title: Liver.SBD.6

description: SBD: biological replicate 6

source_name: Liver: SBD


title: Muscle.SBD.6

status: Public on Mar 31 2010

type: RNA

city: Bar Harbor

first: Rachael

middle: S

last: Hageman

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description: SBD: biological replicate 6

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Probe set data, mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package

data_processing: log2 transformation quantile normalization

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Muscle: SBD

label_protocol: Standard Illumina hybridization protocol

extract_protocol: Total RNA was isolated by TRIzolTM Plus after tissue homogenization (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocols. RNA quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Total RNA was then reverse transcribed followed by second strand cDNA synthesis. An in vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion, Austin TX). 1.5µg biotin-labeled cRNA was hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C.

tag: strain

tag: tissue

value: Muscle

tag: treatment

value: standard breeding diet


title: Muscle.HFD.4

description: HFD: biological replicate 4

source_name: Muscle: HFD

value: high fat diet


title: Liver.HFD.1

description: HFD: biological replicate 1

source_name: Liver: HFD

value: Liver


title: Liver.SBD.4

description: SBD: biological replicate 4


title: JR4

status: Public on Apr 01 2010

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

hyb_protocol: Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden

data_processing: Microarray Suite version 5.0 (MAS 5.0).

organism: Rattus norvegicus

source_name: Vascular smooth muscle cells

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

growth_protocol: Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.

extract_protocol: Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.

