufacturer recommendations (Roche Diagnostics GmbH Roche Applied Science Mannheim, Germany). RNA quality was determined by by means of 18S:28S ratio.  Hybridization targets were prepared from 250 ng of total RNA and amplified with whole transcriptome amplification kit 2 (Sigma Aldrich, St Louis, MO)

tag: disease state

value: Locally advanced cervical cancer

tag: carcinoma type

value: Squamous cell carcinomas

tag: Stage


title: 532138_A12

description: SAMPLE 89

value: IIB


title: 532138_A11

description: SAMPLE 88

value: IIIA


title: 532138_A08

description: SAMPLE 85

value: IIIB


title: Empty vector (Mock) - GAC10

value: Empty vector (Mock)


title: DEHP repl 2 vs Reference

description: Sample 17

source_name: DEHP

value: DEHP


title: Empty vector (Mock) - GAC9


title: BJ fibroblast cell line - wild-type MYOD1 transfected

label_protocol: According to manufacturer's instructions

value: wild-type MYOD1 transfected


title: DEHP repl 3 vs Reference

description: Sample 18

value: a mixture of equal aliquots from control and exposed samples


title: 532138_A09

description: SAMPLE 86


title: 532138_A04

description: SAMPLE 81


title: BJ fibroblast cell line - GFP transfected

value: GFP transfected


title: EB repl 1 vs Reference

description: Sample 13

source_name: EB

value: EB


title: EB repl 2 vs Reference

description: Sample 14


title: EB repl 3 vs Reference

description: Sample 15


title: DEHP repl 1 vs Reference

description: Sample 16


title: 532138_A05

description: SAMPLE 82


title: 532138_A06

description: SAMPLE 83


title: BP repl 3 vs Reference

description: Sample 12

source_name: BP

value: BP


title: 4_3_G: T4_con

city: Amsterdam

first: Tjalf

last: de Boer

address: Science Park 406

country: Netherlands

institute: MicroLife Solutions

description:
LUFA2.2 control soil
raw data: 254227910004_1_3_Cy3

hyb_protocol: 826 ng of Cy3-labeled or Cy5-labeled cRNA (specific activity >8.0 pmol dye/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x180k array slides (Scan Area 610x21.6 mm, Scan resolution 5um, Dye channel is set to Red & Green and PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 042279_D_F_20120723) to obtain mean Red or Green intensities and median Red or Green background intensities. In limma, edwards method for background correction was used (offset = 30), and global loess normalizing was done.

organism: Enchytraeus crypticus

source_name: untreated control, 4 days

label_protocol: Cyanine-3 (Cy3) or Cyanine-5 (Cy5) labeled cRNA was prepared from 500 ng total RNA using the Low Input Quick Amp Labeling Kit, two-color (Agilent Technologies) according to the manufacturer's guidelines followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from all animals, using the SV Total RNA isolation System (Promega).

treatment_protocol: Approximately 5 - 7 adult animals which had a visible clitellum were exposed for 4 days in glass jars containing ~30 g of soil at 50% of the soil WHC. Exposure was done at same conditions as incubation. After exposure the animals were extracted from soil with tap water via floatation, put in 1.5 mL tubes and frozen in liquid N2.

tag: tissue

value: 5-7 animals


title: BP repl 2 vs Reference

description: Sample 11


title: Human hair follicle, control rep1

city: Boston

first: Andrey

last: Sharov

address: 609 Albans St, J-405

country: United Kingdom

institute: Boston University

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

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

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

source_name: Human hair follicle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human hair follicles were disected from normal scalp skin of five healthy female individuals that underwent the face-lift cosmetic surgery. Disectted Individual hair follicles were cultured in 0.5 ml of supplemented Williams E medium at 37 C in a 5%CO2.

treatment_protocol: After 24 hours of culture, Doxorubicin (1uM) was added to the microdissected anagen hair follicles for 1 hour, and culture medium was replaced after completion of the doxorubicin treatment. Control hair follicles were treated with the PBS solution. All experiments were performed using at least three replicates, and RNA isolated from three experimental and control samples was pooled and processed for microarray analyses using one  sample of pooled RNA per experimental and control group.

