title: TG-KO_3

city: Barcelona

first: Gema

last: Alcarraz-Vizán

address: Rossello 149

department: Diabetes & Obesity Laboratory

country: Spain

institute: IDIBAPS

description: Global gene expression of pancreactic islets from 12-week old hIAPP-TgxBACE2-KO mouse

hyb_protocol: Following fragmentation, cRNA was hybridized to Affymetrix GeneChip® Mouse HT_MG-430_PM arrays, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Expression data were normalized with Robust Multi-array Average (RMA)  from the affy package (www.bioconductor.org)

source_name: Pancreactic islets from 12-week old hIAPP-TgxBACE2-KO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (150 ng starting total RNA).

growth_protocol: Islets from wild type, hIAPP-Tg,  BACE2-KO and hIAPP-TgxBACE2-KO mice were isolated at week 12.

extract_protocol: RNA was extracted with Trizol (R) reagent according to manufacturer protocol.

treatment_protocol: All mice were fed ad libitum with standard chow diet for 12 weeks.

tag: strain

value: Islets of Langerhans

value: 12 weeks

value: Pancreatic islets


title: KO_3

status: Public on May 03 2017

type: RNA

description: Global gene expression of pancreactic islets from 12-week old BACE2-KO mouse

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Pancreactic islets from 12-week old BACE2-KO mouse

tag: tissue

tag: genotype

tag: age

tag: cell type


title: TG_3

description: Global gene expression of pancreactic islets from 12-week old hIAPP-Tg mouse

source_name: Pancreactic islets from 12-week old hIAPP-Tg mouse

value: hIAPP-Tg


title: KO_1


title: Th0, 72h, S2 siRNA, repl. 1

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

country: USA

institute: Flatiron Institute

hyb_protocol: Following fragmentation, cRNA were hybridizedAffymetrix GeneChip Human Genome U219 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Gene TitanTM MC Instrument.

data_processing: Possible batch effects caused by the different hybridizations were corrected for with ComBat tool with default parameters. The data were processed using the robust multi-array average (RMA) algorithm, quantile-normalized (Bioconductor affy package) and log2-transformed. Th17-specific genes were identified between the matched Th17- and Th0-measurements (same time point and culture) in the control-siRNA data using paired and moderated t-statistic (Bioconductor limma package). Genes with false discovery rate (FDR) < 0.1 were defined as changed for each time point. The effect of STAT3 knockdown on the gene expression was assessed using the Th17 measurements from the matched siRNA and scramble samples using the same analysis methods as above.

label: Biotin

organism: Homo sapiens

source_name: human cord blood derived T cells

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

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturers instructions.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit from QIAGEN  according to the manufacturer's instructions.

treatment_protocol: Isolated CD4+ T cells were activated with plate-bound anti-CD3 (750 ng/24well culture plate and 3.75ug/ 6 well culture plate, Immunotech, Marseille, France) and soluble anti-CD28 (1 μg/ml, Immunotech) in X-vivo 20 serum free medium (Lonza, Basel, Switzerland) supplemented with 2 mM L-Glutamine (#G7513, Sigma, St. Louis, MO, USA), and 50 U/ml Penicillin and cultured at 37°C in 5 % CO2. IL-6 (20 ng/ml, Roche, Basel, Switzerland), IL-1β (10 ng/ml) and TGFβ (10 ng/ml) in the presence of neutralizing anti-IFNγ (1 μg/ml) and anti-IL4 (1 μg/ml) were used to initiate Th17 polarization. Control Th0 cells were cultured in a medium containing only the neutralizing antibodies. All cytokines and neutralizing antibodies were purchased from R&D Systems (Minneapolis, MN, USA) unless otherwise stated. For STAT3 target gene identification, cells were harvested at 2, 12, 24, and 72 h time points. Three biological replicates were prepared, each time including all three different individual STAT3 siRNAs and non-targeting control siRNA.

tag: treatment

value: siRNA

tag: time point


title: Th0, 72h, D2 siRNA, repl. 1


title: Th0, 72h, scramble, repl. 1

value: scramble


title: TG_1


title: Th0, 2h, S2 siRNA, repl. 1


title: NO_960

city: Taipei

first: Wen-Chien

last: Chou

address: No. 7, Chung-Shan S. Rd.

department: Department of Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Hybridization processes were performed according to manufacturer's instructions (NanoString Technologies).

scan_protocol: Arrays were scanned by nCounter Analysis system according to manufacturer's instructions (NanoString Technologies).

data_processing: Intensities were processed and normalized by using the nSolver™ Analysis Software following manufacturer's instructions (NanoString Technologies).

label: miRNA-specific probes

source_name: de novo acute myeloid leukemia

label_protocol: Labeling was performed according to manufacturer's instructions (NanoString Technologies).

extract_protocol: RNA was extracted by TriZol reagent according to manufacturer's instructions.

tag: npm1 mutation status

value: wild type

tag: disease

value: AML

value: bone marrow


title: NO_957


title: WT_1

description: Global gene expression of pancreactic islets from 12-week old wild type mouse

source_name: Pancreactic islets from 12-week old wild type mouse


title: NO_962


title: NO_955


title: NO_952


title: NO_961


title: NO_949


title: NO_958


title: NO_947


title: Th0, 24h, S2 siRNA, repl. 1


title: NO_945


title: NO_954


title: Th0, 12h, S2 siRNA, repl. 1


title: KO_2


title: TG_2


title: Th0, 12h, D1 siRNA, repl. 1


title: NO_953


title: Th0, 12h, scramble, repl. 1


title: Th0, 24h, D2 siRNA, repl. 1


title: Th0, 24h, D1 siRNA, repl. 1


title: NO_950


title: Th0, 12h, D2 siRNA, repl. 1


title: NO_942


title: NO_951


title: NO_959


title: TG-KO_2


title: WT_2


title: NO_956


title: NO_939


title: NO_938


title: TG-KO_1


title: WT_3


title: NO_941


title: Th0, 24h, scramble, repl. 1


title: NO_937


title: NO_935


title: NO_946


title: NO_948


title: NO_930


title: NO_943


title: NO_936


title: NO_928


title: NO_926


title: NO_932


title: NO_922


title: NO_944


title: NO_933


title: NO_940


title: NO_925


title: NO_927


title: NO_914

value: mutant


title: NO_915


title: NO_931


title: NO_913


title: NO_917


title: NO_923


title: NO_912


title: NO_929


title: NO_920


title: NO_918


title: NO_916


title: NO_924


title: NO_934


title: NO_919


title: NO_904


title: NO_899


title: NO_906


title: NO_895


title: NO_908


title: NO_894


title: NO_921


title: NO_905


title: NO_909


title: NO_911


title: NO_900


title: NO_907


title: NO_901


title: NO_903


title: NO_897


title: NO_889


title: NO_886


title: NO_898


title: NO_885


title: NO_892


title: NO_887


title: NO_902


title: NO_884


title: NO_910


title: NO_888


title: NO_890


title: NO_896


title: NO_891


title: NO_883


title: NO_881


title: NO_893


title: NO_882


title: NO_780


title: NO_880


title: NO_802


title: NO_807


title: NO_879


title: NO_761


title: NO_776


title: NO_979


title: NO_980


title: NO_749


title: NO_976


title: NO_981


title: NO_977


title: NO_972


title: NO_969


title: NO_975


title: NO_970


title: NO_965


title: NO_966


title: NO_967


title: NO_963


title: NO_971


title: NO_978


title: NO_974


title: NO_964


title: NO_968


title: NO_973


title: Human Colon 2 FAIRE-seq

status: Public on May 02 2017

type: SRA

city: Durham

first: John

last: Rawls

state: North Carolina

address: Duke University 213 Research Drive, Box 3580 DUMC CARL Building 327

institute: Duke University

library_source: genomic

data_processing:
Reads were filtered for a quality score of 20 or greater in at least 90% of nucleotides and adapter contaminated reads were removed with TagDust. No more than 5 reads with identical sequence were retained.
Reads were aligned with GSNAP (with -v option using 1,000 Genomes SNP annotation) to sex-specific hg19 genomes using k-mer size of 15 and allowing 1 mismatch per read.
Peaks were identified using MACS2 2.1.0 with default values except, qvalue = 1.00e-01, broad region calling = off, subpeak summits = on
A post-alignment blacklist step was used to filter reads that were aligned to problematic, highly-artifactual regions identified by ENCODE.
Quantification of RPKM values was conducted using an in-house script with RefSeq gene annotations, yielding a full set of 23,679 genes.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; txt files Contain Gene Expression Information (gene Name, Raw Counts and RPKM data columns)

molecule: genomic DNA

source_name: Intestinal Epithelial Cells_FAIRE-seq

growth_protocol: IEC samples were taken from living subjects

extract_protocol:
Total RNA was isolated from flash-frozen tissue samples (mucosal not whole tissue) from surgical colon resections using the Qiagen RNeasy kit following the manufacturer’s protocol
RNA-sequencing libraries were generated using the Illumina TruSeq polyA+ Sample Prep Kit using manufacturer's protocols.

value: Human Colon Aduilt intestinal Epithelial Cells


title: Control, replicate 6

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations, and immediately scanned.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays and channels were considered to be expressed. Data were normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, log2 transformation with the following adaptation: all data were first normalized by LOWESS.

organism: Rattus norvegicus

source_name: liver, control low fat diet

label_protocol: 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010).

extract_protocol: Total RNA from liver samples was extracted using Tripure Reagent (Roche Diagnostic, Barcelona, Spain) and purified with Qiagen RNeasy Mini Kit spin columns (Izasa SA, Barcelona, Spain). RNA yield was quantified on a Nanodrop ND 1000 spectrophotometer (NanoDrop Technologies Wilmintog, Delaware, USA) and its integrity was measured on an Agilent 2100 Bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, United Kingdom).