tag: stress/flow condition

value: Fluid shear stress

tag: sample pairing


title: Muscle.HFD.3

description: HFD: biological replicate 3


title: Liver.HFD.2

description: HFD: biological replicate 2


title: Liver.HFD.4

description: HFD: biological replicate 4


title: Muscle.SBD.1

description: SBD: biological replicate 1


title: Muscle.HFD.6

description: HFD: biological replicate 6


title: Muscle.HFD.1

description: HFD: biological replicate 1


title: Liver.SBD.5

description: SBD: biological replicate 5


title: SubcutaneousFat.HFD.5

description: HFD: biological replicate 5

source_name: Subcutaneous Fat: HFD

value: Subcutaneous Fat


title: Liver.HFD.5

description: HFD: biological replicate 5


title: SubcutaneousFat.SBD.6

description: SBD: biological replicate 6

source_name: Subcutaneous Fat: SBD


title: Liver.SBD.3

description: SBD: biological replicate 3


title: SubcutaneousFat.HFD.2

description: HFD: biological replicate 2


title: SubcutaneousFat.HFD.4

description: HFD: biological replicate 4


title: Liver.SBD.2

description: SBD: biological replicate 2


title: Liver.SBD.1

description: SBD: biological replicate 1


title: SubcutaneousFat.HFD.6

description: HFD: biological replicate 6


title: SubcutaneousFat.SBD.1

description: SBD: biological replicate 1


title: SubcutaneousFat.SBD.3

description: SBD: biological replicate 3


title: PerirenalFat.HFD.6

description: HFD: biological replicate 6

source_name: Perirenal Fat: HFD

value: Perirenal Fat


title: SubcutaneousFat.SBD.5

description: SBD: biological replicate 5


title: SubcutaneousFat.HFD.3

description: HFD: biological replicate 3


title: PerirenalFat.HFD.3

description: HFD: biological replicate 3


title: SubcutaneousFat.HFD.1

description: HFD: biological replicate 1


title: PerirenalFat.HFD.5

description: HFD: biological replicate 5


title: PerirenalFat.SBD.5

description: SBD: biological replicate 5

source_name: Perirenal Fat: SBD


title: SubcutaneousFat.SBD.4

description: SBD: biological replicate 4


title: PerirenalFat.SBD.4

description: SBD: biological replicate 4


title: PerirenalFat.HFD.2

description: HFD: biological replicate 2


title: SubcutaneousFat.SBD.2

description: SBD: biological replicate 2


title: PerirenalFat.HFD.4

description: HFD: biological replicate 4


title: PerirenalFat.SBD.6

description: SBD: biological replicate 6


title: PerirenalFat.SBD.2

description: SBD: biological replicate 2


title: PerirenalFat.SBD.1

description: SBD: biological replicate 1


title: PerirenalFat.HFD.1

description: HFD: biological replicate 1


title: PerirenalFat.SBD.3

description: SBD: biological replicate 3


title: MesentericFat.HFD.4

description: HFD: biological replicate 4

source_name: Mesenteric Fat: HFD

value: Mesenteric Fat


title: MesentericFat.HFD.6

description: HFD: biological replicate 6


title: MesentericFat.HFD.5

description: HFD: biological replicate 5


title: MesentericFat.HFD.2

description: HFD: biological replicate 2


title: MesentericFat.HFD.3

description: HFD: biological replicate 3


title: MesentericFat.SBD.6

description: SBD: biological replicate 6

source_name: Mesenteric Fat: SBD


title: MesentericFat.SBD.4

description: SBD: biological replicate 4


title: MesentericFat.SBD.2

description: SBD: biological replicate 2


title: MesentericFat.HFD.1

description: HFD: biological replicate 1


title: MesentericFat.SBD.3

description: SBD: biological replicate 3


title: MesentericFat.SBD.5

description: SBD: biological replicate 5


title: InguinalFat.HFD.5

description: HFD: biological replicate 5

source_name: Inguinal Fat: HFD

value: Inguinal Fat


title: InguinalFat.HFD.2

description: HFD: biological replicate 2


title: InguinalFat.HFD.4

description: HFD: biological replicate 4


title: InguinalFat.HFD.3

description: HFD: biological replicate 3


title: GonadalFat.HFD.4

description: HFD: biological replicate 4

source_name: Gonadal Fat: HFD

value: Gonadal Fat


title: InguinalFat.SBD.3

description: SBD: biological replicate 3

source_name: Inguinal Fat: SBD


title: InguinalFat.SBD.1

description: SBD: biological replicate 1


title: InguinalFat.HFD.6

description: HFD: biological replicate 6


title: GonadalFat.HFD.5

description: HFD: biological replicate 5


title: InguinalFat.SBD.4

description: SBD: biological replicate 4


title: InguinalFat.SBD.2

description: SBD: biological replicate 2


title: InguinalFat.SBD.6

description: SBD: biological replicate 6


title: InguinalFat.HFD.1

description: HFD: biological replicate 1


title: GonadalFat.SBD.6

description: SBD: biological replicate 6

source_name: Gonadal Fat: SBD


title: GonadalFat.HFD.6

description: HFD: biological replicate 6


title: GonadalFat.HFD.1

description: HFD: biological replicate 1


title: GonadalFat.SBD.2

description: SBD: biological replicate 2


title: MesentericFat.SBD.1

description: SBD: biological replicate 1


title: InguinalFat.SBD.5

description: SBD: biological replicate 5


title: GonadalFat.HFD.3

description: HFD: biological replicate 3


title: GonadalFat.SBD.5

description: SBD: biological replicate 5


title: GonadalFat.SBD.3

description: SBD: biological replicate 3


title: GonadalFat.SBD.4

description: SBD: biological replicate 4


title: GonadalFat.SBD.1

description: SBD: biological replicate 1


title: BrownFat.HFD.4

description: HFD: biological replicate 4

source_name: Brown Fat: HFD

value: Brown Fat


title: BrownFat.HFD.2

description: HFD: biological replicate 2


title: BrownFat.HFD.3

description: HFD: biological replicate 3


title: BrownFat.HFD.5

description: HFD: biological replicate 5


title: GonadalFat.HFD.2

description: HFD: biological replicate 2


title: BrownFat.SBD.5

description: SBD: biological replicate 5

source_name: Brown Fat: SBD


title: BrownFat.HFD.6

description: HFD: biological replicate 6


title: BrownFat.HFD.1

description: HFD: biological replicate 1


title: BrownFat.SBD.4

description: SBD: biological replicate 4


title: BrownFat.SBD.2

description: SBD: biological replicate 2


title: NGS treatment, replicate 2

city: Pathumwan

first: Kanitha

last: Patarakul

state: Bangkok

address: 1873 Rama IV Road

department: Microbiology

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

description: Analysis used RNA of EMJH-treated control samples for comparison to those of NGS-treated experimental samples.

hyb_protocol: The microarray was prehybridized for 45 min at 50°C using a solution containing 25% formamide, 5x SSC, 0.1% sodium dodecyl sulfate, 10 mg/ml bovine serum albumin, and 1 mg/ml sheared herring sperm DNA.  Hybridization with the cDNA hybridization mix at 50°C overnight and 3DNA hybridization mix at 50°C for 4 h was performed following 3DNA Array 900MPX detection kit (Genisphere) protocol. Slides were washed in ultrapure water and dried by centrifugation at 1,000 xg for 3 min prior to scanning.

scan_protocol: Scanned on GMS model 418 microarray scanner (Genetic Microsystems). The spot intensities were quantitated with ImaGene version 5.1 (Biodiscovery).