value: hair follcile

tag: genotype

value: Females

tag: age

value: various

tag: treatment


title: BJ fibroblast cell line - parental cells

tag: cell line

value: BJ fibroblast

value: parental


title: 4_1_G: T4_50

description:
LUFA2.2 control soil
raw data: 254227910004_1_1_Cy3

source_name: zinc EC50, 4 days


title: Human hair follicle, Doxorubicin, 3 hours, rep1

source_name: Human hair follicle treated with 1uM Doxoribicin

value: hair follicle

value: Doxorubicin 1uM


title: 532138_A03

description: SAMPLE 80

value: Locally advanced cervical cancer

value: Adenocarcinoma

value: IIB


title: 5_4_R: T4_50

description:
LUFA2.2 control soil
raw data: 254227910005_1_4_Cy5


title: 2_3_G: T4_con

description:
LUFA2.2 control soil
raw data: 254227910002_1_3C_Cy3


title: ROSI repl 2 vs Reference

description: Sample 8

source_name: ROSI

value: ROSI


title: ROSI repl 3 vs Reference

description: Sample 9


title: 532137_A12

description: SAMPLE 77

value: Squamous cell carcinomas


title: 532138_A07

description: SAMPLE 84

value: IIIB


title: 4_2_R: T4_50

description:
LUFA2.2 control soil
raw data: 254227910004_1_2_Cy5


title: 532138_A01

description: SAMPLE 78


title: 532137_A09

description: SAMPLE 74


title: 532137_A11

description: SAMPLE 76


title: 532137_A08

description: SAMPLE 73


title: 532137_A07

description: SAMPLE 72


title: Human Normal Mucosal Sample, healthy, by UPPP (U) technique - 8011U

city: Baltimore

first: Joseph

last: Califano

state: MD

address: 1550 Orleans Street

department: School of Medicine

institute: The Johns Hopkins University

hyb_protocol: The samples were ice quenched and combined with the hybridization cocktail (5 ul oligonucleotide B2 control, 15 ul 20X eukaryotic hybridization controls, 150 ul 2X hybridization buffer, 30 ul 100% DMSO and 70 ul water). After 10 minutes of pre-hybridizing Human U133 Plus 2.0 Genome array at 45ºC, 60 rpm, 200 ul of cocktail was loaded onto each array and the arrays were hybridized for 16 hours at 45ºC, 60 rpm. The cocktail was removed and the arrays were stained and washed using the Affymetrix GeneChip Fluidics Station 450 and FS450_001 fluidics script.

scan_protocol: All arrays were scanned in the Affymetrix GeneChip Scanner 3000 and the raw analysis was performed with Affymetrix GeneChip Operating System (GCOS) 1.4.

data_processing:
mRNA gene expression profiling was done using Affymetrix GeneChip Human Genome U133Plus 2.0 Arrays containing 47K probe sets (Affymetrix, Santa Clara, California). Signal intensity and statistical significance was established for each transcript using initially dChip version 2008 and then Significance Analysis of Microarrays (SAM) software to analyze and normalize the array data by us. Default settings for dChip were used, including the perfect match/mismatch difference model, invariant set normalization, and check single/probe/array outlier algorithm.
value definition: Linear, default settings for dChip were used, including the perfect match/mismatch difference model, invariant set normalization, and check single/probe/array outlier algorithm.

source_name: Normal mucosal samples from healthy people, UPPP (U) technique

label_protocol: One ug total RNA was combined with 2 ul T7 oligo(dT) primer and 2 ul Poly-A controls and brought to a volume of 12 ul. The samples were incubated at 70ºC for 10 minutes. A master mix of 4 ul first strand buffer, 2 ul DTT and 1 ul 10 mM dNTPs was added to the samples, followed by a two minute incubation at 42ºC. One ul Superscript II (Invitrogen, Carlsbad, CA) was added to each sample and the samples were incubated at 42ºC for one hour for first strand cDNA synthesis. A master mix of 91 ul water, 30 ul 5X second strand buffer, 3 ul 10 mM dNTPs, 4 ul DNA polymerase I, 1 ul E.coli DNA ligase, and 1 ul RNase H was added to each sample and the samples were incubated for two hours at 16ºC for second strand cDNA synthesis. Two ul of T4 DNA polymerase was added followed by a five minute incubation at 16ºC. Ten ul, 0.5 M EDTA was added to stop the reaction. cDNA clean-up was performed with the Affymetrix GeneChip Sample Clean-up Module, as per manufacturer’s instructions. The cDNA was eluted in 14 ul elution buffer. The final elution volume (~12ul) was combined with 28 ul of IVT mix master mix (4 ul 10X IVT labeling buffer, 12 ul Labeling NTP mix, 4 ul labeling enzyme mix, and 8 ul RNAse-free water) for the in vitro transcription cRNA synthesis reaction. The samples were incubated overnight for 16 hours at 37ºC followed by a hold at 4ºC. Clean-up was performed as per the manufacturer’s protocol using the Affymetrix GeneChip Sample Clean-up Module. The final elution volume was ~19ul. Concentration was checked via a nanodrop spectrophotometer. Six ul 5X fragmentation buffer was then combined with 15 ug cRNA and incubated at 95ºC for 35 minutes to fragment the cRN