treatment_protocol: Male Wistar rats (Charles River Laboratories España, SA, Barcelona, Spain) single-housed at 22° C with a period of light/dark of 12 hours (light  on at 8:00 pm) were used. At the age of two months animals were divided into three groups: a control group (n=7), a high-protein group (HP, n=6), and a high fat group (n=6). Control animals were fed a normolipidic diet (D12450B, Research Diets) containing 70% of energy (kcal ) from carbohydrates, 10% from fats and 20% from proteins. HP animals were fed a high-protein diet (Research Diets) containing 45% of energy from carbohydrates, 10% from fats and 45% from proteins (mainly casein), and the HF animals received a high fat diet (60en% fats, 20en% proteins, 20en% carbohydrates). Diets were purchased from Brogaarden (Gentofte, Denmark). Animals  were sacrificed in the fed state early morning by decapitation.

value: Wistar

tag: gender

value: male

tag: developmental stage

value: adult

value: liver

source_name: liver (reference pool)


title: BBr-NHSM04 vs. BBr-SOF04

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

description: Ovaries obtained from mixed breeds at a local slaughterhouse.

hyb_protocol: Tecan HS4800 hybridization: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan)  * Priming: 5xSSC, 0.1%SDS  * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul  * Hybridization: 45 min at 42C.  * Wash 2x: milliQ  * Wash: 5xSSC, 0.1%SDS  * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul)  * Hybridization: 16 hours at 42C.  * Wash 2x: 1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC, 0.2%SDS at 23C  * Wash 2x: 0.1xSSC at 23C  * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using ImaGene software from Biodiscovery.

data_processing: Genes, no bg corr, hybset spec. dye corr: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Bos taurus

label_protocol: Double-amplification & labeling (robotic): All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman). mRNA amplification protocol description: * 5 ul per RNA is put in a 96-wells plate (4-Titude). All subsequent steps are performed by the robot script. Round1: * mix1 containing 10 ng T7 Mlu VN primer (custom mix) per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNase Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * Plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNaseH (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul . * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems) * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol. Round2: * mix1 containing 100 ng random hexamer primers per 5 ul is added and mixed in each well. * Plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNase Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and 1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 100ng T7 Mlu VN primer (custom mix), 4 ul E.coli DNA polymerase I and 1 ul RNaseH (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul . * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol. * Concentration of cRNA is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C. Labeling protocol description: * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10). All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol. * RNA concentration and labeling incorporation are measured (SpectraMax 190). * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization.

growth_protocol: Bovine in vitro embryo culture: Embryo culture was performed in a humidified atmosphere with 5% CO2 at 39°C, unless stated otherwise. Ovaries were obtained from a local slaughterhouse and follicles 3-8 mm were aspirated to retrieve cumulus oocyte complexes (COCs). COCs were incubated to mature for 23 hrs in groups of 35-60 per 500 ml M199 (Life Technologies, Bleiswijk, The Netherlands) supplemented with 0.05 IU/ml recombinant hFSH (Organon, Oss, The Netherlands) and 1% (v/v) penicillin-streptomycin (Life Technologies). Subsequently, fertilization was performed as described previously including modifications. In short, matured COCs were transferred to fertilization medium (Fert-TALP) supplemented with 10 mg/ml heparin (Sigma-Aldrich, Zwijndrecht, The Netherlands), 20 uM D-penicillamine (Sigma-Aldrich), 10 uM hypotaurine (Sigma-Aldrich), and 1 uM epinephrine (Sigma-Aldrich). Frozen-thawed sperm from a bull with proven fertility was centrifuged over a Percoll gradient (GE Healthcare Europe GmbH, Eindhoven, The Netherlands) and added to the COCs at a final concentration of 1.0 x 10^6 spermatozoa/ml. Fertilization day was considered as day 0. After 20 hrs, incubating oocytes were freed of cumulus cells by vortexing for 3 min and placed in synthetic oviduct fluid (SOF).

extract_protocol: RNA extraction: 1. Add 1 ml Trizol per 5 x 10^6 cells in suspension (1 ml Trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.   2. Incubate 5 min at room temperature.   3. Add chloroform (200 ul per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.   4. Centrifuge 20 min at 14000 rpm 4°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.   5. Add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml Trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.   6. Wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 µg/column).  7. Adjust each sample to a volume of 300 ul with sterile MilliQ water. Add 160 ul buffer RLT to the samples, and mix (= lysis buffer).   8. Add 240 ul ethanol (100% stored at -20 °C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.   9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at room temperature. DNase treatment: D1. Pipet 350 ul Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 ul/reaction): add 10 ul DNase I stock solution to 70 ul Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 ul) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 ul Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.   10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 ul buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps.  11. Pipet 500 ul buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.   12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).   13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 ul milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 ul milliQ.   14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 °C.

treatment_protocol: Bovine embryo treatment, harvest and dissection: After 4 days culturing in a humidified atmosphere with 5% CO2 and 7% O2 at 39°C, embryos were transferred to fresh SOF or to naive human stem cell medium (NHSM) containing KO DMEM (Life Technologies) supplemented with 20% knock-out serum replacement (Life Technologies), 12.5 mg/ml bovine insulin (Sigma), 1mM glutamine (Life Technologies), 1% non-essential amino acids (Sigma), 0.1mM beta-mercaptoethanol (Life Technologies), 1% pen/strep (Life Technologies), 20 ng/ml recombinant human LIF (Prospec, Rehovot, Isreael), 8 ng/ml recombinant bFGF (Peprotech, Rocky Hill NJ, USA), 1 ng/ml recombinant TGFbeta1 (Peprotech) and the small molecule inhibitors: 1 mM PD0325901 (Erk1/2; Stemgent, Cambridge MA; USA), 3 mM CHIR99021 (GSK3beta, Bioconnect, Huissen, The Netherlands), 5 mM Go6983 (PKC, Tocris, Bristol, UK), 10 mM SP600125 (JNK, Tocris) and 10 mM SB203580 (p38, Tocris). Subsequent culture continued until day 9 to obtain a higher percentage of stage 9 blastocysts facilitating ICM separation. To ensure good quality embryos, only blastocysts scored as stage 7-9 with quality code 1 or 2 were collected. ICMs were separated from the TE as described before. In short, blastocysts were placed in wash buffer and sharpened tungsten needles were used to separate the ICM from the TE. The procedure was performed under a stereo microscope. Isolated ICMs were collected and stored in RLT (Qiagen, Venlo, The Netherlands) in groups of 11-24 at -80°C until RNA isolation.

value: inner cell mass (ICM)

tag: culture condition

value: naive human stem cell medium (NHSM)

value: SOF (control)


title: HF, replicate 1

source_name: liver, high fat diet


title: HF, replicate 3


title: HP, replicate 1

source_name: liver, high protein diet


title: Control, replicate 5


title: Control, replicate 4


title: HF, replicate 2


title: HF, replicate 5


title: HF, replicate 6


title: Human Colon 1 FAIRE-seq


title: HP, replicate 5


title: Control, replicate 3


title: Human Colon 3 FAIRE-seq


title: Control, replicate 1


title: HP, replicate 4


title: hIEC5 mRNA

library_source: transcriptomic

source_name: Intestinal Epithelial Cells_RNA-seq


title: BBr-NHSM02 vs. BBr-SOF02


title: HF, replicate 4


title: Control, replicate 7


title: BBr-SOF01 vs. BBr-NHSM01


title: HP, replicate 6


title: HP, replicate 3


title: BBr-SOF03 vs. BBr-NHSM03


title: hIEC6 mRNA


title: Control, replicate 2


title: hIEC7 mRNA


title: HP, replicate 2


title: hIEC4 mRNA


title: hIEC1 mRNA


title: hIEC3 mRNA


title: hIEC2 mRNA


title: 4C_24h_8h

city: Thuwal

first: Katsuhiko

last: Mineta

address: 4700 KAUST

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

hyb_protocol: All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: Data were analyzed by Bioconductor of R. To extract the expression level of the probe set, the Robust Multichip Average (RMA) method implemented in the Affy package was used. Log-transformed RMA value was delogged and then normalized with the average expression level of poly(A) RNA controls derived from Bacillus subtilis genes.

organism: Arabidopsis thaliana

source_name: T87 cultured cell

growth_protocol: Arabidopsis T87 suspension cells derived from Columbia ecotype were grown in JPL media (Axelos et al. 1992) at 22°C under constant light (80 μmol m–2 s–1) with orbital shaking (120 rpm). Cells were transferred to new medium every two weeks at ~20-fold dilution. Seven days after subculturing, cells were divided into two conditions. Control cells were grown under the same condition, and the cold treated cells were transferred to 4°C under dim light (40 μmol m–2 s–1) and cultured for 12, 24 and 36 h.

extract_protocol: Total RNA was extracted from the cells by using RNeasy Plant Mini kit (Qiagen)

treatment_protocol: Cells were collected prior to the cordycepin treatment (0 h) and 0.5, 2, 4 h after cordycepin addition in the control cells. Incubation time after cordycepin addition was 4, 8 and 12 h in the cold treated cell.

tag: ecotype

tag: cell line


title: 4C_36h_12h

scan_protocol: All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.


title: 4C_12h_0h

label_protocol: All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.


title: 4C_24h_12h


title: 4C_24h_4h


title: 4C_36h_4h


title: 4C_6h_12h


title: 4C_12h_4h


title: 4C_12h_12h


title: 22C_0h_4h


title: 22C_0h_05h


title: 4C_36h_8h


title: 4C_6h_8h


title: 4C_12h_8h


title: 4C_36h_0h


title: 4C_6h_0h


title: 4C_6h_4h


title: 4C_24h_0h


title: 22C_0h_2h


title: 22C_0h_0h


title: Embryo Uvea 11 weeks of gestation (11.2 uvea)

type: genomic

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

description:
11.2 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: Eye

label_protocol: Standard Illumina labelling protocol

growth_protocol: N/A. Primary patient samples.