data_processing:
The web-based program Bioarray Software Environment (BASE) was used for data analysis.  Spot-specific median background intensities were subtracted from spot-specific median signals. Only spots with a corrected intensity of greater than 250 were further analyzed. Data normalization for each array was performed independently using the global median ratio, which scales the intensities such that the median of the ratio between Cy3 and Cy5 channels was 1 and spots within 5% of the lowest and the highest intensities were excluded. Print-tip loess normalization was applied to each array, followed by between-arrays normalization, which scales all replicate arrays such that they had the same median absolute deviation. Direct comparison of gene expression between NGS- and EMJH-treated samples was based on moderated t test and associated P values adjusted for multiple testing by controlling the false discovery rate. Differentially expressed genes were considered to be statistically significant if an absolute relative ratio (NGS/EMJH) was greater than 1.5 fold with an adjusted P value of less than 0.01.

For data analysis, median data before normalization with global median ratio, LIMMA+SMA (bioconductor, print-tip Loess), and LIMMA+SMA (between arrays) were selected.

organism: Leptospira interrogans

source_name: NGS-treated experimental sample

label_protocol: Labeled cDNA probes were synthesized from 2.5 micrograms of total RNA using random primers contained in the 3DNA Array 900MPX expression array detection kit (Genisphere) according to the manufacturer’s instructions.

growth_protocol: L. interrogans serovar Copenhageni strain L533 was grown in EMJH broth medium at 30°C under aerobic conditions. Leptospires were grown to exponential phase at an approximate density of 5-8x108cells/ml before harvesting.

extract_protocol: Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions and then treated with DNase (20 U for 30 min at 37°C). RNA was further puriﬁed using QIAGEN RNeasy minicolumns with on-column DNase treatment according to the manufacturer’s protocol.

treatment_protocol: One hundred ml cultures of exponential-phase grown L. interrogans serovar Copenhageni strain L533 were divided equally between 2 tubes and harvested by centrifugation at 8,000 xg for 20 min at room temperature. The cell pellet in each tube was resuspended in 5 ml of either prewarmed EMJH or prewarmed 50% normal guinea pig serum (NGS) in EMJH. After incubation at 37°C for 30 min, 0.5 ml of ice-cold killing buffer (50 mM Tris-HCl, pH 7.5, 15 mg/ml sodium azide, 0.6 mg/ml chloramphenicol) was immediately added to each tube before chilling on ice for 5 min. The NGS- and EMJH-treated cells were harvested by centrifugation at 4°C for 15 min before RNA isolation was performed.

tag: serovar

value: Copenhageni

value: normal guinea pig serum (NGS)

source_name: EMJH-treated control sample

value: EMJH broth medium


title: BrownFat.SBD.6

description: SBD: biological replicate 6


title: Mercuric chloride treated for 48hr, 3

city: Singapore

first: Choong Yong

last: UNG

state: Singapore

address: Science Drive 4

department: Biological Sciences Department

country: Singapore

institute: National University of Singapore

description: Biological replicate 3 of 3: mercury-treated at 48 Hr

hyb_protocol: Reference RNA was obtained by pooling equal amount of total RNA extracted from male and female wildtype fish. Reference RNA is co-hybridized with RNA samples extracted either from treated or control fish on a glass array spotted with 16,416 zebrafish oligo probes (16,244 LEADS clusters and 172 copies of β-actin controls)

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized.Normalized ratio of means defined by CH1/CH2

organism: Danio rerio

source_name: Zebrafish liver tissue

label_protocol: For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were reared at room temperature (27°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

treatment_protocol: Treatment for microarray analyses was carried out in 4 days, using one concentration (200 µg/L) of mercuric chloride with liver RNA sampling at 8, 24, 48, and 96 hours, respectively. Treatment was conducted using triplicate groups of four zebrafishes.

tag: tissue type

value: liver

tag: agent

value: Mercuric chloride

tag: time point

tag: reference

value: Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues of wild-type zebrafish.