growth_protocol: None, biopsied materials

extract_protocol: We prepared total RNA from HNSCC tumor and normal mucosa samples using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: Frozen in liquid nitrogen and stored in -80° C

value: male

tag: smoker

value: no

tag: tumor site

tag: overall stage


title: Human Normal Mucosal Sample, healthy, by UPPP (U) technique - 8108U

tag: gender


title: Human Normal Mucosal Sample, healthy, by UPPP (U) technique - 8115U


title: 1_3_G: T4_50

description:
LUFA2.2 control soil
raw data: 254227910001_1_3_Cy3


title: Human Head and Neck Tumor (T) sample - 3957T

source_name: HNSCC primary tumor tissue, biopsy

value: yes

value: larnyx


title: Human Head and Neck Tumor (T) sample - 8140T

value: female

value: oropharynx


title: 2_2_R: T4_con

description:
LUFA2.2 control soil
raw data: 254227910002_1_2C_Cy5

value: 5-7 animals


title: Human Head and Neck Tumor (T) sample - 2801T


title: MDI repl 2 vs Reference

description: Sample 5

tag: reference composition

value: a mixture of equal aliquots from control and exposed samples

source_name: MDI (positive control)

tag: agent

value: MDI


title: MDI repl 3 vs Reference

description: Sample 6


title: 532137_A10

description: SAMPLE 75


title: MDI repl 1 vs Reference

description: Sample 4


title: control 8 days 2

source_name: CD34+ cells_control 8 days

tag: cell type

value: primary human CD34+ cells

tag: transduced/nucleofected with

value: empty retroviral vector (control)

tag: culture time (hrs)


title: 532138_A02

description: SAMPLE 79

tag: disease state

value: Locally advanced cervical cancer


title: Human Head and Neck Tumor (T) sample - 2765T


title: DMSO repl 3 vs Reference

description: Sample 3

source_name: DMSO (solvent control)

value: DMSO


title: Human Head and Neck Tumor (T) sample - 2779T


title: 532137_A03

description: SAMPLE 68

tag: carcinoma type

value: Adenocarcinoma

value: IIB


title: 532137_A05

description: SAMPLE 70

value: Squamous cell carcinomas

tag: Stage


title: DMSO repl 1 vs Reference

description: Sample 1


title: 532137_A02

description: SAMPLE 67


title: Human Head and Neck Tumor (T) sample - 2411T

value: oral cavity


title: Human Normal Mucosal Sample, healthy, by UPPP (U) technique - 8199U


title: Human Head and Neck Tumor (T) sample - 2414T

value: male


title: Human Head and Neck Tumor (T) sample - 2365T


title: 532137_A04

description: SAMPLE 69

value: IIA


title: Human Head and Neck Tumor (T) sample - 2075T


title: geFA-52T iPSCs clon 16

city: Madrid

first: Javier

last: Suela

state: M

address: Faraday 7

institute: NIMGenetics

hyb_protocol: Hybridization and washing was done according to Agilent protocol (65C 24h, 20rpm in hyb chambers)

scan_protocol: Scanned on an Agilent G2565C scanner (3um and Cy5/Cy3 analysis). Images were quantified using Agilent Feature Extraction Software (version 10.7.1).