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

treatment_protocol: Untreated.

tag: disease state

value: normal

value: uvea

tag: health state

value: Healthy donor

tag: time

value: 11 weeks of gestation


title: Embryo Uvea 11 weeks of gestation (11.3 uvea)

description:
11.3 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Retina 17 weeks of gestation (17.2 retina)

description:
17.2 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt

value: retina

value: 17 weeks of gestation


title: Embryo Sclera 21 weeks of gestation (21.1 sclera)

description:
21.1 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt

value: sclera

value: 21 weeks of gestation


title: Embryo Retina 21 weeks of gestation (21.3 retina)

description:
21.3 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 21 weeks of gestation (21.2 uvea)

description:
21.2 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Sclera 17 weeks of gestation (17.1 sclera)

description:
17.1 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 21 weeks of gestation (21.3 uvea)

description:
21.3 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Sclera 17 weeks of gestation (17.2 sclera)

description:
17.2 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 11 weeks of gestation (11.1 uvea)

description:
11.1 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 14 weeks of gestation (14.1 uvea)

description:
14.1 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt

value: 14 weeks of gestation


title: Embryo Retina 17 weeks of gestation (17.1 retina)

description:
17.1 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Retina 17 weeks of gestation (17.3 retina)

description:
17.3 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Sclera 14 weeks of gestation (14.3 sclera)

description:
14.3 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Retina 14 weeks of gestation (14.2 retina)

description:
14.2 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 14 weeks of gestation (14.2 uvea)

description:
14.2 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma RB_39-2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

value: Retinoblastoma

value: Eye

value: Diseased donor


title: Embryo Sclera 11 weeks of gestation (11.1 sclera)

description:
11.1 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 17 weeks of gestation (17.3 uvea)

description:
17.3 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Sclera 21 weeks of gestation (21.3 sclera)

description:
21.3 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 21 weeks of gestation (21.1 uvea)

description:
21.1 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Sclera 14 weeks of gestation (14.2 sclera)

description:
14.2 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Uvea 17 weeks (17.1 uvea)

description:
17.1 uvea
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma RB_32-2


title: Embryo Retina 11 weeks of gestation (11.1 retina)

description:
11.1 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma RB_50-2


title: Embryo sclera 14 weeks of gestation (14.1 sclera)

description:
14.1 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma RB_47-2


title: Embryo Retina 14 weeks of gestation (14.3 retina)

description:
14.3 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Embryo Sclera 21 weeks of gestation (21.2 sclera)

description:
21.2 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma RB_34-2


title: Retinoblastoma RB_33-2


title: Embryo Retina 21 weeks of gestation (21.2 retina)

description:
21.2 retina
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma RB_48-2


title: Retinoblastoma blood_RB44

source_name: Blood

value: Retinoblastoma blood

value: Blood


title: Retinoblastoma RB_44-2


title: Retinoblastoma blood_RB57


title: Retinoblastoma blood_RB51


title: Retinoblastoma RB_38-2


title: Retinoblastoma blood_RB56


title: Retinoblastoma blood_RB47


title: Retinoblastoma blood_RB46


title: Retinoblastoma blood_RB49


title: Retinoblastoma blood_RB55


title: Retinoblastoma RB_46-2


title: Retinoblastoma blood_RB54


title: Retinoblastoma blood_RB48


title: Retinoblastoma blood_RB41


title: Retinoblastoma blood_RB38


title: Retinoblastoma blood_RB52


title: Retinoblastoma blood_RB43


title: Embryo Sclera 17 weeks of gestation (17.3 sclera)

description:
17.3 esclera
Embryo_retinas_Unmeth_signal.txt
Embryo_retinas_meth_signal.txt
Embryo_retinas_pval.txt


title: Retinoblastoma blood_RB36


title: Retinoblastoma blood_RB40


title: Retinoblastoma blood_RB37


title: Retinoblastoma blood_RB50


title: Retinoblastoma blood_RB39


title: Retinoblastoma blood_RB45


title: Retinoblastoma blood_RB53


title: Retinoblastoma blood_RB42


title: Retinoblastoma blood_RB33


title: Retinoblastoma blood_RB35


title: Retinoblastoma blood_RB32


title: Uveal melanoma MEL_63 12072

value: Uveal melanoma


title: Uveal melanoma MEL_61 12070


title: Uveal melanoma MEL_57 12066


title: Uveal melanoma MEL_62 12071


title: Uveal melanoma MEL_55 12064


title: Uveal melanoma MEL_59 12068


title: Uveal melanoma MEL_51 12060


title: Uveal melanoma MEL_60 12069


title: Uveal melanoma MEL_44 12053


title: Uveal melanoma MEL_43 12052


title: Uveal melanoma MEL_50 12059


title: Uveal melanoma MEL_48 12057


title: Uveal melanoma MEL_52 12061


title: Uveal melanoma MEL_56 12065


title: Uveal melanoma MEL_54 12063


title: Uveal melanoma MEL_42 12051


title: Uveal melanoma MEL_41 12050


title: Uveal melanoma MEL_49 12058


title: Uveal melanoma MEL_38 12047


title: Uveal melanoma MEL_58 12067


title: Uveal melanoma MEL_45 12054


title: Uveal melanoma MEL_36 12045


title: Uveal melanoma MEL_47 12056


title: Uveal melanoma MEL_46 12055


title: Uveal melanoma MEL_37 12046


title: Uveal melanoma MEL_53 12062


title: Retinoblastoma blood_RB31


title: Retinoblastoma blood_RB34


title: Uveal melanoma MEL_34 12043


title: Uveal melanoma MEL_35 12044


title: Uveal melanoma MEL_18 12027


title: Uveal melanoma MEL_26 12035


title: Uveal melanoma MEL_17 12026


title: Uveal melanoma MEL_16 12025


title: Uveal melanoma MEL_25 12034


title: Uveal melanoma MEL_28 12037


title: Uveal melanoma MEL_23 12032


title: Uveal melanoma MEL_20 12029


title: Uveal melanoma MEL_19 12028


title: Uveal melanoma MEL_31 12040


title: Uveal melanoma MEL_32 12041


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_6

value: Choroid and ciliary muscle

value: Healthy


title: Uveal melanoma MEL_27 12036


title: Uveal melanoma MEL_24 12033


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_8

value: normal


title: Uveal melanoma MEL_22 12031


title: Uveal melanoma MEL_30 12039


title: Uveal melanoma MEL_29 12038


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_9


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_5


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_3


title: Uveal melanoma MEL_40 12049


title: Uveal melanoma MEL_39 12048


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_4


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_12


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_2


title: Uveal melanoma MEL_21 12030


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_10


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_1


title: Normal Sclera SCLERA_9

value: Sclera


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_11


title: Uveal melanoma MEL_33 12042


title: Normal Sclera SCLERA_8


title: Normal Sclera SCLERA_12


title: Normal Choroid and ciliary muscle Choroid and ciliary muscle_7


title: Normal Sclera SCLERA_3


title: Normal Sclera SCLERA_5


title: Normal Retina RETINA_6

value: Retina


title: Normal Sclera SCLERA_7


title: Normal Retina RETINA_12


title: Normal Sclera SCLERA_10


title: Normal Retina RETINA_4


title: Normal Sclera SCLERA_1


title: Normal Sclera SCLERA_6


title: Retinoblastoma RB_9

value: neuroretina


title: Normal Retina RETINA_8


title: Normal Retina RETINA_5


title: Normal Retina RETINA_9


title: Normal Retina RETINA_7


title: Normal Sclera SCLERA_4


title: Normal Retina RETINA_11


title: Retinoblastoma RB_8


title: Normal Retina RETINA_1


title: Normal Retina RETINA_3


title: Normal Retina RETINA_10


title: Normal Retina RETINA_2


title: Retinoblastoma RB_7


title: Normal Sclera SCLERA_2


title: Retinoblastoma RB_57


title: Retinoblastoma RB_54


title: Retinoblastoma RB_55


title: Retinoblastoma RB_51


title: Retinoblastoma RB_53


title: Retinoblastoma RB_5


title: Retinoblastoma RB_46


title: Retinoblastoma RB_44


title: Retinoblastoma RB_56


title: Retinoblastoma RB_52


title: Retinoblastoma RB_38


title: Retinoblastoma RB_34


title: Retinoblastoma RB_47


title: Retinoblastoma RB_43


title: Retinoblastoma RB_50


title: Retinoblastoma RB_35


title: Retinoblastoma RB_33


title: Retinoblastoma RB_40


title: Retinoblastoma RB_36


title: Retinoblastoma RB_42


title: Retinoblastoma RB_39


title: Retinoblastoma RB_6


title: Retinoblastoma RB_48


title: Retinoblastoma RB_49


title: Retinoblastoma RB_31


title: Retinoblastoma RB_37


title: Retinoblastoma RB_4


title: Retinoblastoma RB_32


title: Retinoblastoma RB_30


title: Retinoblastoma RB_26


title: Retinoblastoma RB_27


title: Retinoblastoma RB_2


title: Retinoblastoma RB_45


title: Retinoblastoma RB_24


title: Retinoblastoma RB_3


title: Retinoblastoma RB_25


title: Retinoblastoma RB_28


title: Retinoblastoma RB_22


title: Retinoblastoma RB_21


title: Retinoblastoma RB_41


title: Retinoblastoma RB_13


title: Retinoblastoma RB_20


title: Retinoblastoma RB_17


title: Retinoblastoma RB_12


title: Retinoblastoma RB_16


title: Retinoblastoma RB_15


title: Retinoblastoma RB_23


title: Retinoblastoma RB_19


title: Retinoblastoma RB_18


title: Retinoblastoma RB_11


title: Membrane from proliferative vitreoretinopathy  PVR_8

value: proliferative vitreoretinopathy

value: eye membrane


title: Retinoblastoma RB_29


title: Retinoblastoma RB_10


title: Retinoblastoma RB_14


title: Retinoblastoma RB_1


title: Membrane from proliferative vitreoretinopathy  PVR_5


title: Membrane from proliferative vitreoretinopathy  PVR_3


title: Membrane from proliferative vitreoretinopathy  PVR_6


title: Membrane from proliferative vitreoretinopathy  PVR_7


title: Membrane from proliferative vitreoretinopathy  PVR_2


title: Membrane from proliferative vitreoretinopathy  PVR_4


title: Uveal melanoma MEL_4


title: Uveal melanoma MEL_9


title: Uveal melanoma MEL_14


title: Uveal melanoma MEL_5


title: Uveal melanoma MEL_2


title: Uveal melanoma MEL_3


title: Uveal melanoma MEL_15


title: Uveal melanoma MEL_16


title: Uveal melanoma MEL_10


title: Uveal melanoma MEL_1


title: Uveal melanoma MEL_11


title: Uveal melanoma MEL_8


title: Membrane from proliferative vitreoretinopathy  PVR_1


title: Normal iris IRIS_5


title: Uveal melanoma MEL_7


title: Normal iris IRIS_3


title: Normal iris IRIS_8


title: Uveal melanoma MEL_6


title: Normal iris IRIS_4


title: Fibrovascular membranes from diabetic retinopathy FVM_7

value: diabetic retinopathy

value: eye fibrovascular membranes


title: Normal iris IRIS_6


title: Fibrovascular membranes from diabetic retinopathy FVM_6


title: Normal iris IRIS_12


title: Normal iris IRIS_2


title: Normal iris IRIS_1


title: Normal iris IRIS_10


title: GH-ref vs. GH-59

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

organism: Canis lupus familiaris

source_name: GH-ref

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA extraction cellLine

tag: breed

value: Labrador retriever

tag: subject id

value: Pool of 10 individuals

value: liver biopsy

tag: diagnosis

value: healthy

value: high copper (hC)


