title: Poplar inclined for 45 min (basal part 1) tree1, dye-swap

city: Tunis

first: Wassim

last: Azri

address: Campus universitaire

country: Tunisia

institute: Biology

description:
Slide13040225_730_550
Analysis used non-inclined plants RNA as control samples for comparison to the experimental samples inclined for 45 min.

hyb_protocol: Labelled RNA with dyes Cy3 and Cy5 was denatured for 1 min at 95°C and collected in a 60 µl hybridization buffer containing 25% formamide, 5 x SCC, and 0.1% SDS. RNA was then incubated for 2 min at 65°C. The samples were loaded on the slide, which was then placed in a hybridization chamber and incubated in a water bath at 42°C for 18 h. After hybridization, the slide was washed for 10 min in 1 x SSC and 0.2% SDS, then in 0.1 x SSC and 0.2% SDS and finally in 0.1 x SSC. All washing steps were carried out at 55°C. The slides were dried by centrifuging for 10 seconds at 800 rpm, prior to scanning.

scan_protocol: Array slides were scanned by a GenePix 4000B microarray reader (Axon Instrument Inc., Molecular Devices Corporation, Union City, CA, USA).

data_processing: Data analysis was carried out using the Anapuce package developed to the URGV by Aubert et al. (2004) and which is available in the website: (http://cran.r-project.org/web/packages/anapuce/index.html). The mean values from each sample were log2 transformed and normalized using the LOWESS algorithm to remove intensity-dependent effects within the calculated values. Normalised values were used to calculate the inclined/control fluorescence ratios from experimental and biological repeats (seperate chemostat runs) with all replicates combined. Data was compiled from two inclined and two non-inclined plants, each with a dye-swap replicate, thus providing two biological repeats within two technical repeats.

organism: Populus tremula x Populus alba

source_name: Poplar control non-inclined

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using a kit (CyDy Post labelling reactive Dye, ref RPN 5661, Amersham) as per the manufacturer's instructions. Samples were purified according to the recommendation of the manufacturer (Kit Amino Allyl Message-Amp II aRNA).

growth_protocol: Hybrid poplars (Populus tremula x Populus alba), clone INRA n° 717-1-B4, were multiplied clonally in vitro on Murashige and Skoog medium (Murashige and Skoog 1962). When they were approximately 4 cm height, poplar micropropagated shoots were gradually acclimatized on hydroponic solution (Herbette et al. 2004). Then, they were kept in a controlled environment growth chamber with 22/18°C (day/night), photon flux density 60 µmol. m-2.s-1, 16h photoperiod and relative humidity of 70 ± 10%.

extract_protocol: Total RNA was extracted from almost 200 mg of stems using CTAB extraction buffer as described by Chang et al. (2003), and then treated with RNase-free RQ1 DNase (Promega, Charbonnières les Bains, France).

treatment_protocol: Poplars showing 20 developed internodes were inclined at 35° from the vertical axis for 45 min, as previously described by Azri et al. (2009).

tag: clone

value: INRA n° 717-1-B4

value: basal region of stem

value: non-inclined

source_name: Poplar inclined for 45 min

value: inclined

tag: tree identifier


title: Poplar inclined for 45 min (basal part 1) tree1

status: Public on Apr 12 2013

type: RNA

description:
Slide13040224_730_550
Analysis used non-inclined plants RNA as control samples for comparison to the experimental samples inclined for 45 min.

molecule: total RNA

tag: tissue

tag: treatment


title: Poplar inclined for 45 min (basal part 2) tree2, dye-swap

description:
Slide13059810_730_550
Analysis used non-inclined plants RNA as control samples for comparison to the experimental samples inclined for 45 min.


title: WT.2093

city: San Francisco

first: Brian

last: Biehs

state: CA

address: 505 Parnassus Ave

country: USA

institute: UCSF

hyb_protocol: Hybridizations were performed for 17 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

organism: Mus musculus

source_name: Mouse incisor dental epithelia

label_protocol: standard Agilent protocol

extract_protocol: Whole incisors were incubated in accumax, dental epithlial were mechanically separated from mesenchyme and total RNA was extracted using the Qiagen Rneasy mini kit.

tag: genotype

value: WT

value: incisor dental epithelia

tag: genetic background

value: mixed


title: Poplar inclined for 45 min (basal part 2) tree2

description:
Slide13059809_730_550
Analysis used non-inclined plants RNA as control samples for comparison to the experimental samples inclined for 45 min.


title: Bmi1KO.1488


title: WT.2091


title: WT.2086


title: peripheral white blood cell 585

city: Milwaukee

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Medicine

institute: Medical College of Wisconsin

description: Illumina Human WG-6 v3 expression

hyb_protocol: A total of 1.5 µg aRNA was hybridized to Illumina HumanWG-6 version 2 or version 3 chips

scan_protocol: Samples were scanned on the Illumina BeadArray 500GX Reader using Illumina BeadScan image data acquisition software (version 2.3.0.13).

data_processing: Illumina GenomeStudio software (version 2010.3) was used for preliminary data analysis with standard background normalization.

label: biotin

organism: Homo sapiens

source_name: peripheral white blood cell

label_protocol: Biotin-16-UTP (Roche) labeled aRNA was synthesized using Ambion’s proprietary MEGAscript in vitro transcription IVT)  technology and T7 RNA Polymerase. Purification of aRNA samples was carried out using QIAGEN’s RNeasy 96 protocol for RNA cleanup using spin technology.

extract_protocol: 2.5ml blood was collected into a PAXgene® Blood RNA Tube (BD, Franklin Lakes, NJ) following an overnight fast. Total RNA was isolated from each tube using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) and anti-sense RNA (aRNA) was synthesized using the MessageAmp II-Biotin aRNA kit (Ambion, Austin, TX)

tag: race

value: Caucasian

tag: age

tag: gender

value: female

tag: leptin


title: peripheral white blood cell 584

description: Illumina Human WG-6 v3 expression


title: WT.2824


title: ovary_mid-vitellogenesis_rep3 miRNA

status: Public on Apr 11 2013

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description: miRNAs expression

hyb_protocol: Hybridization was performed with hybridizations Spike-In were performed at 55°C, 20 rpm for 20 hours. Slides were washed for 5 minutes with Wash 1 and 2 and immediately proceeded to scan.

scan_protocol: Agilent C Scan (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France)and Scan Control software were used with the following protocol: profile: AgilentHD_miRNA, channels: Green, resolution: 3µm, TIFF: 20 bit.

data_processing: Signal intensities were then quantified using FeatureExtraction software (Agilent). Spot with low signal (lower than three times the background level) were excluded. Data were processed by GeneSpring software (Agilent v.11.5.0) using GmedianSignal. Data were subsequently normalized using the 75th percentile of each array.

organism: Oncorhynchus mykiss

source_name: mid-vitellogenesis ovary replicate 3

label_protocol: MiRNA microarray was performed using miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent v2.2) according to the manufacturer procedure with slight modifications. Total RNA (200 ng) from ovary at different stages with labeling Spike-In were dephosphorylated for 30 minutes at 37°C. RNA was denatured with DMSO at 100°C for 7 minutes. RNA was then labeled by terminal ligation of cyanine3-pCp using T4 ligase for 2 hours at 16°C. Purification of labeled RNA was done using Micro Bio-Spin column (Bio-Rad) to eliminate free cyanine3-pCp

extract_protocol: Tissues was homogeneized in Tri-Reagent and total RNA was extracted  following manufacturer protocol. Due to high vitellogenic content, total RNA was then purified with NucleoSpin miRNA kit (Macherey-Nagel)

value: whole ovary

tag: developmental stage

value: mid-vitellogenesis

tag: rna subtype

value: miRNA


title: ovary_post-vitellogenesis_rep1 miRNA

description: miRNAs expression

source_name: post-vitellogenesis ovary replicate 1

value: post-vitellogenesis


title: ovary_immature_rep2 miRNA

description: miRNAs expression

source_name: immature pre-vitellogenic ovary (5 months old) replicate 2

value: pre-vitellogenic


title: ovary_mid-vitellogenesis_rep2 miRNA

description: miRNAs expression

source_name: mid-vitellogenesis ovary replicate 2


title: ovary_late-vitellogenesis_rep3 miRNA

description: miRNAs expression

source_name: late-vitellogenesis ovary replicate 3

value: late-vitellogenesis


title: ovary_mature_rep3 miRNA

description: miRNAs expression

source_name: mature ovary (meiotic maturation in progress) replicate 3

value: mature ovary


title: ovary_immature_rep1 miRNA

description: miRNAs expression

source_name: immature pre-vitellogenic ovary (5 months old) replicate 1


title: ovary_mature_rep4 mRNA

description: gene expression

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Scanning was performed with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (channels: Green, resolution: 3µm, TIFF: 20 bit)

data_processing: Data were then obtained with the Agilent Feature Extraction software (v10.5.1.1) according to the appropriate GE protocol (GE1_107_Sep09). Before analysis, saturated spot, non-uniform spots and spots not significantly different from background (k=5) were flagged using the Agilent GeneSpring GX software (v.10.0.2). Probes were considered valid when corresponding spots remained present in at least 80% of the replicates of each experimental condition after the flagging procedure. Data were subsequently scale-normalized using the median value of each array.

source_name: mature ovary (meiotic maturation in progress) replicate 4

label_protocol: 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop. 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array.

value: mRNA


title: Steere 3

type: protein

city: Irvine

first: Elisabeth

last: Baum

address: Med Surge II

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 (human) or 1:100 (P. leucopus) in Protein Array Blocking (PAB) buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5alpha E. coli lysate (MCLAB, San Francisco, CA). This suspension was incubated for 30 min at 22°C, with gentle constant shaking. Arrays were re-hydrated with PAB buffer for 30 min at 22°C. Primary antibody was placed on re-hydrated array pads and incubated for 12 h at 4°C on a rocker platform (Bellco, Vineland, NJ). Pads were rinsed 6 times, followed by three 5-minute washes in Tween-TBS. Cy3-conjugated secondary antibody, goat anti-human IgG heavy and light chain or goat anti-Peromyscus leucopus IgG heavy and light chain (KPL, Gaithersburg, MD), were diluted 1:200 in PAB buffer, and incubated with pads in the dark for 1 h at 22°C on a rocking platform. Arrays were washed in Tween-TBS as described above and this process repeated with TBS alone.

scan_protocol: Slides were dismounted from their frames, rinsed in double-distilled H2O and centrifuged 20 min at 500 x g to dry. Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to OspC proteins on the microarray the following steps were taken: (i) raw values of antibody binding measured as the mean pixel intensity of spots of printed protein were log10-transformed; raw values less than 1.0 were set to 0; (ii) the mean, standard deviation, 95% confidence intervals and z-scores of antibody binding intensity to each OspC type were calculated for the human LD patient, P. leucopus and respective control sera groups.  Inclusion criterion for cross-reactivity analysis was a minimum reactivity corresponding to a z score of 2 to at least one OspC protein.