title: Mercuric chloride treated for 96hr, 1

description: Biological replicate 1 of 3: mercury-treated at 96 Hr


title: NGS treatment, replicate 3


title: Mercuric chloride treated for 24hr, 3

description: Biological replicate 3 of 3: mercury-treated at 24 Hr


title: Mercuric chloride treated for 48hr, 2

description: Biological replicate 2 of 3: mercury-treated at 48 Hr


title: Mercuric chloride treated for 48hr, 1

description: Biological replicate 1 of 3: mercury-treated at 48 Hr


title: BrownFat.SBD.3

description: SBD: biological replicate 3


title: Mercuric chloride treated for 24hr, 1

description: Biological replicate 1 of 3: mercury-treated at 24 Hr


title: Mercuric chloride treated for 8hr, 3

description: Biological replicate 3 of 3: mercury-treated at 8 Hr


title: Mercuric chloride treated for 96hr, 3

description: Biological replicate 3 of 3: mercury-treated at 96 Hr


title: Mercuric chloride treated for 8hr, 1

description: Biological replicate 1 of 3: mercury-treated at 8 Hr


title: NGS treatment, replicate 1


title: Mercuric chloride treated for 96hr, 2

description: Biological replicate 2 of 3: mercury-treated at 96 Hr


title: Mercuric chloride treated for 24hr, 2

description: Biological replicate 2 of 3: mercury-treated at 24 Hr


title: Mercuric chloride treated for 8hr, 2

description: Biological replicate 2 of 3: mercury-treated at 8 Hr


title: BrownFat.SBD.1

description: SBD: biological replicate 1


title: Control at 96hr, 3

description: Biological replicate 3 of 3: control at 96 Hr

value: Control


title: Control at 96hr, 2

description: Biological replicate 2 of 3: control at 96 Hr


title: Control at 48hr, 1

description: Biological replicate 1 of 3: control at 48 Hr


title: Control at 96hr, 1

description: Biological replicate 1 of 3: control at 96 Hr


title: Control at 48hr, 2

description: Biological replicate 2 of 3: control at 48 Hr


title: Control at 24hr, 1

description: Biological replicate 1 of 3: control at 24 Hr


title: Control at 8hr, 1

description: Biological replicate 1 of 3: control at 8 Hr


title: Control at 8hr, 3

description: Biological replicate 3 of 3: control at 8 Hr


title: Control at 48hr, 3

description: Biological replicate 3 of 3: control at 48 Hr


title: Control at 24hr, 2

description: Biological replicate 2 of 3: control at 24 Hr


title: Control at 8hr, 2

description: Biological replicate 2 of 3: control at 8 Hr


title: Control at 24hr, 3

description: Biological replicate 3 of 3: control at 24 Hr


title: CB fraction of MDA231 cell line replicate 3

status: Public on Mar 30 2010

city: Vancouver

first: Ivan

middle: Robert

last: Nabi

state: British columbia

address: LSI, 2350 health sciences Mall

department: CPS

country: Canada

institute: University of British Columbia

description: Gene expression from CB fraction

hyb_protocol: 15 μg of labeled cRNA was hybridized to Human GeneChips for 16 hours at 45°C as described in the Affymetrix Technical Analysis Manual (Affymetrix, Santa Clara, CA). GeneChips were stained with Streptavidin-Phycoerythrin, followed by an antibody solution and a second Streptavidin-Phycoerythrin solution, with all liquid handling performed by a GeneChip Fluidics Station 400

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA). All GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrgc.ca)

data_processing: RMA normalization was performed on the 36 Affymetrix Human Genome U133 plus 2.0 arrays. To determine significant differences in gene expression levels between the pseudopodia and cell body, 1way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 36 samples.

organism: Homo sapiens

source_name: MDA231 cell body fraction

label_protocol: Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the BioArray High-Yield RNA Transcript Labeling kit (Enzo Biochem, New York) incorporating biotinylated UTP and CTP. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA) and the RNA 6000 Nano kit (Caliper Life Sciences, Mountain View, CA). Quality data was then analyzed using the Degradometer (www.dnaarrays.org) (mean degradation factor 1.99, SD 0.0678)

growth_protocol: U87, U251, HT1080 cells were grown in high glucose Dulbecco’s modified Eagle’s medium  and  MDA435, MDA231 and DU145 were grown in RPMI-1640 media supplemented with nonessential amino acids, glutamine, and vitamins(for DMEM) and 10% fetal bovine serum (Immunocorp,Laval, QC) in a 5% CO2/air humidified incubator as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).

extract_protocol: Total RNA was purified using RNeasy kit from Qiagen (Silica technology). Biotinylated complimentary RNA (cRNA) was prepared from 100 ng of total RNA as per the Affymetrix GeneChip Technical Analysis Manual (Affymetrix, Santa Clara, CA) using the two cycle target labeling assay. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers

treatment_protocol: 107 cells from each of the cell lines were plated on 100-mm 1- mm pore filters mounted between two 76.2–88.9 mm custom-made washers (Boulons Plus, Anjou, QC) in a 100-mm Falcon Petri dish, and the exterior was sealed with agarose to prevent cell leakage to the bottom of the filter. After a 24-h culture, the filter was washed four times with cold phosphate-buffered saline/CM (0.1 mM calcium chloride and 1 mM magnesium chloride) and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass coverslip (Jia et al, J. Biol. Chem. 280, 30564-73, 2005).