title: GH-ref vs. GH-70

tag: tissue

value: high copper chronic hepatitis (high copper (hC)cH)


title: GH-ref vs. GH-77


title: Uveal melanoma MEL_12

value: Uveal melanoma

value: Diseased donor


title: Normal iris IRIS_9

value: Healthy


title: Fibrovascular membranes from diabetic retinopathy FVM_1


title: Fibrovascular membranes from diabetic retinopathy FVM_5


title: Fibrovascular membranes from diabetic retinopathy FVM_3


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_444

value: non-proliferative diabetic retinopathy


title: GH-ref vs. GH-193

value: normal (N)


title: Fibrovascular membranes from diabetic retinopathy FVM pool2


title: GH-ref vs. GH-166


title: Fibrovascular membranes from diabetic retinopathy FVM_2


title: GH-ref vs. GH-156

value: high copper hepatitis (high copper (hC)H)


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_251

value: neuroretina


title: GH-ref vs. GH-122


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_438


title: GH-ref vs. GH-33


title: GH-ref vs. GH-164


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_443


title: GH-ref vs. GH-123


title: GH-ref vs. GH-117


title: GH-ref vs. GH-115


title: GH-ref vs. GH-113


title: Fibrovascular membranes from diabetic retinopathy FVM_4


title: Normal neuroretina C_434

value: normal


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_465


title: GH-ref vs. GH-106


title: GH-ref vs. GH-103


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_406


title: GH-ref vs. GH-197


title: GH-77 vs. GH-ref


title: GH-ref vs. GH-162


title: GH-33 vs. GH-ref


title: GH-193 vs. GH-ref


title: GH-156 vs. GH-ref


title: GH-197 vs. GH-ref


title: GH-122 vs. GH-ref


title: GH-ref vs. GH-114


title: GH-70 vs. GH-ref


title: GH-115 vs. GH-ref


title: GH-114 vs. GH-ref


title: GH-113 vs. GH-ref


title: GH-162 vs. GH-ref


title: GH-106 vs. GH-ref


title: GH-59 vs. GH-ref


title: GH-164 vs. GH-ref


title: Normal neuroretina C_325


title: Normal neuroretina C_418


title: Normal neuroretina C_416


title: GH-123 vs. GH-ref


title: GH-166 vs. GH-ref


title: GH-117 vs. GH-ref


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_209


title: Normal iris IRIS_7


title: GH-103 vs. GH-ref


title: Liver_warm_control_3

city: Salt Lake City

first: Patrice

middle: Kurnath

last: Connors

state: UT

address: 257 south 1400 east

department: Biology

institute: University of Utah

description:
10654E11_596
Gene expression after warm temperature and control diet acclimation in liver

hyb_protocol: Fluorescently labelled cRNA samples wer fragmente dand combined with Agilent Hi-RPM hybridization buffer.  Microarray bhybridizations were performed using Agilent SureHyb and inducbated at 65degC for 17 hours, 10 RPM.  Slides were washed for 1 minute in each of the two wash buffers (6x SSPE, 0.005% N-lauroylsacrosine and 0.06x SSPE, 0.005% N-lauroylsacrosine), dipped in a solution of acetonitrile and dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505B) using one color scan setting (resolution 5um).

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.  Prior to analysis, all control spots and nonuniform spots were removed from the data set.  Data from dupliate probes were combined, but different probes with the same annotation were maintained separately because it is possible that the original contigs were from different isoforms despite the shared match to a rodent gene.

organism: Neotoma lepida

source_name: Liver tissue_warm temp_control diet

label_protocol: Agilent one-Color Quick Amp Labeling Kit was used to generate fluorescently labelled cRNA for one-color microarray hybridizations.  After cDNA synthesis, cyanine-3-CTP nuecleotides were combined with reaction mixture. Fluorescently labelled cRNA molecules were purified with RNAeasy columns (QIAGEN, Valencia, CA).  Purified sample yield were checked with the NanoDrop ND-1000 spectrophotometer.  More details in Malenke et al, 2013, Mol Ecol Resour.

extract_protocol: RNA was prepared using the RNAqueous Purification kit (Ambion Inc., Austin, TX) as per manufacture's instructions.  RNA was quantified  and quality was measured with the Agilent Bioanalyzer  RNA Nanochip (Agilent Technologies, Santa Clara, CA).

tag: Sex

value: female

tag: temperature

value: warm, 27C

tag: diet

value: control

value: liver


title: Fibrovascular membranes from diabetic retinopathy FVM pool1

value: diabetic retinopathy

value: eye fibrovascular membranes


title: Normal neuroretina C_348


title: Liver_warm_toxic_3

description:
10654E15_572
Gene expression after warm temperature and creosote diet acclimation in liver

source_name: Liver tissue_warm temp_toxic diet

value: toxic - creosote resin


title: Liver_warm_toxic_1

description:
10654E13_652
Gene expression after warm temperature and creosote diet acclimation in liver


title: Liver_warm_control_4

description:
10654E12_647
Gene expression after warm temperature and control diet acclimation in liver

value: male


title: Liver_warm_control_1

description:
10654E9_631
Gene expression after warm temperature and control diet acclimation in liver


title: Liver_warm_toxic_4

description:
10654E16_640
Gene expression after warm temperature and creosote diet acclimation in liver


title: Liver_warm_toxic_2

description:
10654E14_654
Gene expression after warm temperature and creosote diet acclimation in liver


title: Normal neuroretina C_318


title: Liver_cool_toxic_4

description:
10654E8_584
Gene expression after cool temperature and creosote diet acclimation in liver

source_name: Liver tissue_cool temp_toxic diet

value: cool, 22C


title: Liver_cool_toxic_1

description:
10654E5_641
Gene expression after cool temperature and creosote diet acclimation in liver


title: Liver_cool_toxic_2

description:
10654E6_619
Gene expression after cool temperature and creosote diet acclimation in liver


title: Liver_cool_toxic_3

description:
10654E7_560
Gene expression after cool temperature and creosote diet acclimation in liver


title: Liver_cool_control_4

description:
10654E4_592
Gene expression after cool temperature and control diet acclimation in liver

source_name: Liver tissue_cool temp_control diet


title: Normal iris IRIS_11


title: Liver_cool_control_3

description:
10654E3_557
Gene expression after cool temperature and control diet acclimation in liver


title: Normal neuroretina C_389


title: Liver_cool_control_1

description:
10654E1_657
Gene expression after cool temperature and control diet acclimation in liver


title: Liver_cool_control_2

description:
10654E2_581
Gene expression after cool temperature and control diet acclimation in liver


title: MEF_OSKZE_ day6_biological_rep3

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA16 implemented in the GeneSpring 12.6.

source_name: retroviral OSKZE, day6

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) were used according to Affymetrix protocol.

growth_protocol: Cells infected with retrovirus were cultured in KSR medium [DMEM with high glucose, 15% Knockout Serum Replacement (Life Technologies), 100 uM 2-mercaptoethanol, 1 x MEM nonessential amino acids, 0.5 x penicillin-streptomycin, 1 x L-glutamine, LIF] from the next day of infection, and medium was changed every other day.

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).

treatment_protocol: MEFs were seeded on plastic coated with gelatin and infected with indicated retroviral vectors with 4 mg/mL polybrane the next day.

tag: condition

value: OSK, Zic3, Esrrb


title: MEF_OSKN_ day6_biological_rep3

source_name: retroviral OSKN, day6

value: OSK, Nr5a2


title: MEF_OSKZN_ day6_biological_rep2

source_name: retroviral OSKZN, day6

value: OSK, Zic3, Nr5a2


title: MEF_OSKZN_ day6_biological_rep3


title: MEF_OSKN_ day6_biological_rep2


title: MEF_OSKZ_ day6_biological_rep3

source_name: retroviral OSKZ, day6

value: OSK, Zic3


title: MEF_OSKZE_ day6_biological_rep2


title: MEF_OSK_ day6_biological_rep2

source_name: retroviral OSK, day6

value: OSK


title: MEF_OSK_ day6_biological_rep3


title: MEF_OSKZ_ day6_biological_rep2


title: Neuroretina from non- proliferative diabetic retinopathy  DBT_288

value: non-proliferative diabetic retinopathy

value: Diseased donor


title: MEF_OSKE_ day6_biological_rep2

source_name: retroviral OSKE, day6

value: OSK, Esrrb


title: MEF_OSKZE_ day6_biological_rep1


title: MEF_OSKZN_ day6_biological_rep1


title: MEF_OSKE_ day6_biological_rep1


title: MEF_OSKN_ day6_biological_rep1


title: MEF_OSK_ day6_biological_rep1


title: MEF_OSKZ_ day6_biological_rep1


title: MEF_OSKE_ day6_biological_rep3


title: Normal neuroretina C_410

value: normal

value: neuroretina

value: Healthy


title: BM-wild type rep1

city: Tsukuba

first: Takayasu

last: Kato

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix). AGCC used for image processing.