molecule: protein

source_name: serum

tag: serum type

value: infected

tag: lyme disease stage

value: Lyme Arthritis

tag: infecting ospc type

value: unknown


title: ovary_late-vitellogenesis_rep2 miRNA

description: miRNAs expression

source_name: late-vitellogenesis ovary replicate 2


title: ovary_immature_rep3 miRNA

description: miRNAs expression

source_name: immature pre-vitellogenic ovary (5 months old) replicate 3


title: peripheral white blood cell 3947

description: Illumina Human WG-6 v3 expression

value: male

tag: adiponectin

tag: fatmass(kg)

tag: fatmass(pct)

tag: leanmass(kg)

tag: leanmass(pct)


title: ovary_late-vitellogenesis_rep1 miRNA

description: miRNAs expression

source_name: late-vitellogenesis ovary replicate 1

tag: tissue


title: ovary_post-vitellogenesis_rep2 miRNA

description: miRNAs expression

source_name: post-vitellogenesis ovary replicate 2


title: ovary_mature_rep2 miRNA

description: miRNAs expression

source_name: mature ovary (meiotic maturation in progress) replicate 2


title: ovary_mature_rep3 mRNA

description: gene expression


title: ovary_mid-vitellogenesis_rep1 miRNA

description: miRNAs expression

source_name: mid-vitellogenesis ovary replicate 1


title: ovary_mature_rep1 miRNA

description: miRNAs expression

source_name: mature ovary (meiotic maturation in progress) replicate 1


title: ovary_post-vitellogenesis_rep2 mRNA

description: gene expression


title: ovary_late-vitellogenesis_rep2 mRNA

description: gene expression


title: ovary_mid-vitellogenesis_rep3 mRNA

description: gene expression


title: ovary_late-vitellogenesis_rep3 mRNA

description: gene expression


title: ovary_post-vitellogenesis_rep3 mRNA

description: gene expression

source_name: post-vitellogenesis ovary replicate 3


title: ovary_post-vitellogenesis_rep1 mRNA

description: gene expression


title: ovary_late-vitellogenesis_rep1 mRNA

description: gene expression


title: ovary_mid-vitellogenesis_rep2 mRNA

description: gene expression


title: ovary_mature_rep2 mRNA

description: gene expression


title: ovary_immature_rep2 mRNA

description: gene expression


title: ovary_immature_rep1 mRNA

description: gene expression


title: ovary_immature_rep3 mRNA

description: gene expression


title: 474864A02 - Col-20µM-Phosphate+40µM-Phosphatin_BR3 vs Col-20µM-Phosphate_BR3

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Identification of transcriptomic modifications promoted by phosphatin (AC6) (a molecule mimicking Pi addition effects on Pi starved plants).

hyb_protocol: Col-20µM-Phosphate_BR3 Cy5 / Col-20µM-Phosphate+40µM-Phosphatin_BR3 Cy3 : 40pmol.

scan_protocol: InnoScan900_MAPIX, Cy3:pmt voltage 532nm,650V,laser power 5%, Cy5:635nm,pmt voltage 700V,laser power 5%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Media=MS/10 medium supplemented with 20 microM Phosphate Temperature=24°C/18°C Light=16h light/8h night

extract_protocol: Col 20µM Phosphate Repet3:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Phosphate 20uM - environmental treatment - abiotic stress,phosphate:quantity 20uM . All seedlings are wild type of the accession Col-0. Seedlings were germinated and grown for 13 days on a 10 times diluted MS medium containing 20µM phosphate. Plates without phosphatine were suppemented with DMSO.

tag: ecotype/cultivar

value: columbia

tag: dev.stage (boyes et al. plant cell 2001)

growth_protocol: roots - Media=MS/10 medium supplemented with 20 microM Phosphate + 40µM Phosphatin. Temperature=24°C/18°C Light=16h light/8h night

extract_protocol: Col 20µM Phosphate+40µM Phosphatin Repet3:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Phosphatine 40uM - compound based treatment - abiotic stress,phosphatine:quantity 40uM . All seedlings are wild type of the accession Col-0. Seedlings were germinated and grown for 13 days on a 10 times diluted MS medium containing 20µM phosphate with 40 µM phosphatine.


title: NORMAL-WEIGHT-4

city: Copenhagen N

first: Morten

last: Rasmussen

address: Panum Building 6.6 Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

description: Vastus Lateralis Gene expression data from lean female controls

hyb_protocol: According to the GeneTitan® Hybridization, Wash, and Stain Kit standard protocol

scan_protocol: The array plate was processed in GeneTitan according to manufacturer's instructions

data_processing: RMA summarized signal intensities were generated in BRB ArrayTools using justRMA

source_name: Vastus Lateralis lean control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from100ng total RNA (GeneChip 3' IVT Express kit, Affymetrix).

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

value: Vastus Lateralis Muscle


title: NORMAL-WEIGHT-6


title: 474864A05 - Col-20µM-Phosphate_BR3 vs Col-500µM-Phosphate_BR3

hyb_protocol: Col-500µM-Phosphate_BR3 Cy5 / Col-20µM-Phosphate_BR3 Cy3 : 40pmol.

growth_protocol: roots - Media=MS/10 medium supplemented with 500 microM Phosphate. Temperature=24°C/18°C Light=16h light/8h night

extract_protocol: Col 500µM PhosphateRepet3:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Phosphate 500uM - environmental treatment - abiotic stress,phosphate:quantity 500uM . All seedlings are wild type of the accession Col-0. Seedlings were germinated and grown for 13 days on a 10 times diluted MS medium containing 500 µM of Phosphate. Plates without phosphatine were suppemented with DMSO.


title: PRE-GBP-5

description: Vastus Lateralis Gene expression data from female patiens before GBP surgery

source_name: Vastus Lateralis pre gastric bypass (GBP)


title: 474825A07 - Col-20µM-Phosphate_BR2 vs Col-20µM-Phosphate+40µM-Phosphatin_BR2

hyb_protocol: Col-20µM-Phosphate+40µM-Phosphatin_BR2 Cy5 / Col-20µM-Phosphate_BR2 Cy3 : 40pmol.

extract_protocol: Col 20µM Phosphate+40µM Phosphatin Repet2:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: Col 20µM Phosphate Repet2:5ug. (Qiagen_RNeasy.pdf)


title: 474864A10 - Col-500µM-Phosphate_BR3 vs Col-20µM-Phosphate_BR3

hyb_protocol: Col-20µM-Phosphate_BR3 Cy5 / Col-500µM-Phosphate_BR3 Cy3 : 40pmol.


title: PRE-GBP-3


title: PRE-GBP-4


title: 474824A10 - Col-20µM-Phosphate_BR1 vs Col-500µM-Phosphate_BR1

hyb_protocol: Col-500µM-Phosphate_BR1 Cy5 / Col-20µM-Phosphate_BR1 Cy3 : 40pmol.

extract_protocol: Col 500µM PhosphateRepet1:5ug. (Qiagen_RNeasy.pdf)

extract_protocol: Col 20µM Phosphate Repet1:5ug. (Qiagen_RNeasy.pdf)


title: 474825A02 - Col-500µM-Phosphate_BR1 vs Col-20µM-Phosphate_BR1

hyb_protocol: Col-20µM-Phosphate_BR1 Cy5 / Col-500µM-Phosphate_BR1 Cy3 : 40pmol.


title: NORMAL-WEIGHT-1


title: PRE-GBP-1


title: 911844

value: Early


title: 474825A11 - Col-20µM-Phosphate+40µM-Phosphatin_BR2 vs Col-20µM-Phosphate_BR2

hyb_protocol: Col-20µM-Phosphate_BR2 Cy5 / Col-20µM-Phosphate+40µM-Phosphatin_BR2 Cy3 : 40pmol.


title: NORMAL-WEIGHT-5


title: PRE-GBP-2


title: NORMAL-WEIGHT-3


title: 474847A06 - Col-500µM-Phosphate_BR2 vs Col-20µM-Phosphate_BR2

hyb_protocol: Col-20µM-Phosphate_BR2 Cy5 / Col-500µM-Phosphate_BR2 Cy3 : 40pmol.

extract_protocol: Col 500µM PhosphateRepet2:5ug. (Qiagen_RNeasy.pdf)


title: POST-GBP-4

description: Vastus Lateralis Gene expression data from female patiens after GBP surgery

source_name: Vastus Lateralis post gastric bypass (GBP)


title: POST-GBP-3


title: 474847A02 - Col-20µM-Phosphate_BR2 vs Col-500µM-Phosphate_BR2

hyb_protocol: Col-500µM-Phosphate_BR2 Cy5 / Col-20µM-Phosphate_BR2 Cy3 : 40pmol.


title: NORMAL-WEIGHT-2


title: POST-GBP-5


title: 474824A05 - Col-20µM-Phosphate+40µM-Phosphatin_BR1 vs Col-20µM-Phosphate_BR1

hyb_protocol: Col-20µM-Phosphate_BR1 Cy5 / Col-20µM-Phosphate+40µM-Phosphatin_BR1 Cy3 : 40pmol.

extract_protocol: Col 20µM Phosphate+40µM Phosphatin Repet1:5ug. (Qiagen_RNeasy.pdf)


title: 474847A09 - Col-20µM-Phosphate_BR3 vs Col-20µM-Phosphate+40µM-Phosphatin_BR3

hyb_protocol: Col-20µM-Phosphate+40µM-Phosphatin_BR3 Cy5 / Col-20µM-Phosphate_BR3 Cy3 : 40pmol.


title: POST-GBP-2


title: Adipocyte

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Adipocyte derived from MSC after 3 week of differentiation culture

hyb_protocol: Fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays.

scan_protocol: GeneChip were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.5 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average analysis.

source_name: MSC derived Adipocyte

label_protocol: Biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: hMSCs were isolated from BM aspirates of normal donors after obtaining informed consent, as previously described (Aluigi et al., 2006). Briefly, the mononuclear cell fraction was separated by centrifugation over a Ficoll-Paque gradient (Amersham Bioscience, Piscataway, NJ, USA), resuspended in proliferation medium consisting of low-glucose Dulbecco’s modified Eagle’s medium (DMEM, Lonza, Milan, Italy), 10% bovine serum albumine (BSA) (Gibco-Invitrogen, Carlsbad, CA, USA), 2 mM L-glutamine, and 1% antibiotics (MP Biomedicals, Verona, Italy), and plated at an initial seeding density of 1.6x105 cells/cm2. After 3 days, the non-adherent cell fraction was removed by washing with phosphate-buffered saline (PBS), and monolayers of adherent cells were cultured until they reached 70%–90% confluence. Cells were then trypsinized (0.25% trypsin with 0.1% EDTA) (EuroClone, Pero, Italy), subcultured at a density of 3.5 x 103 cells/cm2, and used for further experiments within passages 3 to 5.