tag: cell line


title: CB fraction of MDA231 cell line replicate 2

description: Gene expression from CB fraction


title: CB fraction of U251 cell line replicate 2

description: Gene expression from CB fraction

source_name: U251 cell body fraction


title: CB fraction of MDA435 cell line replicate 2

description: Gene expression from CB fraction

source_name: MDA435 cell body fraction


title: CB fraction of HT1080 cell line replicate 3

description: Gene expression from CB fraction

source_name: HT1080 cell body fraction


title: CB fraction of HT1080 cell line replicate 1

description: Gene expression from CB fraction


title: CB fraction of MDA435 cell line replicate 1

description: Gene expression from CB fraction


title: CB fraction of U87 cell line replicate 2

description: Gene expression from CB fraction

source_name: U87 cell body fraction


title: CB fraction of U87 cell line replicate 3

description: Gene expression from CB fraction


title: CB fraction of MDA435 cell line replicate 3

description: Gene expression from CB fraction


title: CB fraction of U251 cell line replicate 1

description: Gene expression from CB fraction


title: CB fraction of DU145 cell line replicate 1

description: Gene expression from CB fraction

source_name: DU145 cell body fraction


title: CB fraction of HT1080 cell line replicate 2

description: Gene expression from CB fraction


title: CB fraction of DU145 cell line replicate 2

description: Gene expression from CB fraction


title: CB fraction of MDA231 cell line replicate 1

description: Gene expression from CB fraction


title: PS fraction of MDA231 cell line replicate 3

description: Gene expression from PS fraction

source_name: MDA231 pseudopod fraction


title: PS fraction of MDA435 cell line replicate 3

description: Gene expression from PS fraction

source_name: MDA435 pseudopod fraction


title: PS fraction of MDA435 cell line replicate 1

description: Gene expression from PS fraction


title: PS fraction of MDA231 cell line replicate 2

description: Gene expression from PS fraction


title: CB fraction of U87 cell line replicate 1

description: Gene expression from CB fraction


title: PS fraction of U251 cell line replicate 2

description: Gene expression from PS fraction

source_name: U251 pseudopod fraction


title: PS fraction of U251 cell line replicate 3

description: Gene expression from PS fraction


title: CB fraction of DU145 cell line replicate 3

description: Gene expression from CB fraction


title: CB fraction of U251 cell line replicate 3

description: Gene expression from CB fraction


title: PS fraction of MDA435 cell line replicate 2

description: Gene expression from PS fraction


title: PS fraction of DU145 cell line replicate 3

description: Gene expression from PS fraction

source_name: DU145 pseudopod fraction


title: PS fraction of MDA231 cell line replicate 1

description: Gene expression from PS fraction


title: PS fraction of HT1080 cell line replicate 2

description: Gene expression from PS fraction

source_name: HT1080 pseudopod fraction


title: PS fraction of U251 cell line replicate 1

description: Gene expression from PS fraction


title: PS fraction of HT1080 cell line replicate 3

description: Gene expression from PS fraction


title: PS fraction of HT1080 cell line replicate 1

description: Gene expression from PS fraction


title: PS fraction of DU145 cell line replicate 2

description: Gene expression from PS fraction


title: PS fraction of U87 cell line replicate 3

description: Gene expression from PS fraction

source_name: U87 pseudopod fraction


title: PS fraction of U87 cell line replicate 1

description: Gene expression from PS fraction


title: zMNCs, day 7, replicate D, batch 2

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
7_D_081507

hyb_protocol: Affymetrix hybridization protocol for the Zebrafish Whole Genome Arrays, 1 µg of cRNA.

scan_protocol: Scanning was carried out on an Affymetrix GeneChip® Scanner 3000 7G with autoloader. The scanner settings are included in the 'characteristics' field. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.

data_processing: CEL files were inputted into Bioconductor/R to derive Affymetrix Microarray Suite version 5.0 (MAS 5.0)-normalized output.

source_name: zebrafish mononuclear myogenic cells from day 7 differentiation

label_protocol: cRNA was biotin-labeled by the Children's Hospital Boston Molecular Genetics Core Facility.

growth_protocol: Zebrafish mononuclear myogenic cells were expanded in Promocell growth media, supplemented with 20% FBS, 1x antibiotics/antimycotics, 1x Glutamax, 3 ng/ml rhFGF.

extract_protocol: Zebrafish mononuclear myogenic cells were isolated with Tripure (Roche Applied Sciences) following the manufacturer's protocol.

treatment_protocol: Zebrafish mononuclear myogenic cells were differentiated in Differentiation media, Promocell human differentiation media, supplemented with 2% horse serum, 1x antibiotics/antimyocotics, 1x Glutamax.