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

source_name: leukemic whole BM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was isolated using an RNeasy kit (QIAGEN).

tag: strain

value: bone marrow

tag: genotype

value: Wild type


title: BM-wild type rep2


title: BM-Hes1 null rep2

value: Hes1 null


title: BM-Hes1 null rep1


title: CD133+GFP+_tech replicate 3

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
Human infant kidney-derived cells, passage 5, CD133+GFP+ tech replicate 3
S_133_plus_3

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

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

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

growth_protocol: The human infant kidney-derived cells were isolated from a healthy donor. The bulk population was plated in DMEM/F12 additioned with FCS (5%), ITS (1x), hEGF (10μg/L), Hydrocortisone  (36 μg/L), 3,3',5-triiodo-L-thyronine sodium salt (4 ng/L). At passage 1, the bulk population was transduced with an anmodified eGFP vector (pHIV-eGFP, Addgene), with a MOI of 5, yielding >90% labelling efficiency. At passage 2, the cells were sorted by FACS for the expression of CD133/1 and GFP and both CD133+/GFP+ and CD133-/GFP+ were maintained in culture for 2 additional passages. The expression of CD133 in both populations was monitored during expansion by FACS, and MACS were used at  passage 3 and 4 in the CD133- population to eliminate eventual residual CD133+ cells.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions from approximately 500 thousand cells per sample

treatment_protocol: the cells were not treated

tag: subject status

value: healthy donor

tag: cell type

value: Human infant kidney-derived cells

tag: passage

value: passage 5

value: plus


title: U112 24 hpi J774 rep 1

city: Hannibal

first: Siva

middle: Tej

last: Sarva

state: Missouri

address: 6500 Hospital Dr

department: Division of Pulmonary Critical Care

institute: Hannibal Regional Medical Group

hyb_protocol: Following fragmentation, cDNA was hybridized for 16 hr at 45C on custom Nimble Express Affymetrix microarray. The microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using the Genechip Scanner 3000 (Affymetrix).

data_processing: Data was scaled using GCOS (Affymetrix) to a mean intensity of 1000 using the Francisella Traditional Probe Sets (please see platform annotation files for details) as a scaling mask

organism: Francisella tularensis subsp. novicida U112

source_name: U112 isolated from J774 macrophages 24 hours post infection

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

growth_protocol: Francisella tularensis novicida was grown to optical density of 0.6 in a chemical defined medium (Chamberlain medium) and was used to infect J774 monolayers grown using Dulbecco's Modified Eagle's Medium with 10% Fetal Bovine Serum with a final a multiplicity of infection ranging between 50 and 250.

extract_protocol: Total RNA isolated from the pellet using TRIZOL (Invitrogen) and DNase treated using Turbo DNA-free (Ambion) according to manufacture instructions.

treatment_protocol: After two hours of incubation, the monolayer was washed two times and fresh media with 50µg / ml of gentamicin was added. The antibodic supplemented medium was removed after 1 hour and fresh medium without antibiotic was added. This was considered as time zero for the infection. 24 hours post infection the monolayer was washed twice and scraped in half diluted ice cold Phosphate Buffered Saline (P.B.S). The scraped medium was spun at 20,000g to obtain the cell pellet. The cell pellet was resuspended in equal volume half diluted ice cold P.B.S. Equal pellet volume of 40 µm glass beads were added and the macrophages were lysed by vortexing for 30 sec 3 times with incubations of 45 sec on ice in between the vortexes. The solution was spun at 800g for 10 minutes and the pellet was discarded. The supernatant was spun at 20,000g for 10 min and the supernatant was discarded.

tag: isolated from

value: J774 macrophages


title: CD133-GFP+_tech replicate 1

description:
Human infant kidney-derived cells, passage 5, CD133-GFP+ _tech replicate 1
S_133_minus_1

value: minus


title: CD133-GFP+_tech replicate 3

description:
Human infant kidney-derived cells, passage 5, CD133-GFP+ _tech replicate 3
S_133_minus_3


title: U112 24 hpi J774 rep 2


title: CD133+GFP+_tech replicate 1

description:
Human infant kidney-derived cells, passage 5, CD133+GFP+ tech replicate 1
S_133_plus_1


title: CD133+GFP+_tech replicate 2

description:
Human infant kidney-derived cells, passage 5, CD133+GFP+ tech replicate 2
S_133_plus_2


title: X38_TP_B04.05707B6_2_1

status: Public on May 01 2017

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: PM Formalin-fixed paraffin-embedded tissue (X38_TP_B04.05707B6_2_1)

hyb_protocol: Total RNA was extracted from FFPE tissues with the miRNeasy FFPE kit (Qiagen), labeled using the Agilent miRNA Labeling and Hybridization Kit (Agilent Technologies Incorporated, Santa Clara CA, USA), hybridized to Agilent Human miRNA microarrays

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: Raw data were normalized by quantile algorithm using Bioconductor (v.3.3)

source_name: Formalin-fixed paraffin-embedded tissue

tag: idc

value: primary IDC with regional LN involvement (PM)


title: X39_TP_B04.02756B6_1_2

description: PM Formalin-fixed paraffin-embedded tissue (X39_TP_B04.02756B6_1_2)

extract_protocol: Total RNA was extracted from FFPE tissues with the miRNeasy FFPE kit (Qiagen), labeled using the Agilent miRNA Labeling and Hybridization Kit


title: CD133-GFP+_tech replicate 2

description:
Human infant kidney-derived cells, passage 5, CD133-GFP+ _tech replicate 2
S_133_minus_2


title: X35_TP_B03.5711B1_2_2

description: PM Formalin-fixed paraffin-embedded tissue (X35_TP_B03.5711B1_2_2)


title: U112 24 hpi J774 rep 3


title: X40_TP_B04.06079C2_2_3

description: PM Formalin-fixed paraffin-embedded tissue (X40_TP_B04.06079C2_2_3)


title: X34_TP_B04.14779B2_1_3

description: PM Formalin-fixed paraffin-embedded tissue (X34_TP_B04.14779B2_1_3)


title: X36_TP_B05.276255_1_2

description: PM Formalin-fixed paraffin-embedded tissue (X36_TP_B05.276255_1_2)


title: T4A_Rtt103

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

description: Rtt103 ChIP-chip in T4A

hyb_protocol: 24 pmol of ChIP DNA and an equivalent mass of input DNA were mixed in a speedvac on medium heat for 30 min. The samples were resuspended in 18 uL of hybrdization buffer and loaded using NimbleGen X1 mixers and hybridzed on a MAUI instrument.

scan_protocol: Arrays were scanned on a GenePix 4000B instrument as previously described (Tietjen, et al., 2010).

data_processing: Probe intensities were extracted with NimbleScan using the .ndf file. Global and local normalization was performed using in-house R code available upon request, log2-transformed and averaged with a five-probe moving average to smooth the data.

organism: Saccharomyces cerevisiae

source_name: Rtt103 input DNA from T4A

label_protocol: ChIP DNA was end-repaired, linkers were ligated and ligation-mediated PCR was performed as previously described (Tietjen, et al., 2010).

growth_protocol: grow in YPD to OD600=0.5 at 30°C

extract_protocol: For every immunoprecipitation, 50 ul of protein G conjugated Dynabeads (Life Technologies), pre-washed with lysis buffer (50mM HEPES-KOH [pH 7.5], 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 1mM, Aprotinin, 1mM Leupeptin, 1mM PMSF, 1mM Benzamidine, 1.45mM Pepstatin, 1mM NaN3, 1mM Na3VO4, 1mM NaF), were mixed with the whole cell extract-antibody mixture to pulldown Pol II complexes. Washes and elution were performed as previously described (Tietjen et al., 2010).

value: MATalpha his3delta200 leu2-3,112 ura3-52 rpb1delta187::HIS3 pY1-T4A19

tag: antibody

value: FLAG - M2 - Sigma

source_name: Rtt103 IP DNA from T4A


title: X37_TP_B05.07307B6_1_1

description: PM Formalin-fixed paraffin-embedded tissue (X37_TP_B05.07307B6_1_1)


title: X28_TP_B00.10744B6_1_4

description: PM Formalin-fixed paraffin-embedded tissue (X28_TP_B00.10744B6_1_4)


title: Liver_warm_control_2

description:
10654E10_574
Gene expression after warm temperature and control diet acclimation in liver

value: male

value: warm, 27C

value: control

value: liver


title: WT_RNA

description: RNA expression analysis in WT

hyb_protocol: Hybridization on Maui hyb station according to Nimblegen and Maui protocols

scan_protocol: Axon GenePix scanner

data_processing: Background-subtracted signal intentisties for all probes were normalized by quantile normalization, removing probes with missing signal,

source_name: S. cerevisiae WT

label_protocol: Amino-allyl-dUTP incorporated into generated cDNA; post-synthesis coupling to cyanine dyes (see Lee & Topper. 2011. Mol Sys Bio 7:514)

growth_protocol: Cells were grow in YPD to OD600=0.5 at 30°C

extract_protocol: Hot phenol lysis to isolate total RNA

value: MATalpha his3delta200 leu2-3,112 ura3-52 rpb1delta187::HIS3 pY1-WT21


title: WT_Rtt103

description: Rtt103 ChIP-chip in WT

source_name: Rtt103 input DNA from WT

source_name: Rtt103 IP DNA from WT


title: WT_pThr4

description: pThr4 ChIP-chip in WT

source_name: pThr4 input DNA from WT

value: pThr4 - 1G7

source_name: pThr4 IP DNA from WT


title: X21_TP_B04.7477A4_1_2

description: PM Formalin-fixed paraffin-embedded tissue (X21_TP_B04.7477A4_1_2)


title: X23_TP_B05.13236.4_1_3

description: PM Formalin-fixed paraffin-embedded tissue (X23_TP_B05.13236.4_1_3)


title: X26_TP_B03.13616D2_1_1

description: PM Formalin-fixed paraffin-embedded tissue (X26_TP_B03.13616D2_1_1)


title: X29_TP_B00.10222C2_1_1

description: PM Formalin-fixed paraffin-embedded tissue (X29_TP_B00.10222C2_1_1)


title: X22_TP_B05.9647.6_2_2

description: PM Formalin-fixed paraffin-embedded tissue (X22_TP_B05.9647.6_2_2)


title: X27_TP_B04.19478E_2_3

description: PM Formalin-fixed paraffin-embedded tissue (X27_TP_B04.19478E_2_3)


title: X25_TP_B06.2582.1_1_3

description: PM Formalin-fixed paraffin-embedded tissue (X25_TP_B06.2582.1_1_3)