extract_protocol: ATP pre-treated or untreated adipocyte, osteoblast and BM-hMSCs were collected and lyzed in QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from BM-hMSCs was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: BM-hMSCs were treated with 1 mM ATP or with solvent alone 24 hours before to initiate osteogenic or adipogenic differentiation protocols. To induce adipogenic differentiation BM-hMSC cells were seeded at 2.1 x 104 cells/cm2 on Lab-Tek II coverglass chamber (Nalge-Nunc, Roskilde, Denmark), were grown for 3 days in Adipogenic induction medium (Lonza) containing additional h-Insulin, L-glutamine, MCGS, Dexamethasone, Indomethacin, 3-isobuty-I-methyl-xanthine, Pen/Strep followed by 3 days in Adipogenic maintenance medium containing h-Insulin, L-glutamine, MCGS, Pen/Strep. Both cycles were repeated and cell cultures were stopped at day 12 and 18, for histological staining and total RNA extraction. To induce osteogenic differentiation BM-hMSC cells were seeded at 3.1 x 103 cells/cm2, were grown in Osteogenic Differentiation medium (Lonza) containing L-glutamine, MCGS, Dexamethasone, Ascorbate, β-Glycerophosphate, Pen/Strep. The media was replaced every 3-4 days. Cell cultures were stopped at day 14 and 21 for histological staining and total RNA extraction.

value: MSC derived Adipocyte

tag: time

value: 3 weeks

tag: treatment


title: ATP pre-treatment Adipocyte

description: Adipocyte derived from ATP pre-treated MSC after 3 week of differentiation culture

value: treated with 1 mM ATP


title: ATP pre-treatment Osteocyte

description: Osteocyte derived from ATP pre-treated MSC after 3 week of differentiation culture

source_name: MSC derived Osteocyte

value: MSC derived Osteocyte


title: POST-GBP-1

tag: gender

value: female


title: Osteocyte

description: Osteocyte derived from MSC after 3 week of differentiation culture


title: 474824A01 - Col-20µM-Phosphate_BR1 vs Col-20µM-Phosphate+40µM-Phosphatin_BR1

hyb_protocol: Col-20µM-Phosphate+40µM-Phosphatin_BR1 Cy5 / Col-20µM-Phosphate_BR1 Cy3 : 40pmol.


title: Serum_diabetic_6

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

country: Germany

institute: Zentrum für klinische Tiermedizin

description: miRNA expression profile in the serum of a cat suffering from diabetes

hyb_protocol: Microarray analysis was performed using custom-made Agilent miRNA microarrays. Cy3-labeled miRNA was hybridized to the microarrays according the manufacturer’s instructions (User Manual G4170-90011_miRNA_complete_2.3).

scan_protocol: Hybridized and washed slides were scanned at 2 µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing:
Image processing was performed with Feature Extraction Software 10.7.3.1 (Agilent Technologies).
The gProcessedSignal column contains the original values from the FE software. For further statistical analysis gProcessedSignals were 1) filtered based on “Is well above background” flags (A feature was listed as detectable if > 50% of the signals in at least one of the two measured groups were above detection limit, and a probe was considered as detectable if ≥ 50% of the replicated features were detectable); 2) detectable probes were summarized (calculation of mean signal intensities for each probe); and 3) normalized with the BioConductor package vsn.

organism: Felis catus

source_name: Serum

label_protocol: Labeling of miRNAs with Cy3-CTP was performed with the miRNA Complete Labeling and Hybridization Kit (Cat.-No. 5190-1934; Agilent Technologies) according the manufacturer’s instructions.

growth_protocol: All cats were client-owned adult animals (Age 6 -14 years) that were presented as patients or for health checks to the clinic of Small Animal Veterinary Medicine, LMU University of Munich, Germany

extract_protocol: Total RNA was isolated from  16 serum samples using Qiazol® Reagent (Qiagen, Hilden Germany) and the miRNeasy Mini Kit (QIAGEN, Valencia, CA, USA) according to the supplementary protocol “Purification of total RNA, including small RNAs, from serum or plasma". Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany).

treatment_protocol: Blood was collected by venipuncture in serum tubes and left to clot for 20 min. The blood was centrifuged at 600g for 5 min and the serum was stored at -80°C until RNA extraction.

tag: condition

value: diseased


title: Serum_healthy_7

description: miRNA expression profile in the serum of a healthy cat

value: healthy


title: Mesenchymal Stem Cells (MSC)

description: Mesenchymal Stem Cells (MSC)

source_name: Bone Marrow Mesenchymal Stem Cells

value: Bone Marrow Mesenchymal Stem Cells

value: untreated


title: ovary_mature_rep1 mRNA

description: gene expression

hyb_protocol: Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

value: whole ovary

tag: developmental stage

value: mature ovary

value: mRNA


title: Serum_healthy_6


title: Serum_healthy_5


title: Serum_healthy_8


title: Serum_diabetic_7


title: PSP07SB

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User's Guide (V 3.2).

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche). Background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: berry pericarp at mid-ripening, year 2007, PSP vineyard

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: Vitis vinifera cultivar Corvina clone 48 berries were harvested from 11 different vineyards, each located in one of the three most important wine production macro-areas of the Verona region: Bardolino, Valpolicella and Soave, on the basis of the site geographical coordinates. For each of the selected vineyards, specific environmental conditions (altitude and type of soil) and farming and agricultural practices used (training system, rows facing direction, planting layout, vineyard age and rootstock type) were recorded. Vineyards were selected in order to maximize differences in locations and in microenvironmental and farming conditions.

extract_protocol: Total RNA was extracted from ~400 mg of liquid-nitrogen-ground berry pericarp tissue (entire berries without seeds) using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO), with some modifications, as reported in Fasoli et al., 2012 (PMID 22948079). RNA quality and quantity were determined using a NanoDrop 2000 instrument (Thermo Scientific, Wilmington, DE) and a Bioanalyzer Chip RNA 7500 series II (Agilent, Santa Clara, CA).

tag: cultivar

value: Corvina

value: berry pericarp

value: mid-ripening

tag: year

tag: vineyard name

value: PSP

tag: vineyard location

value: S. Pietro Incariano

tag: macro-area of verdona region

value: Valpolicella

tag: vineyard site

tag: replica

value: B


title: PSP063A

source_name: berry pericarp at harvest, year 2006, PSP vineyard

value: harvest

value: A


title: PSP073A

source_name: berry pericarp at harvest, year 2007, PSP vineyard


title: PSP073C

value: C


title: PSP073B


title: PSP063B


title: Serum_diabetic_5

value: diseased


title: ATP pre-treatment Mesenchymal Stem Cells (MSC)

description: Mesenchymal Stem Cells (MSC) pre-treated with 1mM ATP

value: 3 weeks

value: treated with 1 mM ATP


title: PSP063C


title: PSP072A


title: PSP071B

source_name: berry pericarp at veraison, year 2007, PSP vineyard

value: veraison


title: PSP071A


title: PSP072C


title: PSP071C


title: ovary_mid-vitellogenesis_rep1 mRNA

description: gene expression

value: whole ovary

value: mid-vitellogenesis

tag: rna subtype


title: Serum_healthy_4

value: healthy


title: Serum_healthy_3


title: Serum_diabetic_2


title: Serum_diabetic_4


title: CS072B

source_name: berry pericarp at mid-ripening, year 2007, CS vineyard

value: Corvina

value: CS

value: Sona

value: Bardolino


title: Serum_diabetic_1


title: PSP062B

source_name: berry pericarp at mid-ripening, year 2006, PSP vineyard

value: berry pericarp

value: mid-ripening

value: PSP

value: S. Pietro Incariano


title: CS073B

source_name: berry pericarp at harvest, year 2007, CS vineyard

value: harvest

value: B


title: CS072C

value: C


title: AM073C

source_name: berry pericarp at harvest, year 2007, AM vineyard

value: AM

value: Marcellise

value: Soave


title: Serum_healthy_2


title: Patient 7_BV_8wks_CD8

city: Seattle

first: Tao

last: Peng

state: WA

address: 1100 Fairview Ave N/FHCRC/E5-110

institute: University of Washington

description: Illumina Chip Bar Code: 5388892001

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using CubicSpline with background subtraction using Illumina Genome Studio (V2010.3)

label_protocol: cDNA were synthesized  using NuGEN pico kits from the extracted total RNA and biotinylated cDNA were prepared using a NuGEN labeling kit for Illumina arrays (Ref8_v3)

extract_protocol: RNA from laser captured cells was extracted with Arturus PicoPure RNA isolation kits in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: skin biopsy

tag: cell type

tag: biopsy location

value: deeper dermal area near blood vessel


title: Serum_diabetic_3

value: diseased


title: Patient 6_BV_8wks_CD8

description: Illumina Chip Bar Code: 5388892001

tag: tissue


title: Patient 7_JC_8wks_CD8

description: Illumina Chip Bar Code: 5388892003

value: dermal-epidermal junction


title: PSP062A

value: Corvina

value: Valpolicella

value: A


title: Serum_healthy_1

value: healthy


title: CS073C

value: berry pericarp

value: CS

value: Sona

value: Bardolino


title: CS071A

source_name: berry pericarp at veraison, year 2007, CS vineyard

value: veraison


title: PSP061C

source_name: berry pericarp at veraison, year 2006, PSP vineyard

value: PSP

value: S. Pietro Incariano

value: C


title: PSP061A


title: CS071C


title: AM073A

value: harvest

value: AM

value: Marcellise

value: Soave


title: AM073B

value: B


title: PSP061B

value: Corvina


title: AM072C

source_name: berry pericarp at mid-ripening, year 2007, AM vineyard

value: mid-ripening


title: CS072A

value: A


title: PSP062C

value: Valpolicella


title: CS071B

value: berry pericarp


title: CS073A

value: CS


title: Healthy vac_X098_source

city: Stanford

first: David

last: Furman

institute: Stanford University

hyb_protocol: 750 ng of total RNA were hybridized to Beadchips (HumanHT-12v3 Expression Bead Chip, Illumina, San Diego, CA) that contain 47,231 probes for around 28,700 genes.

scan_protocol: The hybridized Beadchips were scanned on an Illumina BeadScan confocal scanner and analyzed by Illumina's GenomeStudio software, version 2.0.