value: dorsal muscle

tag: cell type

value: mononuclear myogenic cells

value: day 7

tag: microarray hybridization date

tag: microarray data quality

value: good

tag: microarray scanning scale factor

tag: microarray scanning target intensity

tag: microarray batch


title: zMNCs, day 7, replicate C, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
7_C_081507


title: zMNCs, day 7, replicate E, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
7_E_081507


title: zMNCs, day 7, replicate B, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
7_B_080107

value: poor


title: zMNCs, day 7, replicate A, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
7_A_080107


title: zMNCs, day 4, replicate D, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
4_D_080107

source_name: zebrafish mononuclear myogenic cells from day 4 differentiation

value: day 4


title: PS fraction of U87 cell line replicate 2

description: Gene expression from PS fraction


title: zMNCs, day 14, replicate B, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 14 differentiation.
14_B_081507

source_name: zebrafish mononuclear myogenic cells from day 14 differentiation

value: day 14


title: zMNCs, day 4, replicate B, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
4_B_072407


title: zMNCs, day 0, replicate A, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 0 differentiation.
0_A_070507

source_name: zebrafish mononuclear myogenic cells from day 0 differentiation

value: day 0


title: zMNCs, day 10, replicate C, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 10 differentiation.
10_C_080107

source_name: zebrafish mononuclear myogenic cells from day 10 differentiation

value: day 10


title: zMNCs, day 4, replicate A, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
4_A_070507


title: zMNCs, day 4, replicate C, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
4_C_072407


title: zMNCs, day 10, replicate B, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 10 differentiation.
10_B_080107


title: zMNCs, day 1, replicate A, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 1 differentiation.
1_A_070507

source_name: zebrafish mononuclear myogenic cells from day 1 differentiation

value: day 1


title: zMNCs, day 1, replicate B, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 1 differentiation.
1_B_072407


title: zMNCs, day 1, replicate B, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 1 differentiation.
D1B_082709

tag: initial number of cells plated


title: zMNCs, day 14, replicate A, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 14 differentiation.
14_A_080107

tag: tissue


title: zMNCs, day 10, replicate A, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 10 differentiation.
10_A_070507


title: PS fraction of DU145 cell line replicate 1

description: Gene expression from PS fraction


title: zMNCs, day 7, replicate A, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
D7A_082709


title: zMNCs, day 0, replicate B, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 0 differentiation.
0_B_072407


title: zMNCs, day 1, replicate A, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 1 differentiation.
D1A_082709


title: zMNCs, day 1, replicate C, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 1 differentiation.
1_C_080107


title: zMNCs, day 4, replicate A, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
D4A_082709


title: zMNCs, day 7, replicate B, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 7 differentiation.
D7B_082709


title: zMNCs, day 14, replicate B, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 14 differentiation.
D14B_082709


title: zMNCs, day 0, replicate C, batch 2

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 0 differentiation.
0_C_080107


title: zMNCs, day 14, replicate A, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 14 differentiation.
D14A_082709


title: zMNCs, day 10, replicate B, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 10 differentiation.
D10B_082709


title: R_aetherivorans-glucose-rep2-technical_rep1

status: Public on Mar 20 2010

city: Cambridge

first: Matt

middle: J

last: Cahill

address: Downing Street

department: Genetics

country: United Kingdom

institute: University of Cambridge

description: This is the second of three biological replicates of the reference treatment (minimal media + glucose). These data are derived from the first technical replicate.

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

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

data_processing: Raw probe-level intensities were initially processed with Nimblescan using default settings (Roche NimbleGen, Inc, Madison, Wis.). Data were subjected to quantile normalization and gene expression summary values were then calculated using the robust multiarray average (RMA) algorithm (Bolstad et al. Bioinformatics 19(2):185, Irizarry et al. Biostatistics 4(2):249).

organism: Rhodococcus aetherivorans

source_name: Wild-type Rhodococcus aetherivorans I24

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

growth_protocol: R. aetherivorans I24 was grown overnight in 10 ml LB before inoculating 1 L of minimal medium (MM) (Priefert et al. Appl Microbiol Biotechnol 65(2):168) supplemented with glucose (3 g L-1) and biphenyl (4.5 μM). Cells were incubated overnight at 30°C on a rotary shaker before repeating biphenyl supplementation and incubating for a further 3 hours. Prior to treatment, the cells were washed twice in 1 L phosphate buffered saline (PBS) and then resuspended in MM containing 3 g L-1 glucose (OD600 = 0.5). For treatments, 60 ml aliquots of this culture were then dispensed into 500 ml flasks.