data_processing: FE extraction was done following protocol CGH_107_Sep09. Agilent Genomic Workbench using ADM-2 method (ADM=6) using at least 5 consecutive probes for aberration detection

source_name: geFA-52T fibroblasts-derived iPSCs

label_protocol: 500 ng were labeled using Agilent CGH enzymatic protocol 7.2 (Agilent Technologies)

growth_protocol: Skin fibroblasts from FA patient were maintained in DMEM (Invitrogen) supplemented with 20% FBS (Biowhitaker) and 1% penicillin/streptomycin solution (Gibco) at 37C under hypoxic conditions (5% of O2 and 5% of CO2).

extract_protocol: Qiagen Dneasy blood and tissue kit

treatment_protocol: IPSCs were mantained in hES medium composed by DMEM-KO (Gibco), non-essential aminoacides, 1% NEEA (Lonza, Biowhitlaker), glutamax (2 mM; Gibco), 1% penicillin/streptomycin (Gibco), 10% KO-Serum Replacement (Gibco), β-Mercaptoetanol (50 μM; Gibco) and hrFGF (10 ng/ml; Prepotech).

tag: subject status

value: Fanconi anemia (FA) patient

value: Induced pluripotent stem cells (iPSCs)

tag: genotype/variation

value: control (beofre excision of geFA-52T)

source_name: FA-52 Fibroblasts

value: Fibroblasts

tag: sample type

value: reference


title: 4_1_R: T4_con

description:
LUFA2.2 control soil
raw data: 254227910004_1_1_Cy5

tag: tissue

value: 5-7 animals


title: 532137_A01

description: SAMPLE 66


title: Human Head and Neck Tumor (T) sample - 2328T

value: yes

value: larnyx


title: geFA-52T iPSCs excised clone 16.1

value: after excision of geFA-52T


title: 509837_A06

description: SAMPLE 65

value: Locally advanced cervical cancer


title: 509837_A05

description: SAMPLE 64


title: 509837_A03

description: SAMPLE 63


title: Human Head and Neck Tumor (T) sample - 1683T

value: female

value: no


title: Human Normal Mucosal Sample, healthy, by UPPP (U) technique - 8209U


title: ROSI repl 1 vs Reference

description: Sample 7

source_name: Reference

tag: cell line

value: a mixture of equal aliquots from control and exposed samples

value: ROSI


title: 509837_A02

description: SAMPLE 62

source_name: Cervical tissue

value: Squamous cell carcinomas

value: IIB


title: DMSO repl 2 vs Reference

description: Sample 2

value: DMSO


title: FA-52 Fibroblasts

source_name: FA-52 fibroblast

value: Fanconi anemia (FA) patient

value: skin fibroblasts

value: control (before gene editing)

source_name: Female Control

value: reference (pooled DNA)


title: Human Head and Neck Tumor (T) sample - 12020T

value: male

tag: smoker


title: 509837_A01

description: SAMPLE 61


title: PBMC_284_day-7

status: Public on Apr 10 2014

city: Bethesda

first: Yuri

last: Kotliarov

address: 4 Memorial Dr., room 134

department: CHI

institute: NHLBI

description:
284_day-7
Gene expression data from PBMC extracted from individual 284 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

hyb_protocol: Labeled cDNA were hybridized to Human 1.0 ST GeneChip arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturers' instructions.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw intensities of gene probesets in the CEL files were processed using Affymetrix Power Tools. The apt-probeset_summarize script was used for background correction and normalization (RMA with sketch, quantile normalization). The Bioconductor package arrayQualityMetrics was used to assess the quality of the microarray data.

source_name: Individual 284 at day-7

label_protocol: Fragmented single-stranded sense cDNA were terminally labeled with biotin according to the standard Affymetrix protocol.

growth_protocol: Blood specimens were collected in heparinized syringes and peripheral blood mononuclear cells (PBMC) were isolated using Leucosep tubes with Ficoll-Paque Plus density gradient media and centrifugation. Fresh isolated PBMC were directly lysed in 700ul of Qiazol and stored at -80C till isolation.

extract_protocol: Total RNA was isolated from 1e7 freshly isolated PBMC using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and eluted in 40ul of elution buffer with the addition of 1ul of RNase inhibitor (Invitrogen).

treatment_protocol: Individuals were vaccinated with the 2009 Fluvirin seasonal influenza (Novartis), and H1N1 pandemic (Sanofi-Aventis) vaccines, both without adjuvant.