title: X7_noM_B04.11037_2_2

description: PNM Formalin-fixed paraffin-embedded tissue (X7_noM_B04.11037_2_2)

value: primary IDC without LN involvement (PNM)


title: X9_noM_B04.18306_2_1

description: PNM Formalin-fixed paraffin-embedded tissue (X9_noM_B04.18306_2_1)


title: X8_noM_B03.12900_2_3

description: PNM Formalin-fixed paraffin-embedded tissue (X8_noM_B03.12900_2_3)


title: X31_TP_B00.12535B_1_2

description: PM Formalin-fixed paraffin-embedded tissue (X31_TP_B00.12535B_1_2)


title: X71_Pool_PoolNormalesSanos_1_4

description: N Formalin-fixed paraffin-embedded tissue (X71_Pool_PoolNormalesSanos_1_4)

value: normal breast epithelial tissue


title: X24_TP_B03.1733A3_2_3

description: PM Formalin-fixed paraffin-embedded tissue (X24_TP_B03.1733A3_2_3)


title: T4A_RNA

description: RNA expression analysis in T4A/WT

source_name: S. cerevisiae T4A


title: X6_noM_B03.5512G2.1._1_1

description: PNM Formalin-fixed paraffin-embedded tissue (X6_noM_B03.5512G2.1._1_1)


title: X2_noM_B01.14480A2_1_2

description: PNM Formalin-fixed paraffin-embedded tissue (X2_noM_B01.14480A2_1_2)


title: X5_noM_B03.5537B2_1_3

description: PNM Formalin-fixed paraffin-embedded tissue (X5_noM_B03.5537B2_1_3)


title: X4_noM_B02.17197C1_1_4

description: PNM Formalin-fixed paraffin-embedded tissue (X4_noM_B02.17197C1_1_4)


title: X30_TP_B00.11952A3_2_1

description: PM Formalin-fixed paraffin-embedded tissue (X30_TP_B00.11952A3_2_1)


title: X33_TP_B03.15905D2_2_3

description: PM Formalin-fixed paraffin-embedded tissue (X33_TP_B03.15905D2_2_3)


title: T4A_Rpb3

description: Rpb3 ChIP-chip in T4A

source_name: Rpb3 input DNA from T4A

value: Rpb3 - 1Y26 - Biolegend

source_name: Rpb3 IP DNA from T4A


title: WT_Rpb3

description: Rpb3 ChIP-chip in WT

source_name: Rpb3 input DNA from WT

source_name: Rpb3 IP DNA from WT


title: X32_TP_B02.12885B2_2_2

description: PM Formalin-fixed paraffin-embedded tissue (X32_TP_B02.12885B2_2_2)


title: X18_noM_B04.22803A2_2_1

description: PNM Formalin-fixed paraffin-embedded tissue (X18_noM_B04.22803A2_2_1)


title: X20_noM_B04.19804B_2_3

description: PNM Formalin-fixed paraffin-embedded tissue (X20_noM_B04.19804B_2_3)


title: X17_noM_B04.10045A1_1_1

description: PNM Formalin-fixed paraffin-embedded tissue (X17_noM_B04.10045A1_1_1)


title: X15_noM_B03.7648C2_2_3

description: PNM Formalin-fixed paraffin-embedded tissue (X15_noM_B03.7648C2_2_3)


title: X12_noM_B03.17701C_1_2

description: PNM Formalin-fixed paraffin-embedded tissue (X12_noM_B03.17701C_1_2)


title: X11_noM_B04.08120E1_2_2

description: PNM Formalin-fixed paraffin-embedded tissue (X11_noM_B04.08120E1_2_2)


title: X10_noM_B03.14463B_1_2

description: PNM Formalin-fixed paraffin-embedded tissue (X10_noM_B03.14463B_1_2)


title: X14_noM_B03.22683D1_1_3

description: PNM Formalin-fixed paraffin-embedded tissue (X14_noM_B03.22683D1_1_3)


title: X51_MD_B99.8522C_1_4

description: DM Formalin-fixed paraffin-embedded tissue (X51_MD_B99.8522C_1_4)

value: distant metastases (DM)


title: X53_MD_B05.5041A_1_4

description: DM Formalin-fixed paraffin-embedded tissue (X53_MD_B05.5041A_1_4)


title: X48_MD_B98.2507A2_2_4

description: DM Formalin-fixed paraffin-embedded tissue (X48_MD_B98.2507A2_2_4)


title: X47_MD_B97.9330A_2_2

description: DM Formalin-fixed paraffin-embedded tissue (X47_MD_B97.9330A_2_2)


title: X56_MD_B99.1991A5_1_1

description: DM Formalin-fixed paraffin-embedded tissue (X56_MD_B99.1991A5_1_1)


title: X54_MD_B04.1172A_2_2

description: DM Formalin-fixed paraffin-embedded tissue (X54_MD_B04.1172A_2_2)


title: X57_MD_B08.163411_2_1

description: DM Formalin-fixed paraffin-embedded tissue (X57_MD_B08.163411_2_1)


title: X55_MD_B00.4809_2_4

description: DM Formalin-fixed paraffin-embedded tissue (X55_MD_B00.4809_2_4)


title: X59_MD_B08.73563_2_1

description: DM Formalin-fixed paraffin-embedded tissue (X59_MD_B08.73563_2_1)


title: X48_MD_B98.12112A_1_3

description: DM Formalin-fixed paraffin-embedded tissue (X48_MD_B98.12112A_1_3)


title: X46_MD_B98.12439_1_2

description: DM Formalin-fixed paraffin-embedded tissue (X46_MD_B98.12439_1_2)


title: X1_noM_B01.14360A2_1_1

description: PNM Formalin-fixed paraffin-embedded tissue (X1_noM_B01.14360A2_1_1)


title: X49_MD_B97.11955D_2_3

description: DM Formalin-fixed paraffin-embedded tissue (X49_MD_B97.11955D_2_3)


title: X16_noM_B03.16743C_1_4

description: PNM Formalin-fixed paraffin-embedded tissue (X16_noM_B03.16743C_1_4)


title: X3_noM_B02.23804_2_1

description: PNM Formalin-fixed paraffin-embedded tissue (X3_noM_B02.23804_2_1)


title: X50_MD_B01.2889A1_2_4

description: DM Formalin-fixed paraffin-embedded tissue (X50_MD_B01.2889A1_2_4)


title: X19_noM_B05.84543_1_3

description: PNM Formalin-fixed paraffin-embedded tissue (X19_noM_B05.84543_1_3)


title: X58_MD_B07.8851_1_3

description: DM Formalin-fixed paraffin-embedded tissue (X58_MD_B07.8851_1_3)


title: X52_MD_B01.15125P_2_4

description: DM Formalin-fixed paraffin-embedded tissue (X52_MD_B01.15125P_2_4)


title: X41_MD_B97.16075P_1_4

description: DM Formalin-fixed paraffin-embedded tissue (X41_MD_B97.16075P_1_4)


title: X44_MD_B97.10649B1_1_1

description: DM Formalin-fixed paraffin-embedded tissue (X44_MD_B97.10649B1_1_1)


title: X43_MD_B97.7125A3_2_1

description: DM Formalin-fixed paraffin-embedded tissue (X43_MD_B97.7125A3_2_1)


title: X13_noM_B04.19825C_2_2

description: PNM Formalin-fixed paraffin-embedded tissue (X13_noM_B04.19825C_2_2)


title: X45_MD_B00.13_2_1

description: DM Formalin-fixed paraffin-embedded tissue (X45_MD_B00.13_2_1)


title: X39_G_B04.02851BT_1_3

description: LNM Formalin-fixed paraffin-embedded tissue (X39_G_B04.02851BT_1_3)

value: node-positive primary tumors (LNM)


title: X40_G_B04.6080C_2_4

description: LNM Formalin-fixed paraffin-embedded tissue (X40_G_B04.6080C_2_4)


title: X42_MD_B99.5167_1_1

description: DM Formalin-fixed paraffin-embedded tissue (X42_MD_B99.5167_1_1)


title: X37_G_B05.07308B_1_2

description: LNM Formalin-fixed paraffin-embedded tissue (X37_G_B05.07308B_1_2)


title: X38_G_B04.05799G2_2_2

description: LNM Formalin-fixed paraffin-embedded tissue (X38_G_B04.05799G2_2_2)


title: X33_G_B03.15928E_2_4

description: LNM Formalin-fixed paraffin-embedded tissue (X33_G_B03.15928E_2_4)


title: S2A_RNA

description: RNA expression analysis in S2A/WT

source_name: S. cerevisiae S2A

value: MATalpha his3delta200 leu2-3,112 ura3-52 rpb1delta187::HIS3 pY1-S2A8-WT7


title: X36_G_B05.276265_1_3

description: LNM Formalin-fixed paraffin-embedded tissue (X36_G_B05.276265_1_3)


title: X26_G_B03.13682C_1_2

description: LNM Formalin-fixed paraffin-embedded tissue (X26_G_B03.13682C_1_2)


title: X23_G_B05.13238.10_1_4

description: LNM Formalin-fixed paraffin-embedded tissue (X23_G_B05.13238.10_1_4)


title: X31_G_B00.12639C_1_3

description: LNM Formalin-fixed paraffin-embedded tissue (X31_G_B00.12639C_1_3)


title: X21_G_B04.7493B_1_3

description: LNM Formalin-fixed paraffin-embedded tissue (X21_G_B04.7493B_1_3)


title: X27_G_B04.19533A_2_4

description: LNM Formalin-fixed paraffin-embedded tissue (X27_G_B04.19533A_2_4)


title: X29_G_B10338D_1_2

description: LNM Formalin-fixed paraffin-embedded tissue (X29_G_B10338D_1_2)


title: X22_G_B05.9648.1_2_3

description: LNM Formalin-fixed paraffin-embedded tissue (X22_G_B05.9648.1_2_3)


title: X34_G_B04.16289B_1_4

description: LNM Formalin-fixed paraffin-embedded tissue (X34_G_B04.16289B_1_4)


title: X30_G_B00.11980E_2_2

description: LNM Formalin-fixed paraffin-embedded tissue (X30_G_B00.11980E_2_2)