data_processing: Only non-normalized data was provided

label: unknown

source_name: Healthy vac_X098_sample

label_protocol: not provided

extract_protocol: Total RNA was extracted from whole blood of healthy individuals using PAXgene blood RNA tubes (PreAnalytiX, USA) and the QIAcube automation RNA extraction procedure according to the manufacturer's protocol (Qiagene, Valencia, CA). The amount of total RNA, and A260/A280 and A260/A230 nm ratios were assessed using the NanoDrop 1000 (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). For each sample,

value: peripheral whole blood from healthy individual

tag: age (years)

value: Male


title: Healthy vac_X097_source

source_name: Healthy vac_X097_sample

value: Female


title: Patient 6_JC_8wks_CD8

description: Illumina Chip Bar Code: 5412581003

value: skin biopsy

value: dermal-epidermal junction


title: Healthy vac_X096_source

source_name: Healthy vac_X096_sample


title: Healthy vac_X095_source

source_name: Healthy vac_X095_sample


title: Healthy vac_X094_source

source_name: Healthy vac_X094_sample


title: Healthy vac_X093_source

source_name: Healthy vac_X093_sample


title: AM072B


title: Patient 3_JC_8wks_CD8

description: Illumina Chip Bar Code: 5412581003


title: AM072A


title: Healthy vac_X092_source

source_name: Healthy vac_X092_sample


title: Patient 2_BV_8wks_CD8

description: Illumina Chip Bar Code: 5388892001

value: deeper dermal area near blood vessel


title: Patient 2_JC_8wks_CD8

description: Illumina Chip Bar Code: 5388892003


title: AM071C

source_name: berry pericarp at veraison, year 2007, AM vineyard

value: veraison

value: C


title: AM071A

value: AM

value: Marcellise


title: Patient 1_BV_8wks_CD8

description: Illumina Chip Bar Code: 5388892001


title: MN073B

source_name: berry pericarp at harvest, year 2007, MN vineyard

value: harvest

value: MN

value: Negrar

value: B


title: MN073C

value: Corvina

value: Valpolicella


title: Patient 3_BV_8wks_CD8

description: Illumina Chip Bar Code: 5388892003


title: Healthy vac_X091_source

source_name: Healthy vac_X091_sample


title: Patient 5_JC_2wks_CD8

description: Illumina Chip Bar Code: 5412581007


title: MN072C

source_name: berry pericarp at mid-ripening, year 2007, MN vineyard

value: berry pericarp

value: mid-ripening


title: Healthy vac_X089_source

source_name: Healthy vac_X089_sample

value: peripheral whole blood from healthy individual


title: Patient 5_BV_2wks_CD8

description: Illumina Chip Bar Code: 5412581004


title: MN072A

value: A


title: MN073A


title: MN072B


title: Patient 1_JC_8wks_CD8

description: Illumina Chip Bar Code: 5412581003

value: skin biopsy


title: Healthy vac_X088_source

source_name: Healthy vac_X088_sample

value: Female


title: Healthy vac_X090_source

source_name: Healthy vac_X090_sample


title: AM062C

source_name: berry pericarp at mid-ripening, year 2006, AM vineyard

value: Soave


title: Patient 3_BV_2wks_CD8

description: Illumina Chip Bar Code: 5412581007

value: deeper dermal area near blood vessel


title: MN071B

source_name: berry pericarp at veraison, year 2007, MN vineyard

value: veraison


title: AM063A

source_name: berry pericarp at harvest, year 2006, AM vineyard

value: AM


title: AM061B

source_name: berry pericarp at veraison, year 2006, AM vineyard

value: Marcellise


title: Healthy vac_X087_source

source_name: Healthy vac_X087_sample


title: AM061C

value: C


title: AM061A


title: MN071A

value: MN


title: AM062A


title: Patient 3_JC_2wks_CD8

description: Illumina Chip Bar Code: 5412581008

value: dermal-epidermal junction


title: AM063C

value: harvest


title: Patient 4_JC_2wks_CD8

description: Illumina Chip Bar Code: 5412581007


title: MN071C

value: Corvina

value: Negrar


title: Patient 4_BV_2wks_CD8

description: Illumina Chip Bar Code: 5412581008


title: Patient 2_BV_2wks_CD8

description: Illumina Chip Bar Code: 5412581007


title: AM063B

value: berry pericarp

value: B


title: Patient 2_JC_2wks_CD8

description: Illumina Chip Bar Code: 5412581004


title: AM071B


title: CS063C

source_name: berry pericarp at harvest, year 2006, CS vineyard

value: CS

value: Sona

value: Bardolino


title: Healthy vac_X086_source

source_name: Healthy vac_X086_sample

value: peripheral whole blood from healthy individual

value: Male


title: Healthy vac_X085_source

source_name: Healthy vac_X085_sample


title: CS063B


title: CS063A

value: A


title: Healthy vac_X084_source

source_name: Healthy vac_X084_sample


title: CS062B

source_name: berry pericarp at mid-ripening, year 2006, CS vineyard

value: mid-ripening


title: CS062C


title: AM062B

value: AM

value: Soave


title: Healthy vac_X083_source

source_name: Healthy vac_X083_sample

value: Female


title: Healthy vac_X081_source

source_name: Healthy vac_X081_sample


title: Healthy vac_X082_source

source_name: Healthy vac_X082_sample


title: Healthy vac_X080_source

source_name: Healthy vac_X080_sample


title: Healthy vac_X079_source

source_name: Healthy vac_X079_sample


title: Healthy vac_X078_source

source_name: Healthy vac_X078_sample


title: Patient 1_JC_2wks_CD8

description: Illumina Chip Bar Code: 5412581004

value: skin biopsy


title: Patient 1_BV_2wks_CD8

description: Illumina Chip Bar Code: 5412581007

value: deeper dermal area near blood vessel


title: CS062A


title: Healthy vac_X076_source

source_name: Healthy vac_X076_sample


title: LT-HSC_CD41KO_12mo_rep3

city: Barcelona

first: Christos

last: Gekas

address: Carrer del Doctor Aiguader 88, Lab277

country: Spain

institute: Centre for Genomic Regulation (CRG)

description: Gene expression in CD41-KO long-term HSCs in 12mo old mice

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized to Agilent SurePrint G2 Mouse Gene Expression 8x60K microarray for 40h at 65ºC 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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Bone marrow CD41-KO LT-HSCs, 12mo, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of ds cDNA using the DNA Enzymatic Labeling kit (Agilent 5190-0449) according to manufacturer’s instructions followed by column pufirication (Amicon 30kDa). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectophotometer.

growth_protocol: Freshly FACS sorted HSCs from mouse bone marrow

extract_protocol: Total RNA was extracted from 1000 FACS sorted cells with RNAClean XP kit– Agentcourt A63987 following the manufacturer’s instructions and immediately amplified using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma WTA2) to generate the cDNA