tag: individual id

tag: age

tag: ethnicty

value: White

tag: sample collection time

value: 7 days prior to vaccination (day-7)


title: PBMC_284_day0

description:
284_day0
Gene expression data from PBMC extracted from individual 284 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 284 at day0

value: peripheral blood mononuclear cells (PBMC)

tag: gender

value: immediately before vaccination (day0)


title: PBMC_283_day-7

description:
283_day-7
Gene expression data from PBMC extracted from individual 283 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 283 at day-7


title: PBMC_284_day70

description:
284_day70
Gene expression data from PBMC extracted from individual 284 70 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 284 at day70

value: 70 days post vaccination (day70)


title: PBMC_283_day70

description:
283_day70
Gene expression data from PBMC extracted from individual 283 70 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 283 at day70

value: female


title: PBMC_281_day1

description:
281_day1
Gene expression data from PBMC extracted from individual 281 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 281 at day1

value: 1 day post vaccination (day1)


title: PBMC_283_day1

description:
283_day1
Gene expression data from PBMC extracted from individual 283 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 283 at day1


title: PBMC_282_day70

description:
282_day70
Gene expression data from PBMC extracted from individual 282 70 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 282 at day70


title: PBMC_282_day7

description:
282_day7
Gene expression data from PBMC extracted from individual 282 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 282 at day7

value: 7 days post vaccination (day7)


title: PBMC_282_day1

description:
282_day1
Gene expression data from PBMC extracted from individual 282 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 282 at day1


title: PBMC_282_day-7

description:
282_day-7
Gene expression data from PBMC extracted from individual 282 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 282 at day-7


title: BP repl 1 vs Reference

description: Sample 10

tag: reference composition

value: a mixture of equal aliquots from control and exposed samples

source_name: BP

tag: agent

value: BP


title: PBMC_282_day0

description:
282_day0
Gene expression data from PBMC extracted from individual 282 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 282 at day0


title: PBMC_283_day7

description:
283_day7
Gene expression data from PBMC extracted from individual 283 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 283 at day7


title: PBMC_283_day0

description:
283_day0
Gene expression data from PBMC extracted from individual 283 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 283 at day0


title: PBMC_284_day7

description:
284_day7
Gene expression data from PBMC extracted from individual 284 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 284 at day7


title: PBMC_281_day7

description:
281_day7
Gene expression data from PBMC extracted from individual 281 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 281 at day7


title: PBMC_281_day-7

description:
281_day-7
Gene expression data from PBMC extracted from individual 281 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 281 at day-7


title: PBMC_280_day-7

description:
280_day-7
Gene expression data from PBMC extracted from individual 280 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 280 at day-7

value: Hispanic


title: PBMC_284_day1

description:
284_day1
Gene expression data from PBMC extracted from individual 284 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 284 at day1


title: PBMC_281_day0

description:
281_day0
Gene expression data from PBMC extracted from individual 281 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 281 at day0


title: PBMC_280_day7

description:
280_day7
Gene expression data from PBMC extracted from individual 280 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 280 at day7


title: PBMC_280_day1

description:
280_day1
Gene expression data from PBMC extracted from individual 280 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 280 at day1


title: PBMC_280_day70

description:
280_day70
Gene expression data from PBMC extracted from individual 280 70 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 280 at day70


title: PBMC_280_day0

description:
280_day0
Gene expression data from PBMC extracted from individual 280 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 280 at day0


title: PBMC_279_day1

description:
279_day1
Gene expression data from PBMC extracted from individual 279 1 day post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 279 at day1


title: PBMC_277_day-7

description:
277_day-7
Gene expression data from PBMC extracted from individual 277 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 277 at day-7

value: Asain


title: PBMC_279_day0

description:
279_day0
Gene expression data from PBMC extracted from individual 279 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 279 at day0


title: PBMC_279_day-7

description:
279_day-7
Gene expression data from PBMC extracted from individual 279 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 279 at day-7


title: PBMC_274_day-7

description:
274_day-7
Gene expression data from PBMC extracted from individual 274 7 days prior to vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 274 at day-7


title: PBMC_273_day0

description:
273_day0
Gene expression data from PBMC extracted from individual 273 immediately before vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 273 at day0

value: African American


title: PBMC_273_day70

description:
273_day70
Gene expression data from PBMC extracted from individual 273 70 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 273 at day70


title: PBMC_277_day7

description:
277_day7
Gene expression data from PBMC extracted from individual 277 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.

source_name: Individual 277 at day7