title: X66_DCIS_B02.3587B2_2_4

description: DCIS Formalin-fixed paraffin-embedded tissue (X66_DCIS_B02.3587B2_2_4)

value: ductal carcinomas in situ (DCIS)


title: X28_G_B00.10744G3_2_1

description: LNM Formalin-fixed paraffin-embedded tissue (X28_G_B00.10744G3_2_1)


title: X25_G_B062582.14_1_4

description: LNM Formalin-fixed paraffin-embedded tissue (X25_G_B062582.14_1_4)


title: X24_G_B03.1734A_2_4

description: LNM Formalin-fixed paraffin-embedded tissue (X24_G_B03.1734A_2_4)


title: X65_DCIS_B02.5323C_1_4

description: DCIS Formalin-fixed paraffin-embedded tissue (X65_DCIS_B02.5323C_1_4)


title: X32_G_B02.12886A7_2_3

description: LNM Formalin-fixed paraffin-embedded tissue (X32_G_B02.12886A7_2_3)


title: X64_DCIS_B00.13642A4_2_3

description: DCIS Formalin-fixed paraffin-embedded tissue (X64_DCIS_B00.13642A4_2_3)


title: X63_DCIS.B04.2756B91_4

description: DCIS Formalin-fixed paraffin-embedded tissue (X63_DCIS.B04.2756B91_4)


title: X62_DCIS_B04.5707A1_2_1

description: DCIS Formalin-fixed paraffin-embedded tissue (X62_DCIS_B04.5707A1_2_1)


title: Mutant hypoxia 50 hpf

city: Bad Nauheim

first: Claudia

last: Gerri

address: Ludwigstraße 43

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

description: hif1α mutant at 50 hpf after hypoxia incubation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8 x 60K zebrafish expression array (XS-5090; Agilent 60-mer SurePrint technology)

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: Danio rerio

source_name: Zebrafish hif1α mutants, 50 hpf, hypoxia

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

growth_protocol: Zebrafish embryos were grown at 28 degree celsius in their medium

extract_protocol: RNA was extracted using TRIZOL (Life Technologies) from 30 hif1α double mutants (hif1aabns89/bns89;hif1abbns90/bns90) and 30 WT siblings.

treatment_protocol: Two different conditions were considered: 50 hpf mutants and WT in normoxia, 50 hpf mutants and WT after hypoxia chamber treatment (2 hours after 3% O2)

tag: developmental stage

value: 50 hpf

tag: sample type

value: 30 embryos


title: X61_DCIS_B03.18584A7_1_2

description: DCIS Formalin-fixed paraffin-embedded tissue (X61_DCIS_B03.18584A7_1_2)


title: WT normoxia 50 hpf

description: WT embryos at 50 hpf normoxia

source_name: Zebrafish WT embryos, 50 hpf, normoxia


title: X60_DCIS_B05.926A2_2_1

description: DCIS Formalin-fixed paraffin-embedded tissue (X60_DCIS_B05.926A2_2_1)


title: WT hypoxia 50 hpf

description: WT embryos at 50 hpf after hypoxia incubation

source_name: Zebrafish WT embryos, 50 hpf, hypoxia


title: X35_G_B03.5711I2_2_3

description: LNM Formalin-fixed paraffin-embedded tissue (X35_G_B03.5711I2_2_3)

source_name: Formalin-fixed paraffin-embedded tissue


title: Mutant normoxia 50 hpf

description: hif1α mutant at 50 hpf normoxia

source_name: Zebrafish hif1α mutants, 50 hpf, normoxia


title: X67_DCIS_B04.14269L_2_2

description: DCIS Formalin-fixed paraffin-embedded tissue (X67_DCIS_B04.14269L_2_2)


title: case9_N_SNP

city: FUKUOKA

first: RYUTARO

last: UCHI

state: FUKUOKA

institute: KYUSHUUNIVERSItY

description: SAMPLE 70

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Illumina's GenomeStudio software was used to obtain B allele frequencies (BAF) and log R ratios (LRR) from the raw output data.

source_name: Normal colon tissue

extract_protocol: Total DNA was isolated by standard procedures with Qiagen AllPrep DNA/RNA Mini Kit

tag: case

tag: gender

value: Female

tag: age

tag: primary tumor differentiation

value: moderately differentiated

tag: tumor or normal colon location

value: ascending colon

tag: tissue sample

value: normal colon tissue


title: case8_T8_SNP

description: SAMPLE 69

source_name: Primary colorectal tumor tissue

value: sigmoid colon

value: primary colorectal tumor tissue


title: case8_T4_SNP

description: SAMPLE 66


title: case9_T8_SNP

description: SAMPLE 75


title: case7_T8_SNP

description: SAMPLE 62

value: well to moderately differentiated

value: rectum


title: case7_T7_SNP

description: SAMPLE 61


title: case6_T2_SNP

description: SAMPLE 51


title: case7_T1_SNP

description: SAMPLE 57


title: case6_T8_SNP

description: SAMPLE 55


title: case8_T5_SNP

description: SAMPLE 67


title: case6_N_SNP

description: SAMPLE 49


title: case8_N_SNP

description: SAMPLE 63


title: case8_T1_SNP

description: SAMPLE 64


title: case7_N_SNP

description: SAMPLE 56


title: case5_T8_SNP

description: SAMPLE 48

value: Male

value: well differentiated


title: case9_T2_SNP

description: SAMPLE 72


title: case7_T4_SNP

description: SAMPLE 59


title: case5_T5_SNP

description: SAMPLE 46


title: case7_T6_SNP

description: SAMPLE 60


title: case6_T1_SNP

description: SAMPLE 50


title: case6_T7_SNP

description: SAMPLE 54


title: case6_T3_SNP

description: SAMPLE 52


title: case6_T6_SNP

description: SAMPLE 53


title: case7_T2_SNP

description: SAMPLE 58


title: case9_T6_SNP

description: SAMPLE 74


title: case5_T6_SNP

description: SAMPLE 47


title: case8_T3_SNP

description: SAMPLE 65


title: case9_T3_SNP

description: SAMPLE 73


title: case9_T1_SNP

description: SAMPLE 71


title: case8_T6_SNP

description: SAMPLE 68


title: case5_T3_SNP

description: SAMPLE 45


title: case5_N_SNP

description: SAMPLE 42


title: case4_T8_SNP

description: SAMPLE 41


title: case4_T5_SNP

description: SAMPLE 39


title: case5_T2_SNP

description: SAMPLE 44


title: case5_T1_SNP

description: SAMPLE 43


title: case3_po1_SNP

description: SAMPLE 30

value: descending colon


title: case3_S_SNP

description: SAMPLE 35


title: case3_M_SNP

description: SAMPLE 28


title: case4_T6_SNP

description: SAMPLE 40


title: case4_N_SNP

description: SAMPLE 36


title: case3_po2_SNP

description: SAMPLE 31


title: case3_G2_SNP

description: SAMPLE 23


title: case3_Q_SNP

description: SAMPLE 33


title: case4_T4_SNP

description: SAMPLE 38


title: case3_I_SNP

description: SAMPLE 25


title: case3_R_SNP

description: SAMPLE 34


title: case3_O_SNP

description: SAMPLE 29


title: case3_H_SNP

description: SAMPLE 24


title: case3_po3_SNP

description: SAMPLE 32


title: case3_J_SNP

description: SAMPLE 26


title: case3_F2_SNP

description: SAMPLE 21


title: case3_E3_SNP

description: SAMPLE 19


title: case3_G1_SNP

description: SAMPLE 22


title: case3_F1_SNP

description: SAMPLE 20


title: DmagOv_MF_rep4

city: Okazaki

first: Kenji

last: Toyota

address: 5-1 Higashiyama

institute: National Institute for Basic Biology

description: Gene expression in response to MF treatment in ovary

hyb_protocol: 165 µg of Cyanine3-labeled cRNA were hybridized to the custom 4x44k D. magna microarray according to the manufacture’s protocol. After 17 h incubation with rotation, the microarrays were washed with Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s procedure.

scan_protocol: DNA microarrays were scanned using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) at 5 µm resolution.

data_processing: The signal intensity of the spots was digitized using the microarray imager software (Combimatrix Molecular Diagnostics, Irvine, CA, USA).

organism: Daphnia magna

source_name: Ovary, methyl farnesoate, replicate 4

label_protocol: 500 ng of total RNA were prepared for hybridization using the Quick Amp Labeling Kit and One-color RNA Spike-in kit (Agilent Technologies), and purified using the RNeasy Micro Kit (Qiagen) following the manufacturer’s protocol. The quality of Cyanine3-labeled complementary RNA (cRNA) was analyzed using the 2100 Bioanalyzer.

extract_protocol: Harvested those ovaries were homogenized using the physcotron NS-310E (Nichion, Tokyo, Japan). Total RNA was extracted by TRIZOL reagent (Invitrogen, Tokyo, Japan), and purified using the RNeasy Micro Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocols. The RNA treated with RNase-free DNase was cleaned up using the RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol. The quality and concentration of total RNA was validated by NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: tissue