value: bone marrow


title: CS061C

source_name: berry pericarp at veraison, year 2006, CS vineyard

value: Corvina

value: veraison

value: C


title: LT-HSC_CD41KO_12mo_rep2

source_name: Bone marrow CD41-KO LT-HSCs, 12mo, replicate 2


title: CS061A

value: berry pericarp


title: MN063C

source_name: berry pericarp at harvest, year 2006, MN vineyard

value: harvest

value: MN

value: Negrar

value: Valpolicella


title: Healthy vac_X077_source

source_name: Healthy vac_X077_sample

value: peripheral whole blood from healthy individual


title: MN063B

value: B


title: LT-HSC_WT_12mo_rep3

description: Gene expression in wild-type long-term HSCs in 12mo old mice

source_name: Bone marrow wild-type LT-HSCs, 12mo, replicate 3


title: LT-HSC_CD41KO_12mo_rep1

source_name: Bone marrow CD41-KO LT-HSCs, 12mo, replicate 1


title: MN061B

source_name: berry pericarp at veraison, year 2006, MN vineyard


title: FA083A

source_name: berry pericarp at harvest, year 2008, FA vineyard

value: FA

value: Arbizzano

value: A


title: MN062A

source_name: berry pericarp at mid-ripening, year 2006, MN vineyard

value: mid-ripening


title: FA082C

source_name: berry pericarp at mid-ripening, year 2008, FA vineyard


title: Healthy vac_X075_source

source_name: Healthy vac_X075_sample

value: Male


title: CS061B

value: CS

value: Sona

value: Bardolino


title: FA082B

value: Corvina


title: FA081C

source_name: berry pericarp at veraison, year 2008, FA vineyard

value: veraison

value: C


title: MN061A

value: berry pericarp


title: MN061C

value: MN


title: FA081B


title: LT-HSC_WT_12mo_rep2

source_name: Bone marrow wild-type LT-HSCs, 12mo, replicate 2

value: bone marrow


title: FA083B

value: harvest

value: Valpolicella


title: FA082A


title: Healthy vac_X074_source

source_name: Healthy vac_X074_sample

value: peripheral whole blood from healthy individual


title: MN062C

value: Negrar


title: MN063A


title: FA083C

value: FA

value: Arbizzano


title: FA081A

value: A


title: MN062B

value: mid-ripening

value: B


title: Healthy vac_X073_source

source_name: Healthy vac_X073_sample

value: Female


title: Healthy vac_X072_source

source_name: Healthy vac_X072_sample


title: Healthy vac_X071_source

source_name: Healthy vac_X071_sample

value: Male


title: Healthy vac_X070_source

source_name: Healthy vac_X070_sample


title: Healthy vac_X069_source

source_name: Healthy vac_X069_sample


title: LT-HSC_WT_12mo_rep1

source_name: Bone marrow wild-type LT-HSCs, 12mo, replicate 1


title: AM083C

source_name: berry pericarp at harvest, year 2008, AM vineyard

value: Corvina

value: AM

value: Marcellise

value: Soave


title: Healthy vac_X067_source

source_name: Healthy vac_X067_sample


title: Healthy vac_X068_source

source_name: Healthy vac_X068_sample


title: LT-HSC_WT_2mo_rep3

description: Gene expression in wild-type long-term HSCs in 2mo old mice

source_name: Bone marrow wild-type LT-HSCs, 2mo, replicate 3


title: AM082C

source_name: berry pericarp at mid-ripening, year 2008, AM vineyard

value: berry pericarp

value: C


title: AM082B


title: LT-HSC_CD41KO_2mo_rep1

description: Gene expression in CD41-KO long-term HSCs in 2mo old mice

source_name: Bone marrow CD41-KO LT-HSCs, 2mo, replicate 1

value: bone marrow


title: LT-HSC_CD41KO_2mo_rep2

source_name: Bone marrow CD41-KO LT-HSCs, 2mo, replicate 2


title: AM083A

value: harvest


title: AM081A

source_name: berry pericarp at veraison, year 2008, AM vineyard

value: veraison


title: BA083C

source_name: berry pericarp at harvest, year 2008, BA vineyard

value: BA

value: Affi

value: Bardolino


title: AM083B


title: LT-HSC_WT_2mo_rep2

source_name: Bone marrow wild-type LT-HSCs, 2mo, replicate 2


title: BA083B


title: HSC_41-pos_rep2

description: Gene expression in CD41-positive HSCs

source_name: Bone marrow wild-type HSCs, CD41-positive, replicate 2


title: AM082A

value: A


title: BA082C

source_name: berry pericarp at mid-ripening, year 2008, BA vineyard

value: mid-ripening


title: Healthy vac_X066_source

source_name: Healthy vac_X066_sample

value: peripheral whole blood from healthy individual


title: HSC_41-pos_rep1

description: Gene expression in CD41-positive HSCs

source_name: Bone marrow wild-type HSCs, CD41-positive, replicate 1


title: HSC_41-pos_rep3

description: Gene expression in CD41-positive HSCs

source_name: Bone marrow wild-type HSCs, CD41-positive, replicate 3


title: LT-HSC_WT_2mo_rep1

source_name: Bone marrow wild-type LT-HSCs, 2mo, replicate 1


title: BA083A


title: Healthy vac_X065_source

source_name: Healthy vac_X065_sample

value: Female


title: BA081A

source_name: berry pericarp at veraison, year 2008, BA vineyard


title: BA082A


title: BA082B

value: B


title: BA081B

value: Corvina


title: Healthy vac_X064_source

source_name: Healthy vac_X064_sample


title: BA081C


title: AM081C

value: AM


title: Healthy vac_X063_source

source_name: Healthy vac_X063_sample


title: Healthy vac_X062_source

source_name: Healthy vac_X062_sample


title: Healthy vac_X061_source

source_name: Healthy vac_X061_sample

value: Male


title: HSC_41-neg_rep3

description: Gene expression in CD41-negative HSCs

source_name: Bone marrow wild-type HSCs, CD41-negative, replicate 3


title: Healthy vac_X059_source

source_name: Healthy vac_X059_sample


title: PSP082C

source_name: berry pericarp at mid-ripening, year 2008, PSP vineyard

value: PSP

value: S. Pietro Incariano

value: Valpolicella


title: PSP083B

source_name: berry pericarp at harvest, year 2008, PSP vineyard

value: berry pericarp


title: PSP083A

value: harvest


title: PSP082A


title: Healthy vac_X057_source

source_name: Healthy vac_X057_sample


title: PSP082B


title: PSP081A

source_name: berry pericarp at veraison, year 2008, PSP vineyard

value: veraison


title: Healthy vac_X060_source

source_name: Healthy vac_X060_sample


title: CS083C

source_name: berry pericarp at harvest, year 2008, CS vineyard

value: CS

value: Sona

value: C


title: HSC_41-neg_rep1

description: Gene expression in CD41-negative HSCs

source_name: Bone marrow wild-type HSCs, CD41-negative, replicate 1

value: bone marrow


title: Healthy vac_X056_source

source_name: Healthy vac_X056_sample


title: CS083B

value: Bardolino


title: CS082C

source_name: berry pericarp at mid-ripening, year 2008, CS vineyard

value: mid-ripening


title: PSP081C


title: CS083A

value: A


title: PSP083C


title: Healthy vac_X058_source

source_name: Healthy vac_X058_sample

value: peripheral whole blood from healthy individual

value: Female


title: CS082B

value: Corvina

value: B


title: PSP081B

value: PSP


title: CS082A


title: Healthy vac_X054_source

source_name: Healthy vac_X054_sample


title: HSC_41-neg_rep2

description: Gene expression in CD41-negative HSCs

source_name: Bone marrow wild-type HSCs, CD41-negative, replicate 2


title: Healthy vac_X053_source

source_name: Healthy vac_X053_sample


title: CS081C

source_name: berry pericarp at veraison, year 2008, CS vineyard


title: Healthy vac_X052_source

source_name: Healthy vac_X052_sample


title: CS081A


title: CC083C

source_name: berry pericarp at harvest, year 2008, CC vineyard

value: CC

value: Colognola

value: Soave


title: CC083B

value: berry pericarp

value: harvest


title: CC083A


title: CS081B

value: veraison

value: CS


title: CC082C

source_name: berry pericarp at mid-ripening, year 2008, CC vineyard

value: C


title: Healthy vac_X051_source

source_name: Healthy vac_X051_sample


title: CC081B

source_name: berry pericarp at veraison, year 2008, CC vineyard


title: MYD88-TRIF (dko) 5 (16h) - vs. MYD88-TRIF (dko) 5 (16h) LPS

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: untreated vs LPS treated

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing:
Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies).
The normalized/processed data are included in the LogRatio column of the Agilent Feature Extraction files (ie, normalized log10 Cy5/Cy3 ratios).
Note: The NA probes of Platform GPL10333 are not present in the Agilent FE files.

source_name: MyD88/TRIF (dko) 5 (16h) untreated

label_protocol: Total RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Bone marrow was collected from femur and tibia of age and gender matched mice of the indicated genotypes. Bone marrow cells were plated on sterile petridishes and incubated in DMEM containing 10% FCS, 5% equine serum, 10 mM HEPES, 1 mM pyruvate, 10 mM L-glutamine, and 20% M-CSF–conditioned medium at 37 °C and 7% CO2. M-CSF–conditioned medium was collected from an L929 M-CSF cell line. Bone marrow derived macrophages were harvested after 6 days and replated in tissue-culture treated dishes. Before the experiment, cells were washed once with serum-free DMEM without phenolred.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.

treatment_protocol: Cells were stimulated with 200 ng/mL LPS (Salmonella minessota, ultrapure, Invivogen) in serum-free DMEM without phenolred or left untreated. At 1, 2, 4, 8 or 16 hours, cell supernatants were collected, passed through a 0.22 µm filter to remove detached cells, aliquotted and immediately frozen in liquid nitrogen.

tag: strain

value: BMDM (bone marrow derived macrophages)

value: naive

tag: genotype/variation

value: MyD88/Trif -/- double KO

tag: time

source_name: MYD88/TRIF (dko) 5 (16h) LPS-treated

tag: cells

value: LPS


title: Healthy vac_X050_source

source_name: Healthy vac_X050_sample

value: peripheral whole blood from healthy individual

tag: gender


title: Healthy vac_X055_source

source_name: Healthy vac_X055_sample

value: Female


title: CC082A

tag: cultivar

value: Corvina

tag: developmental stage

value: mid-ripening

value: A


title: CC082B

tag: year

tag: vineyard name

value: CC

value: B


title: CC081A

tag: vineyard location

value: Colognola

tag: macro-area of verdona region

value: Soave


title: CC081C

value: berry pericarp

tag: vineyard site

tag: replica


title: AM081B

source_name: berry pericarp at veraison, year 2008, AM vineyard

value: veraison

value: AM

value: Marcellise


title: Healthy vac_X048_source

source_name: Healthy vac_X048_sample


title: MYD88-TRIF (dko) 3 (4h) - vs. MYD88-TRIF (dko) 3 (4h) LPS

description: untreated vs LPS treated

source_name: MyD88/TRIF (dko) 3 (4h) untreated

tag: cell type

value: BMDM (bone marrow derived macrophages)

tag: treatment

source_name: MYD88/TRIF (dko) 3 (4h) LPS-treated


title: MN083B

source_name: berry pericarp at harvest, year 2008, MN vineyard

tag: tissue

value: harvest

value: MN

value: Negrar

value: Valpolicella


title: Healthy vac_X049_source

source_name: Healthy vac_X049_sample

value: peripheral whole blood from healthy individual

tag: age (years)

value: Male


title: Healthy vac_X047_source

source_name: Healthy vac_X047_sample


title: MN083A

value: Corvina


title: MYD88-TRIF (dko) 1 (1h) - vs. MYD88-TRIF (dko) 1 (1h) LPS

description: untreated vs LPS treated

source_name: MyD88/TRIF (dko) 1 (1h) untreated

tag: strain

value: naive

value: MyD88/Trif -/- double KO

source_name: MYD88/TRIF (dko) 1 (1h) LPS-treated

value: LPS


title: MYD88-TRIF (dko) 2 (2h) - vs. MYD88-TRIF (dko) 2 (2h) LPS

description: untreated vs LPS treated

source_name: MyD88/TRIF (dko) 2 (2h) untreated

tag: genotype/variation

source_name: MYD88/TRIF (dko) 2 (2h) LPS-treated


title: MN083C

value: C


title: MYD88-TRIF (dko) 4 (8h) - vs. MYD88-TRIF (dko) 4 (8h) LPS

description: untreated vs LPS treated

source_name: MyD88/TRIF (dko) 4 (8h) untreated

tag: time

source_name: MYD88/TRIF (dko) 4 (8h) LPS-treated


title: MN082C

source_name: berry pericarp at mid-ripening, year 2008, MN vineyard

value: mid-ripening


title: Healthy vac_X046_source

source_name: Healthy vac_X046_sample

value: Female


title: MYD88 4 (8h) - vs. MYD88 4 (8h) LPS

description: untreated vs LPS treated

source_name: MyD88 4 (8h) untreated

value: MyD88 -/- KO

source_name: MYD88 4 (8h) LPS-treated

tag: cells


title: MN082B

value: berry pericarp

value: B


title: MN082A

value: A


title: MYD88 5 (16h) - vs. MYD88 5 (16h) LPS

description: untreated vs LPS treated

source_name: MyD88 5 (16h) untreated

value: BMDM (bone marrow derived macrophages)

source_name: MYD88 5 (16h) LPS-treated


title: MN081C

source_name: berry pericarp at veraison, year 2008, MN vineyard

value: veraison

value: MN


title: Healthy vac_X045_source

source_name: Healthy vac_X045_sample

tag: gender


title: MYD88 2 (2h) LPS - vs. MYD88 2 (2h)

description: untreated vs LPS treated

source_name: MyD88 2 (2h) LPS-treated

source_name: MYD88 2 (2h) untreated


title: Healthy vac_X044_source

source_name: Healthy vac_X044_sample


title: MN081B

tag: cultivar

value: Negrar

value: Valpolicella


title: GIV082C

source_name: berry pericarp at mid-ripening, year 2008, GIV vineyard

tag: developmental stage

value: GIV

value: Cavaion

value: Bardolino


title: GIV083B

source_name: berry pericarp at harvest, year 2008, GIV vineyard

value: Corvina

value: harvest

tag: year


title: GIV083A

tag: vineyard name


title: MN081A

tag: vineyard location


title: Healthy vac_X042_source

source_name: Healthy vac_X042_sample

value: peripheral whole blood from healthy individual


title: GIV082A

value: mid-ripening

tag: macro-area of verdona region


title: Healthy vac_X041_source

source_name: Healthy vac_X041_sample

value: Male


title: Healthy vac_X040_source

source_name: Healthy vac_X040_sample

value: Female


title: MYD88 1 (1h) - vs. MYD88 1 (1h) LPS

description: untreated vs LPS treated

source_name: MyD88 1 (1h) untreated

value: naive

value: MyD88 -/- KO

source_name: MYD88 1 (1h) LPS-treated

value: LPS


title: MYD88 3 (4h) - vs. MYD88 3 (4h) LPS

description: untreated vs LPS treated

source_name: MyD88 3 (4h) untreated

value: BMDM (bone marrow derived macrophages)

source_name: MYD88 3 (4h) LPS-treated


title: GIV083C

value: berry pericarp

tag: vineyard site

value: C


title: GIV082B

tag: replica

value: B


title: TRIF 4 (8h) - vs. TRIF 4 (8h) LPS

description: untreated vs LPS treated

source_name: TRIF 4 (8h) untreated

tag: cell type

value: TRIF -/- KO

source_name: TRIF 4 (8h) LPS-treated


title: TRIF 1 (1h) - vs. TRIF 1 (1h) LPS

description: untreated vs LPS treated

source_name: TRIF 1 (1h) untreated

tag: treatment

source_name: TRIF 1 (1h) LPS-treated


title: Healthy vac_X038_source

source_name: Healthy vac_X038_sample

tag: tissue


title: Healthy vac_X039_source

source_name: Healthy vac_X039_sample

tag: age (years)