extract_protocol: RNA was extracted from sediment treatments using the QBIOgen FastRNA Pro Soil Direct Kit as per the manufacturer's recommendations (Morgan Irvine, CA). For non-sediment treatments, the QBIOgen Pro Blue Kit was used. For all treatments, RNA was isolated from 20 mls of culture harvested by centrifugation. Following isolation, RNA samples were subjected to a double DNAse treatment with Qiagen's RNase-free DNase and RNeasy mini kit (Valencia, CA).

treatment_protocol: A 60 ml culture in minimal medium (OD600 = 0.5, 3 g/L glucose, 500ml flask) was incubated at 30°C on a rotary shaker for 48 hrs prior to RNA isolation.

tag: strain


title: R_aetherivorans-glucose-rep3-technical_rep2

description: This is the third of three biological replicates of the reference treatment (minimal media + glucose). These data are derived from the second technical replicate.


title: R_aetherivorans-glucose-rep1-technical_rep2

description: This is the first of three biological replicates of the reference treatment (minimal media + glucose). These data are derived from the second technical replicate.


title: R_aetherivorans-glucose-rep3-technical_rep1

description: This is the third of three biological replicates of the reference treatment (minimal media + glucose). These data are derived from the first technical replicate.


title: R_aetherivorans-glucose-rep2-technical_rep2

description: This is the second of three biological replicates of the reference treatment (minimal media + glucose). These data are derived from the second technical replicate.


title: zMNCs, day 4, replicate B, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 4 differentiation.
D4B_082709


title: R_aetherivorans-PCB-rep3-technical_rep1

description: This is the third of three biological replicates of the PCB treatment in minimal medium. These data are derived from the first technical replicate.

treatment_protocol: A 60 ml culture in minimal medium (OD600 = 0.5, 3 g/L glucose, 500ml flask) was supplemented with the PCB mixture Aroclor 1254  (5 mg/L) and incubated at 30°C on a rotary shaker for 48 hrs prior to RNA isolation.


title: zMNCs, day 0, replicate A, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 0 differentiation.
D0A_082709


title: R_aetherivorans-biphenyl-rep1-technical_rep2

description: This is the first of three biological replicates of the biphenyl treatment in minimal medium. These data are derived from the second technical replicate.

treatment_protocol: A 60 ml culture in minimal medium (OD600 = 0.5, 3 g/L glucose, 500ml flask) was supplemented with 4.5 μM biphenyl and incubated at 30°C on a rotary shaker for 48 hrs prior to RNA isolation.


title: R_aetherivorans-PCB-rep2-technical_rep2

description: This is the second of three biological replicates of the PCB treatment in minimal medium. These data are derived from the second technical replicate.


title: R_aetherivorans-biphenyl-rep2-technical_rep1

description: This is the second of three biological replicates of the biphenyl treatment in minimal medium. These data are derived from the first technical replicate.


title: R_aetherivorans-glucose-rep1-technical_rep1

description: This is the first of three biological replicates of the reference treatment (minimal media + glucose). These data are derived from the first technical replicate.


title: zMNCs, day 0, replicate B, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 0 differentiation.
D0B_082709


title: R_aetherivorans-PCB-rep3-technical_rep2

description: This is the third of three biological replicates of the PCB treatment in minimal medium. These data are derived from the second technical replicate.


title: R_aetherivorans-biphenyl-rep2-technical_rep2

description: This is the second of three biological replicates of the biphenyl treatment in minimal medium. These data are derived from the second technical replicate.


title: R_aetherivorans-biphenyl-rep3-technical_rep1

description: This is the third of three biological replicates of the biphenyl treatment in minimal medium. These data are derived from the first technical replicate.


title: R_aetherivorans-contaminated_sediment-rep3-technical_rep1

description: This is the third of three biological replicates of the contaminated sediment treatment. These data are derived from the first technical replicate.

treatment_protocol: Sediment samples used in this treatment were taken from the Wijnhaven area of Rotterdam harbour (The Netherlands) in 2000. This site has a 30 year history of contamination by several inorganic and organic pollutants, PCBs included. 9 g of this sediment was added to a 500 ml flask containing 60 ml culture (OD600 = 0.5, minimal medium + 3 g/L glucose). Cells were incubated at 30°C on a rotary shaker for 48 hrs before RNA isolation. Sediments were sterilized by autoclaving prior to the experiment.


title: R_aetherivorans-biphenyl-rep3-technical_rep2

description: This is the third of three biological replicates of the biphenyl treatment in minimal medium. These data are derived from the second technical replicate.