value: Whole ovary including in male oocytes

tag: treatment

value: methyl farnesoate


title: DmagOv_DMF(MF)_rep4

description: Gene expression in response to DMF treatment in ovary

source_name: Ovary, DMF(MF), replicate 4

value: Whole ovary including in female oocytes

value: DMF


title: DmagOv_DMF(MF)_rep1

source_name: Ovary, DMF(MF), replicate 1


title: DmagOv_MF_rep3

source_name: Ovary, methyl farnesoate, replicate 3


title: DmagOv_DMF(MF)_rep2

source_name: Ovary, DMF(MF), replicate 2


title: DmagOv_MF_rep2

source_name: Ovary, methyl farnesoate, replicate 2


title: case3_E1_SNP

description: SAMPLE 18


title: DmagOv_MF_rep1

source_name: Ovary, methyl farnesoate, replicate 1


title: DmagOv_DMF(Fx)_rep4

source_name: Ovary, DMF(Fx), replicate 4


title: DmagOv_DMF(MF)_rep3

source_name: Ovary, DMF(MF), replicate 3


title: DmagOv_DMF(Fx)_rep3

source_name: Ovary, DMF(Fx), replicate 3


title: DmagOv_DMF(Fx)_rep2

source_name: Ovary, DMF(Fx), replicate 2


title: case3_D_SNP

description: SAMPLE 17


title: case4_T3_SNP

description: SAMPLE 37


title: DmagOv_Fx_rep2

description: Gene expression in response to Fx treatment in ovary

source_name: Ovary, fenoxycarb, replicate 2

value: fenoxycarb


title: DmagOv_Fx_rep4

source_name: Ovary, fenoxycarb, replicate 4


title: DmagOv_Fx_rep1

source_name: Ovary, fenoxycarb, replicate 1


title: DmagOv_DMF(Fx)_rep1

source_name: Ovary, DMF(Fx), replicate 1


title: case3_C_SNP

description: SAMPLE 16


title: DmagOv_Fx_rep3

source_name: Ovary, fenoxycarb, replicate 3


title: case2_Liver2_SNP

description: SAMPLE 12

source_name: Liver metastasis tumor tissue

value: Liver

value: liver metastasis tumor tissue


title: 7721-EPOR-1

city: shanghai

first: shizhong

last: ke

address: Xietu Road No. 25 Lane 2200

department: Shanghai Cancer Institute

country: China

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression after NS treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1ul of 25x Agilent fragmentation buffer and 5ul of 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60K，Design ID：039494）for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325) and 1 minute with 37Â°C Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2505C) using one color scan (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version13.1,Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 100% of the values in any 1 out of all conditions have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

label_protocol: Cyanine-3-CTP labeled cRNA was prepared from 0.2 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cells were routinely cultured in DMEM medium supplemented with 10% fetal bovine serum within a humidified incubator containing 5% CO2 at 37°C.

extract_protocol: RNA was extracted using Trizol according to the manufacturer's instructions

treatment_protocol: 1×10e6 7721-EPOR cells were plated in 6 cm dishes and starved for 8 hours and then treated with either NS or EPO (10 IU/ml) for 16 hours.

tag: cell line

value: hepatocellular carcinoma cell line 7721-EPOR

tag: agent

value: control


title: case3_Liver_SNP

description: SAMPLE 27


title: Liver_Maf_CKO_rep3

city: Sendai

first: Masayuki

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were analyzed using GeneSpring GX software (Agilent).  Normalization was performed usig Percentile Shift.

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

growth_protocol: All mice were kept in specific-pathogen-free conditions, and allowed water and rodent chow ad libitum.

extract_protocol: Total RNA was extracted from liver tissues using Isogen (Nippon Gene) and further purified by RNAeasy.

tag: strain background

value: mixed; 129Sv/J, C57BL/6J, and ICR

tag: genotype/variation

value: liver-specific small Maf knockout

value: 5 weeks


title: 7721-EPOR+EPO-2

description: Gene expression after EPO treatment

value: EPO


title: 7721-EPOR+EPO-1

description: Gene expression after EPO treatment


title: Liver_Maf_CKO_rep2


title: Liver_Maf_Control_rep2

value: control wild type


title: Liver_Maf_Control_rep1


title: case2_G3_SNP

description: SAMPLE 9

source_name: Primary colorectal tumor tissue

value: Male

value: primary colorectal tumor tissue


title: case3_B_SNP

description: SAMPLE 15

value: well to moderately differentiated

value: descending colon


title: case2_Liver3_SNP

description: SAMPLE 13

value: well differentiated


title: case2_D2_SNP

description: SAMPLE 3


title: case2_I3_SNP

description: SAMPLE 10


title: Liver_Maf_Control_rep3


title: Liver_Maf_CKO_rep1


title: case2_Liver1_SNP

description: SAMPLE 11


title: case2_E2_SNP

description: SAMPLE 5


title: case3_normal_SNP

description: SAMPLE 14

source_name: Normal colon tissue

value: normal colon tissue


title: WholeBlood Unexposed_QQ 47

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

description: Prenatal pesticide unexposed, PON1 192QQ

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Cg-probes were filtered before normalization based on following criteria: probes containing a SNP within 3 bp of the analysed CpG site, bad quality probes based on an iterative greedycut algorithm where a detection p-value of 0.01 was set as a threshold for an unreliable measurement, and probes with missing values in at least one sample. After filtering these cg-probes, beta-values were within-array normalized using the beta mixture quantile dilation (BMIQ) method. Another filtering step was performed after normalization based on following criteria: probes measuring methylation not at CpG sites and probes on sex chromosomes.

label: Cy5 and Cy3

source_name: WholeBlood, pesticide Unexposed, PON1 192QQ

label_protocol: Standard Illumina Protocol

extract_protocol: gDNA was extracted from buffy coat samples using QIAamp DNA Blood Mini kit from Qiagen

tag: pesticide exposure

value: Unexposed

tag: pon1 192 genotype

value: PON1 192QQ

tag: pon1 activity

tag: bmi z-scores

tag: bmi z-score difference

tag: bodyfat (%)

tag: leptin (pg/ml)


title: case2_D3_SNP

description: SAMPLE 4

tag: case

tag: gender

tag: age


title: WholeBlood Unexposed_QR 45

description: Prenatal pesticide unexposed, PON1 192QR

source_name: WholeBlood, pesticide Unexposed, PON1 192QR

value: PON1 192QR


title: case2_F2_SNP

description: SAMPLE 8

tag: primary tumor differentiation

tag: tumor or normal colon location

tag: tissue sample


title: case2_normal_SNP

description: SAMPLE 1


title: 7721-EPOR-2

description: Gene expression after NS treatment

tag: cell line


title: case2_C2_SNP

description: SAMPLE 2


title: WholeBlood Unexposed_QQ 40

value: Female


title: WholeBlood Unexposed_QQ 46


title: WholeBlood Unexposed_QR 43


title: WholeBlood Unexposed_QQ 44


title: WholeBlood Unexposed_QR 48


title: case2_E3_SNP

description: SAMPLE 6


title: WholeBlood Unexposed_QR 28


title: WholeBlood Unexposed_QR 37


title: WholeBlood Unexposed_QQ 41


title: WholeBlood Unexposed_QR 34


title: WholeBlood Unexposed_QR 32


title: case2_E4_SNP

description: SAMPLE 7


title: WholeBlood Exposed_QR 25

description: Prenatal pesticide exposed, PON1 192QR

source_name: WholeBlood, pesticide Exposed, PON1 192QR

value: Exposed


title: WholeBlood Exposed_QQ 26

description: Prenatal pesticide exposed, PON1 192QQ

source_name: WholeBlood, pesticide Exposed, PON1 192QQ


title: WholeBlood Unexposed_QQ 42


title: WholeBlood Unexposed_QQ 27


title: WholeBlood Exposed_QQ 30

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Unexposed_QQ 31


title: WholeBlood Exposed_QQ 21

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Exposed_QR 18

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Unexposed_QQ 36


title: WholeBlood Unexposed_QR 39


title: WholeBlood Exposed_QQ 19

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Unexposed_QR 33


title: WholeBlood Exposed_QR 16

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Unexposed_QQ 35


title: WholeBlood Exposed_QQ 22

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Exposed_QQ 17

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Exposed_QQ 24

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Exposed_QQ 29

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Exposed_QR 20

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QR 14

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QR 12

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QQ 15

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Exposed_QQ 13

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Unexposed_QR 38


title: WholeBlood Exposed_QR 8

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QR 9

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QR 11

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QR 5

description: Prenatal pesticide exposed, PON1 192QR


title: WholeBlood Exposed_QQ 6

description: Prenatal pesticide exposed, PON1 192QQ


title: WholeBlood Unexposed_QR 23


title: rCNT inhalation 4days + 24h M3_4h.4d.24h

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: RNA isolation from the lung samples was done with TRIsure (phenol-chloroform extraction) and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.

treatment_protocol: mice lung tissue samples collected 24h after final exposure. Tissue samples stored in RNAlater in -80ºC

tag: exposure

value: rCNT inhalation 4h per day

tag: exposure method

value: inhalation

tag: time


title: WholeBlood Unexposed_QQ 3

tag: pesticide exposure


title: vehicle (PBS) aspiration 4days + 24h UT1

value: Untreated


title: rCNT inhalation 4days + 24h M1_4h.4d.24h


title: WholeBlood Exposed_QR 7

description: Prenatal pesticide exposed, PON1 192QR

tag: pon1 192 genotype


title: Proband163

city: New York

first: Andrew

last: Sharp

state: NY

address: 1470 Madison Av

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg19 (GRCh37) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.

source_name: Whole Blood

extract_protocol: DNA was acquired from various labs/consortiums

tag: tissue

value: Whole Blood

tag: individual


title: Proband266


title: rCNT aspiration 4days + 24h M4_4d24h

value: 10 ug of rCNT in 50 ul of PBS

value: aspiration


title: Proband268

value: Male


title: Proband166


title: Proband165


title: WholeBlood Unexposed_QR 2

tag: pon1 activity

tag: bmi z-scores

tag: bmi z-score difference


title: WholeBlood Exposed_QR 10

description: Prenatal pesticide exposed, PON1 192QR

tag: bodyfat (%)

tag: leptin (pg/ml)


title: Proband265

tag: gender


title: Proband164


title: Vehicle (PBS) aspiration 4days + 24h C3_4d24h

value: 50 ul of PBS


title: Proband267


title: Proband162


title: WholeBlood Exposed_QQ 4

description: Prenatal pesticide exposed, PON1 192QQ


title: Proband161


title: WholeBlood Exposed_QQ 1

description: Prenatal pesticide exposed, PON1 192QQ


title: Untreated inhalation control 4 days + 24h UT4


title: Proband269


title: Proband264


title: Untreated inhalation control 4 days + 24h UT3


title: Proband259


title: rCNT inhalation 4days + 24h M2_4h.4d.24h


title: Vehicle (PBS) aspiration 4days + 24h C4_4d24h


title: Proband260


title: Untreated inhalation control 4 days + 24h UT2


title: Vehicle (PBS) aspiration 4days + 24h C1_4d24h


title: Proband270


title: Proband263


title: Proband262


title: Proband261


title: rCNT aspiration 4days + 24h M1_4d24h


title: rCNT aspiration 4days + 24h M2_4d24h


title: rCNT aspiration 4days + 24h M3_4d24h