title: TRIF 5 (16h) - vs. TRIF 5 (16h) LPS

description: untreated vs LPS treated

source_name: TRIF 5 (16h) untreated

tag: strain

source_name: TRIF 5 (16h) LPS-treated


title: GIV081B

source_name: berry pericarp at veraison, year 2008, GIV vineyard

value: veraison

value: GIV


title: BM083B

source_name: berry pericarp at harvest, year 2008, BM vineyard

value: BM

value: Marano

value: Valpolicella


title: BM082A

source_name: berry pericarp at mid-ripening, year 2008, BM vineyard

value: Corvina

value: A


title: GIV081C

value: Cavaion

value: Bardolino


title: Healthy vac_X037_source

source_name: Healthy vac_X037_sample

value: peripheral whole blood from healthy individual

value: Male


title: BM083C

value: harvest


title: TRIF 2 (2h) - vs. TRIF 2 (2h) LPS

description: untreated vs LPS treated

source_name: TRIF 2 (2h) untreated

value: BMDM (bone marrow derived macrophages)

value: naive

tag: genotype/variation

source_name: TRIF 2 (2h) LPS-treated

value: LPS


title: GIV081A

value: berry pericarp


title: BM082C

value: mid-ripening

value: C


title: BM083A


title: BM081C

source_name: berry pericarp at veraison, year 2008, BM vineyard

value: veraison


title: TRIF 3 (4h) - vs. TRIF 3 (4h) LPS

description: untreated vs LPS treated

source_name: TRIF 3 (4h) untreated

value: TRIF -/- KO

tag: time

source_name: TRIF 3 (4h) LPS-treated


title: BM072B

value: BM

value: Marano

value: B


title: WT 5 (16h) - vs. WT 5 (16h) LPS

description: untreated vs LPS treated

source_name: WT 5 (16h) untreated

value: wild type

source_name: WT 5 (16h) LPS-treated

tag: cells


title: WT 4 (8h) - vs. WT 4 (8h) LPS

description: untreated vs LPS treated

source_name: WT 4 (8h) untreated

source_name: WT 4 (8h) LPS-treated


title: Healthy vac_X036_source

source_name: Healthy vac_X036_sample

tag: gender

value: Female


title: Healthy vac_X035_source

source_name: Healthy vac_X035_sample


title: BM081A

tag: cultivar

value: Corvina

value: Valpolicella

value: A


title: BM081B

tag: developmental stage


title: PM083C

source_name: berry pericarp at harvest, year 2008, PM vineyard

value: harvest

tag: year

value: PM

value: Montorio

value: Soave


title: PM083A

value: berry pericarp

tag: vineyard name


title: PM083B

tag: vineyard location


title: PM082C

source_name: berry pericarp at mid-ripening, year 2008, PM vineyard

value: mid-ripening

tag: macro-area of verdona region


title: Healthy vac_X034_source

source_name: Healthy vac_X034_sample

value: peripheral whole blood from healthy individual


title: Healthy vac_X033_source

source_name: Healthy vac_X033_sample

value: Male


title: Healthy vac_X032_source

source_name: Healthy vac_X032_sample


title: Healthy vac_X031_source

source_name: Healthy vac_X031_sample


title: Healthy vac_X029_source

source_name: Healthy vac_X029_sample


title: WT 1 (1h) - vs. WT 1 (1h) LPS

description: untreated vs LPS treated

source_name: WT 1 (1h) untreated

value: BMDM (bone marrow derived macrophages)

value: naive

source_name: WT 1 (1h) LPS-treated

value: LPS


title: WT 3 (4h) - vs. WT 3 (4h) LPS

description: untreated vs LPS treated

source_name: WT 3 (4h) untreated

source_name: WT 3 (4h) LPS-treated


title: PM082A

tag: vineyard site


title: Healthy vac_X028_source

source_name: Healthy vac_X028_sample


title: WT 2 (2h) - vs. WT 2 (2h) LPS

description: untreated vs LPS treated

source_name: WT 2 (2h) untreated

source_name: WT 2 (2h) LPS-treated


title: PM082B

tag: replica

value: B


title: PM081C

source_name: berry pericarp at veraison, year 2008, PM vineyard

value: veraison

value: C


title: VM083C

source_name: berry pericarp at harvest, year 2008, VM vineyard

value: Corvina

value: VM

value: Sommacampagna

value: Bardolino


title: PM081B

value: PM


title: Healthy vac_X025_source

source_name: Healthy vac_X025_sample

value: Female


title: Healthy vac_X024_source

source_name: Healthy vac_X024_sample


title: VM083A

value: harvest

value: A


title: PM081A

value: berry pericarp

value: Montorio

value: Soave


title: VM082C

source_name: berry pericarp at mid-ripening, year 2008, VM vineyard

value: mid-ripening


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Tongue 3

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: Whole genome transcriptome profile of tongue mesenchyme from embryonic day 14.5 mice with a conditional inactivation of Tgfbr2 in the cranial neural crest.

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: Samples were processed by RMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray.

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used

extract_protocol: Embryo was harvested at the designated time point. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from the embryonic tongue.

treatment_protocol: Mice were maintained under standard IACUC protocols.

tag: genotype

value: Tgfbr2 fl/fl; Wnt1-Cre

value: Tongue

tag: age

value: Not determined


title: E14.5 Tgfbr2 Wildtype Mouse Model Tongue 3

description: Whole genome transcriptome profile of tongue mesenchyme from embryonic day 14.5 control mice .

value: Tgfbr2 fl/fl

tag: tissue


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Tongue 1


title: VM083B

value: B


title: Healthy vac_X026_source

source_name: Healthy vac_X026_sample

value: peripheral whole blood from healthy individual

tag: age (years)


title: Healthy vac_X023_source

source_name: Healthy vac_X023_sample

value: Male


title: VM081C

source_name: berry pericarp at veraison, year 2008, VM vineyard

value: Corvina

value: veraison

value: VM

value: Sommacampagna

value: C


title: VM081B

value: Bardolino


title: Healthy vac_X022_source

source_name: Healthy vac_X022_sample

value: Female


title: VM082A

value: berry pericarp

value: A


title: E14.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Tongue 2

tag: strain


title: Healthy vac_X021_source

source_name: Healthy vac_X021_sample


title: E14.5 Tgfbr2 Wildtype Mouse Model Tongue 1


title: E14.5 Tgfbr2 Wildtype Mouse Model Tongue 2


title: VM082B

value: mid-ripening


title: VM081A


title: Healthy vac_X020_source

source_name: Healthy vac_X020_sample


title: Healthy vac_X019_source

source_name: Healthy vac_X019_sample


title: Healthy vac_X016_source

source_name: Healthy vac_X016_sample


title: LHCN-M2 myoblasts, 7 days differentiation - pool of total RNA extracted from three cell cultures.

city: Gif Sur Yvette Cedex

first: Guillaume

last: PINNA

address: Bat. 144 - Point courrier n° 22 - CEA SACLAY

institute: CEA

description: Differentiated cells (7 days post induction of differentation)

data_processing: Amplification efficiency of each individual PCR reaction was calculated using algorithms similar to the LinReg software. All amplification products were inspected individually for distinct melting curves and the Tm was checked to be within known specifications for the assay. The following data filtering criteria were applied:  PCR amplifications that either failed to give a signal all together or with amplification efficiency <1.6 or resulted in products with melt curves with more than one peak or Tm's not within the known specifications of the assay are indicated with the symbol “*” in the raw data sheet and were removed from the dataset. In addition data from reactions that gave Cq values closer than 5 Cq values from the NoEnzymeRT control or Cq>37 were removed.  (marked as ND  in the Matrix non-normalized Template that lists the detected miRNAs).   Using the Bioconducter SLqPCR software package the most stable normalizer was found to be the mean Cq value of assays that passed the filtering criteria. Values in Matrix Normalized template are calculated as the difference between each Cq and the average Cq for the given sample. Fold Changes are calculated as the fold change between the sample 'Proliferation' and samples 'Day3' and 'Day 7'  and difference between Day3 and Day7. When detection of a microRNA in one or two of the samples failed it is indicated as NA.

label: SYBR Green

source_name: Skeletal muscle-derived immortalized human myoblasts LHCN-M2, 4 days differentiation

label_protocol: microRNA profiling with Exiqon PCR panels was performed by Exiqon Services, Vedbaek, Denmark. 40 ng RNA per sample was reverse transcribed in 40 µl reactions using the Universal cDNA synthesis kit from Exiqon. cDNA was diluted 100 x and 4 ul was used in 10 ul PCR reactions with Exiqon SYBR Green master mix according to the protocol for miRCURY LNA™ Universal RT microRNA PCR system. 730 microRNAs (miRBase version 13.0) were assayed once by qPCR on the microRNA Ready-to-Use PCR, Human panel I or panel II V1.R. A negative control excluding enzyme from the reverse transcription reaction was performed on a pool of all 9 samples and profiled like the individual samples.The amplification was performed in a LightCycler® 480 Real-Time PCR System (Roche) in 384 well plates. The LightCycler® 480 software was used to determine the Cp value, and to generate amplification- and melting curves.

growth_protocol: Proliferation of LHCN-M2 cells: on collagen-coated 6-well Falcon plates, 500 000 cells/well, in DMEM supplemented with 20% FCS, cells are collected 24h post-plating.

extract_protocol: Standard total RNA extraction protocol using Trizol (Invitrogen) according to the manufacturer's instructions

treatment_protocol: Differentiation of LHCN-M2 cells:  on collagen-coated 6-well Falcon plates, 500 000 cells/well, DMEM supplemented with 0,01 mg/ml insulin and 0,1 mg/ml transferrin, cells are collected 3 and 7 days post-differentiation induction..

tag: reference

value: Described in (Zhu et al., Aging Cell (2007)

tag: cell type

value: LHCN-M2 myoblasts

tag: differentiation status

source_name: NoEnzymeRT


title: LHCN-M2 myoblasts, 3 days differentiation - pool of total RNA extracted from three cell cultures.

description: Differentiating cells (3 days post induction of differentation)

value: A negative control excluding enzyme from the reverse transcription reaction was performed on a pool of all 9 samples and profiled like the individual samples


title: Healthy vac_X015_source

source_name: Healthy vac_X015_sample

tag: gender


title: Healthy vac_X018_source

source_name: Healthy vac_X018_sample


title: Healthy vac_X014_source

source_name: Healthy vac_X014_sample


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 4 dye-swap

city: Parkville

first: Lynn

last: Rowley

state: Vic

address: Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

hyb_protocol: 825ng Cy labelled aRNA was prepared and hybridised as per the manufacturer's protocol using Agilent Whole Mouse Genome 44k oligoarray (G4122A).

scan_protocol: Scanned on an Agilent G2565BA scanner

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1) using GE2_v_5_95_Feb07.
The arrays were analysed using limma in the statistical package R, The two colour arrays were background corrected using norm exp (offest=50) , normalised within arrays with loess, between arrays with Aquantile. Control probes were given a weight of zero for normalisation and biological replicates were accounted for.  The linear model was constructed to account for dye, and batch effects (data was generated in 3 batches). Duplicate probes were averaged via Probe name.  P values were adjusted for FDR using the Benjamini & Hochberg method

source_name: Adamts5Dcat Sham 6wk

label_protocol: RNA labelling: 5µg of aRNA was labelled with Amersham Cy3 or Cy5 dye as per the Ambion Amino Allyl MessageAmp II protocol.

extract_protocol:
DMM surgery: Medial menisco-tibial ligament was cut to destabilise the meniscus (DMM) preventing it from performing its normal load-bearing and joint stabilizing function. The subsequent increase in load borne directly by the joint surface initiates breakdown of the articular cartilage. The underlying joint capsule was opened, the anterior fat pad, dissected with forceps to expose the medial menisco-tibial ligament which was cut (confirmed by being able to move the meniscus medially). The joint was flushed with sterile saline and the wound, closed in three layers – joint capsule, subcutaneous tissue (using 8/0 absorbable suture) and skin (using surgical tissue glue).  Animals were allowed normal cage exercise immediately after recovery from anaesthesia. The Sham knee joint was also surgically opened as above, the medial menisco-tibial ligament was touched and then the joint closed as described above.
Cartilage collection: Mice were euthanased at 1, 2 or 6 weeks post surgery. Knee joints were dissected and decalcified in RNAlater/EDTA for 72 hours at 4 deg C. Tibial epiphyses were then snap frozen in OCT and stored at -80 deg C. Up to 45 7mM coronal sections were collected within the arthritic lesion zone onto membrane slides. Sections were then laser microdissected to collect the area of cartilage affected by the DMM surgery.
RNA extraction: Total RNA was extracted using Trizol following manufacturer's instructions
RNA amplification: Up to 10ng of total RNA was collected from the microdissected cartilage which and amplified in two rounds using an Ambion Amino Allyl MessageAmp II amplification kit as per the manufacturer's instructions.

value: C57Bl/6 Adamts5Dcat

tag: surgery week

value: 6 week

value: cartilage

tag: surgery

value: Sham

source_name: Adamts5Dcat DMM 6wk

value: DMM


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 1 dye-swap


title: LHCN-M2 myoblasts, proliferation - pool of total RNA extracted from three cell cultures.

description: Proliferating cells

source_name: Skeletal muscle-derived immortalized human myoblasts LHCN-M2, proliferating

value: Proliferating cells


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 2 dye-swap


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 4 dye-swap

source_name: Adamts5Dcat Sham 1wk

value: 1 week

source_name: Adamts5Dcat DMM 1wk


title: Healthy vac_X013_source

source_name: Healthy vac_X013_sample

value: peripheral whole blood from healthy individual


title: Wild Type cartilage 6wk Post Surgery Biol Rep 3 dye-swap

source_name: WT Sham 6wk

source_name: WT DMM 6wk


title: Wild Type cartilage 6wk Post Surgery Biol Rep 2 dye-swap


title: Wild Type cartilage 6wk Post Surgery Biol Rep 4 dye-swap


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 1 dye-swap


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 3 dye-swap


title: Healthy vac_X012_source

source_name: Healthy vac_X012_sample

value: Male


title: Healthy vac_X010_source

source_name: Healthy vac_X010_sample


title: Healthy vac_X011_source

source_name: Healthy vac_X011_sample


title: Wild Type cartilage 2wk Post Surgery Biol Rep 4 dye-swap

source_name: WT Sham 2wk

value: 2 week

source_name: WT DMM 2wk


title: Wild Type cartilage 6wk Post Surgery Biol Rep 1 dye-swap


title: normal prostate from cancer patient array 7

city: Reykjavik

first: Sigrun

middle: Helga

last: Lund

address: Dunhagi 3

country: Iceland

institute: University of Iceland

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

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

data_processing: This experiment was used to estimate general properties of signal intensities for tiled microarrays and therefore are processed data files irrelevant.

source_name: Subject 7

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

extract_protocol: Performed according to NimbleGen protocols

tag: disease state

value: prostate cancer

value: normal prostate


title: normal prostate from cancer patient array 6

source_name: Subject 6


title: Wild Type cartilage 2wk Post Surgery Biol Rep 3 dye-swap


title: Wild Type cartilage 2wk Post Surgery Biol Rep 1 dye-swap


title: Wild Type cartilage 2wk Post Surgery Biol Rep 2 dye-swap


title: Healthy vac_X006_source

source_name: Healthy vac_X006_sample

value: Female


title: WT8 + IL4

city: SAN FRANCISCO

first: Rahul

middle: C

last: Deo

address: 555 Mission Bay Blvd. South

department: Cardiovascular Research Institute

institute: University of California San Francisco

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: lumi - vst and quantile normalization

source_name: fibroadipocyte progenitor

label_protocol: standard as recommended by illumina

extract_protocol: RNA was isolated from plated FAPs using RNeasy purification columns (Qiagen). 25 ug of total RNA was hybridized to Illumina MouseRef-8 v2.0 Expression BeadChip.

value: skeletal muscle

tag: background mouse strain

value: Balb/cJ

tag: genotype/variation

value: wild type

tag: treatment

value: recombinant IL4


title: normal prostate from cancer patient array 5

source_name: Subject 5


title: normal prostate from cancer patient array 4

source_name: Subject 4


title: WT6 + IL4


title: Wild Type cartilage 1wk Post Surgery Biol Rep 3 dye-swap

source_name: WT Sham 1wk

source_name: WT DMM 1wk


title: Healthy vac_X004_source

source_name: Healthy vac_X004_sample


title: T-1542

description: tumor tissue from 1542

value: tumor


title: normal prostate from cancer patient array 2

source_name: Subject 2


title: normal prostate from cancer patient array 3

source_name: Subject 3


title: N-1535

description: normal tissue from 1535


title: WT4

value: vehicle


title: Healthy vac_X003_source

source_name: Healthy vac_X003_sample


title: normal prostate from cancer patient array 1

source_name: Subject 1


title: Healthy vac_X002_source

source_name: Healthy vac_X002_sample


title: Wild Type cartilage 1wk Post Surgery Biol Rep 1 dye-swap

value: cartilage


title: HepG2 cells_Lipid-loaded, Linalool-treated_Replicate 2

city: Seoul

first: Sung-Joon

last: Lee

address: 402, Bioth Building (east) Anam 5 ga, Seungbuk gu

country: South Korea

institute: Korea University

description: Biological replicate 2 of 2. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells Treated with Linalool

hyb_protocol: Labeled cDNA samples were purified using the QIAquick PCR Purification kit (Qiagen) and then hybridized to 32 K Human OneArray (Phalanx biotech group), which contains 30,968 human genome probes, using Maui hybridization system (BioMicro Systems). After hybridization, slides were washed sequential.

scan_protocol: Scanned on an GenePix 4000B microarray scanner (Molecular Devices)

data_processing: Probe-level gene expression values were computed, background corrected, and normalized with the Lowess method using GenePix 5.1 software and Acuity 4.0 software.

source_name: Hepatoblastoma cell line, untreated control

label_protocol: Total RNA was purified with RNeasy MinElute Cleanup kit (Qiagen) following manufacturer's instructions. cDNA was synthesized from 8 μg of purified RNA using the M-MLV Reverse Transcriptase, oligo(dT)20VN primers, and dNTPs and subsequently labeled with the Cy3-dUTP and Cy5-dUTP.

growth_protocol: HepG2 cells were grown in DMEM supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using RNAiso Plus (Takara) following manufacturer's instructions.

treatment_protocol: HepG2 cells were cultured for 24 h in DMEM containing 10% FBS and 1% penicillin/streptomycin as well as 400 μM oleate, which was conjugated to fatty acid-free BSA following the ratio of 6.6 to 1. The lipid-loaded cells were washed with PBS and then incubated with serum-free DMEM with or without 100 μM fenofibrate or 1 mM linalool for 24 h.

tag: cell line

value: HepG2 cells

value: Untreated

source_name: Hepatoblastoma cell line, lipid-loaded, linalool-treated

value: Lipid-loaded (oleate and palmitate), Linalool


title: N-1542

description: normal tissue from 1542


title: HepG2 cells_Lipid-loaded, Linalool-treated_Replicate 1

description: Biological replicate 1 of 2. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells Treated with Linalool


title: T-1535

description: tumor tissue from 1535


title: NILOHYY3

description: Array 5, 3. replicate

source_name: NILOHYY


title: Wild Type cartilage 1wk Post Surgery Biol Rep 2 dye-swap

value: 1 week

value: Sham

value: DMM


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 4

source_name: Adamts5Dcat DMM 6wk

value: C57Bl/6 Adamts5Dcat

value: 6 week

source_name: Adamts5Dcat Sham 6wk


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 2 dye-swap

source_name: Adamts5Dcat Sham 1wk

source_name: Adamts5Dcat DMM 1wk


title: WT3

source_name: fibroadipocyte progenitor


title: WT5 + IL4


title: T-IKBARHW

description: tumor tissue from IKBARHW

source_name: IKBARHW

value: prostate cancer


title: NILOHYY2

description: Array 5, 2. replicate

value: normal prostate


title: Healthy vac_X001_source

source_name: Healthy vac_X001_sample

value: peripheral whole blood from healthy individual

value: Female


title: HepG2 cells_Lipid-loaded, Fenofibrate-treated_Replicate 2

description: Biological replicate 2 of 3. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells Treated with Fenofibrate

source_name: Hepatoblastoma cell line, lipid-loaded, fenofibrate-treated

value: Lipid-loaded (oleate and palmitate), Fenofibrate


title: HepG2 cells_Lipid-loaded, Fenofibrate-treated_Replicate 3

description: Biological replicate 3 of 3. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells Treated with Fenofibrate


title: WT2

value: skeletal muscle

value: Balb/cJ

value: wild type


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 3

value: cartilage


title: HepG2 cells_Lipid-loaded, Fenofibrate-treated_Replicate 1

description: Biological replicate 1 of 3. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells Treated with Fenofibrate

value: HepG2 cells


title: WT7 + IL4

value: recombinant IL4


title: N-IKBARHW

description: normal tissue from IKBARHW


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 2


title: WT1

value: vehicle


title: HepG2 cells_Lipid-loaded_Replicate 3

description: Biological replicate 3 of 3. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells

value: Untreated

source_name: Hepatoblastoma cell line, lipid-loaded

value: Lipid-loaded (oleate and palmitate)


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 3

value: 1 week

value: DMM

value: Sham


title: HepG2 cells_Lipid-loaded_Replicate 2

description: Biological replicate 2 of 3. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells


title: HepG2 cells_Lipid-loaded_Replicate 1

description: Biological replicate 1 of 3. Control Untreated HepG2 Cells vs. Lipid-loaded HepG2 Cells


title: Healthy vac_X008_source

source_name: Healthy vac_X008_sample

value: Male


title: Adamts5Dcat cartilage 6wk Post Surgery Biol Rep 1

value: C57Bl/6 Adamts5Dcat

value: 6 week


title: KO4 + IL4

value: IL4RA -/-


title: KO2 + IL4


title: Wild Type cartilage 6wk Post Surgery Biol Rep 4

source_name: WT DMM 6wk

source_name: WT Sham 6wk


title: NILOHYY1

description: Array 5, 1. replicate

value: normal prostate

value: prostate cancer


title: Wild Type cartilage 6wk Post Surgery Biol Rep 3


title: KO1 + IL4

value: skeletal muscle

value: Balb/cJ


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 1

value: cartilage


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 4


title: KO3 + IL4


title: KO2


title: KO4


title: Adamts5Dcat cartilage 1wk Post Surgery Biol Rep 2

source_name: Adamts5Dcat  DMM 1wk


title: KO3


title: Olfactory epithelium OBX side 3

city: Lexington

first: Paula

last: Heron

address: 800 Rose St.

institute: University of Kentucky

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the University of Kentucky Microarray Core Facility.

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

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data from the 10% of genes with the lowest average signal intensities were discarded.  Statistical analyses via paired t-tests were done in SAS 9.2 (SAS Institute, Cary, NC).  Setting α = 0.05 gave a false discovery rate of 19.3%.
RMA expression value derived from Expression Console software; core-exon analysis
program-name = Expression Console
program-version = 1.1.2800.19935
affymetrix-algorithm-name = rma-exon-core : dabg
affymetrix-algorithm-version = 1.0

source_name: Olfactory epithelium ipsilateral to OBX

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated from epithelial tissue homogenized in 700 µL TriReagent  according to the manufacturer’s instructions. RNA purity was checked using an Agilent Bioanalyzer

treatment_protocol: Unilateral olfactory bulbectomy was perfomed on male mice aged 8 weeks of age. 5 days following bulbectomy, the olfactory epithelial tissue ipsi- and contralateral to the bulbectomized side, was isolated and placed in TriReagent

value: male

value: 8 weeks

value: Olfactory epithelium

tag: time point

value: 5 days following ipsilateral olfactory bulbectomy (OBX)


title: Olfactory epithelium OBX side 2


title: Wild Type cartilage 6wk Post Surgery Biol Rep 1


title: Olfactory epithelium control side 1

source_name: Olfactory epithelium contralateral to OBX


title: Wild Type cartilage 2wk Post Surgery Biol Rep 4

source_name: WT DMM 2wk

value: 2 week

source_name: WT Sham 2wk


title: Wild Type cartilage 2wk Post Surgery Biol Rep 3


title: Olfactory epithelium control side 2


title: H3f3b pcKO1 + CRE-IRES-GFP

city: Sacramento

first: Paul

last: Knoepfler

address: 2425 Stockton Blvd

department: Cell Biology and Human Anatomy

institute: UC Davis

description: Replicate F

hyb_protocol: Standard Illumina hybridization protocol-Direct Hybridization

scan_protocol: Standard Illumina scanning protocol-Illumina iScan System

data_processing: The data were normalized using average normalization using genome studio software

source_name: E12.5 H3f3b Fl/Fl MEFs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini Prep kit. Quality control was performed with Agilent Bioanalyser.
RNA amplification:  Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

tag: genotype

value: H3f3b Fl/Fl

value: Mouse Embryonic Fibroblasts

tag: line

tag: transduced

value: Cre retroviruses


title: Wild Type cartilage 2wk Post Surgery Biol Rep 2

tag: tissue

value: DMM

value: Sham


title: H3f3b pcKO1 + IRES-GFP

description: Replicate E

tag: strain

tag: age

value: GFP vector


title: KO1

value: IL4RA -/-

value: vehicle


title: H3f3b cKO2 (2) + CRE-IRES-GFP

description: Replicate D2


title: Wild Type cartilage 6wk Post Surgery Biol Rep 2

value: 6 week


title: Olfactory epithelium control side 3


title: Olfactory epithelium OBX side 1


title: hMSC CTR

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133 Plus 2 GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 2 μg of total RNA.

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133 Plus 2 GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard FS450_0001 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=200. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

source_name: Human Bone Marrow Mesenchymal Stem Cells

label_protocol: Total cellular RNA pools (2μg) of CTR hMSCs, obtained from six independent experiments, were converted in biotinilated cRNA according to the one-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Cells were then trypsinized (0.25% trypsin with 0.1% EDTA) (EuroClone, Pero, Italy), subcultured at a density of 2.5 x 103 cells/cm2, and used for further experiments within passages 2 to 5.

extract_protocol: hMSCs from 6 healthy donors were seeded at a density of 2.5 x 103 cells/cm2 in the same conditions described above for 24 hours with or without 1mM ATP. Total RNA from hMSCs was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer (Salati 2008). RNAs originating from the 6 donors were pooled in order to obtain at least 2 μg/sample in both untreated and treated cells.

treatment_protocol: Untreated cells.

tag: MSCs were isolated from BM aspirates of normal donors after obtaining informed consent, as previously described (Aluigi M et al, 2006). Briefly, the mononuclear cell fraction was separated by centrifugation over a Ficoll-Paque gradient (Amersham Bioscience, Piscataway, NJ, USA), resuspended in proliferation medium consisting of low-glucose Dulbecco’s modified Eagle’s medium (DMEM, Cambrex Bio Science, Caravaggio, Italy), 10% bovine serum albumine (BSA) (Gibco-Invitrogen, Carlsbad, CA, USA), 2 mM L-glutamine, and 1% antibiotics (MP Biomedicals, Verona, Italy), and plated at an initial seeding density of 5 x 105 cells/ml. After 3 days, the non-adherent cell fraction was removed by washing with phosphate-buffered saline (PBS), and monolayers of adherent cells were cultured until they reached 70%–90% confluence.


title: Wild Type cartilage 1wk Post Surgery Biol Rep 3

source_name: WT DMM 1wk

value: 1 week

source_name: WT Sham 1wk


title: H3f3b cKO2 + CRE-IRES-GFP

description: Replicate D


title: H3f3b cKO2 (2) + IRES-GFP

description: Replicate C2


title: normal prostate from cancer patient array 5

source_name: Subject 5

value: prostate cancer

value: normal prostate


title: Wild Type cartilage 2wk Post Surgery Biol Rep 1

value: cartilage


title: normal prostate from cancer patient array 6

source_name: Subject 6


title: H3f3b cKO2 + IRES-GFP

description: Replicate C


title: hMSC 1mM ATP 24h

label_protocol: Total cellular RNA pools (2μg) of ATP hMSCs, obtained from six independent experiments, were converted in biotinilated cRNA according to the one-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

treatment_protocol: ATP was from Roche Diagnostics (Monza, Italy). hMSCs from 6 healthy donors were seeded at a density of 2.5 x 103 cells/cm2 in the same conditions described above for 24 hours with 1mM ATP.


title: CD34+ HSCs VPA-treated

description: Gene expression data from VPA-treated human CD34+ HSCs from umbilical Cord Blood (CB)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133A GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0004 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.

data_processing: The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human CD34+ cells from umbilical Cord Blood (CB)

label_protocol: Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 2 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

growth_protocol: Human CD34+ cells were purified upon donor’s informed consent from umbilical Cord Blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lymphoprep; Nycomed Pharma, Oslo, Norway) gradient separation, washed twice with PBS, and then CD34+ cells separated using magnetic cell sorting procedure (EasySep Human CD34+ positive selection kit, StemCell Techonologies Inc.; Vancouver, Canada). CD34+ cell purity assessed by flow cytometry was always >95%.   CD34+ hematopoietic cells were seeded in 24-well plates at a density of 5x105cell/ml in Iscove’s modified Dulbecco’s medium (IMDM) (Euroclone, Celbio, Milano, Italy) supplemented with 20% heat inactivated human serum (Lonza, Milano, Italy), 1mM L-Glutamine (Euroclone), SCF (50ng/ml), Flt3-ligand (Flt3-l) (50ng/ml), TPO (20ng/ml), IL-6 (10ng/ml) and IL-3 (10ng/ml) (all from R&D Systems, Minneapolis, MN, USA). CD34+ cells were initially maintained in the media described above and incubated at 37ºC in humidified atmosphere containing 5% CO2.

extract_protocol: Total cellular RNA was extracted 48 hours of treatment from 0.5x106 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA. RNAs originating from five different experiments were pooled in order to obtain at least 2 µg per sample.

treatment_protocol: Valproic acid (VPA) (Sigma-Aldrich, St. Louis, MO, USA) was dissolved in water at concentration of 50mg/ml. After an initial 24 hours of pre-incubation, cells were exposed to VPA at a concentration of 400µg/ml and the culture was continued for an additional 2 days.

value: 400µg/ml VPA

tag: cell type

value: CD34+ cells from umbilical Cord Blood


title: Wild Type cartilage 1wk Post Surgery Biol Rep 1


title: H3f3b cKO1 + CRE-IRES-GFP

description: Replicate B


title: Wild Type cartilage 1wk Post Surgery Biol Rep 2


title: CD34+ HSCs untreated

description: Gene expression data from untreated human CD34+ HSCs from umbilical Cord Blood (CB)

value: untreated


title: H3f3b cKO1 + IRES-GFP

description: Replicate A


title: normal prostate from cancer patient array 3

source_name: Subject 3


title: normal prostate from cancer patient array 2

source_name: Subject 2


title: normal prostate from cancer patient array 4

source_name: Subject 4


title: Growth at 300 min

status: Public on Apr 10 2013

city: Atlanta

first: CHun-Kai

last: Yang

state: GA

address: 166 Jesse Hill Jr. Dr.

department: Biology

institute: Georgia state University

description: Bacillus subtilis 168 in stationary phase

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

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

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

organism: Bacillus subtilis subsp. subtilis str. 168

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

growth_protocol: Bacillus subtilis 168 cells were grown in Luria-Bertani medium supplemented with glucose 0.2 % at 37°C with  vigorous shaking in flasks. Overnight cultures were diluted 100-fold in fresh pre-warmed medium and samples were collected at indicated time points

extract_protocol: Total RNA was extracted by method provided by Qiagen and Qiagen Rneasy kit was used for total RNA extraction

treatment_protocol: Cells were centrifuged at 1,3000rpm and pellets were kept at -80OC for further extraction

tag: growth time

value: 300 min

tag: growth stage

value: stationary phase

tag: optical density


title: Growth at 260 min

description: Bacillus subtilis 168 in transition phase

value: 260 min

value: transition phase


title: Growth at 420 min

source_name: Bacillus subtilis 168 in stationary phase

value: 420 min


title: Growth at 360 min

value: 360 min