title: R_aetherivorans-contaminated_sediment-rep2-technical_rep2

description: This is the second of three biological replicates of the contaminated sediment treatment. These data are derived from the second technical replicate.


title: R_aetherivorans-contaminated_sediment-rep1-technical_rep2

description: This is the first of three biological replicates of the contaminated sediment treatment. These data are derived from the second technical replicate.


title: R_aetherivorans-contaminated_sediment-rep2-technical_rep1

description: This is the second of three biological replicates of the contaminated sediment treatment. These data are derived from the first technical replicate.


title: R_aetherivorans-biphenyl-rep1-technical_rep1

description: This is the first of three biological replicates of the biphenyl treatment in minimal medium. These data are derived from the first technical replicate.


title: R_aetherivorans-PCB-rep1-technical_rep2

description: This is the first of three biological replicates of the PCB treatment in minimal medium. These data are derived from the second technical replicate.


title: zMNCs, day 10, replicate A, batch 1

description:
Zebrafish mononuclear myogenic cells from dorsal muscle from day 10 differentiation.
D10A_082709


title: R_aetherivorans-PCB-rep1-technical_rep1

description: This is the first of three biological replicates of the PCB treatment in minimal medium. These data are derived from the first technical replicate.


title: R_aetherivorans-contaminated_sediment-rep1-technical_rep1

description: This is the first of three biological replicates of the contaminated sediment treatment. These data are derived from the first technical replicate.


title: R_aetherivorans-PCB-rep2-technical_rep1

description: This is the second of three biological replicates of the PCB treatment in minimal medium. These data are derived from the first technical replicate.


title: R_aetherivorans-sediment-rep3-technical_rep2

description: This is the third of three biological replicates of the uncontaminated sediment treatment. These data are derived from the second technical replicate.

treatment_protocol: Sediment samples used in this treatment were taken from an uncontaminated site in the vicinity of the Wijnhaven area of Rotterdam harbour (The Netherlands) in 2000. 9 g of this sediment was added to a 500 ml flask containing 60 ml culture (OD600 = 0.5, minimal medium + 3 g/L glucose). Cells were incubated at 30°C on a rotary shaker for 48 hrs before RNA isolation. Sediments were sterilized by autoclaving prior to the experiment.


title: R_aetherivorans-sediment-rep2-technical_rep2

description: This is the second of three biological replicates of the uncontaminated sediment treatment. These data are derived from the second technical replicate.


title: R_aetherivorans-contaminated_sediment-rep3-technical_rep2

description: This is the third of three biological replicates of the contaminated sediment treatment. These data are derived from the second technical replicate.


title: Group A Streptococcus grown in human amniotic fluid, stationary phase, replicate 2

status: Public on Mar 15 2010

city: Warsaw

first: Izabela

last: Sitkiewicz

address: Chełmska 30/34

department: Epidemiology and Clinical Microbiology

country: Poland

institute: National Medicines Institute

description: Part of the study on the adaptation of group A Streptococcus to human amniotic fluid

hyb_protocol: Overnight 45C, Standard Affymetrix procedure

scan_protocol: Affymetrix GeneChip scanner 3000

data_processing: Raw data was normalized to total signal intensity of GAS probes on chip. Individual hybridization values of each probe were divided by sum of all hybridization values.

organism: Streptococcus pyogenes MGAS6180

source_name: AF, S phase replicate 2

label_protocol: Standard Affymetrix

extract_protocol: 5ml culture was added to 10ml RNA protect (Qiagen), and GAS collected by centrifugation and stored at -80C. RNA was extracted from bacterial cell pellets through mechanical disruption using glass beads (MatrixB tubes) in a FastPrep machine. RNA was purified using hot acid phenol (Ambion) extraction and re-purified on Qiagen miRNeasy columns using standard protocol. DNA was removed with DNA-free (Ambion). RNA quality was assessed by bioanalyzer and O.D. measurements.

tag: growth condition

value: human amniotic fluid

tag: growth phase

value: stationary


title: Group A Streptococcus grown in human amniotic fluid, late log phase, replicate 3

source_name: AF, LL phase replicate 3

value: mid logarithmic


title: R_aetherivorans-sediment-rep2-technical_rep1

description: This is the second of three biological replicates of the uncontaminated sediment treatment. These data are derived from the first technical replicate.


title: Group A Streptococcus grown in human amniotic fluid, stationary phase, replicate 1

source_name: AF, S phase replicate 1


title: Group A Streptococcus grown in human amniotic fluid, late log phase, replicate 2

source_name: AF, LL phase replicate 2

value: late logarithmic


title: Group A Streptococcus grown in human amniotic fluid, mid log phase, replicate 2

source_name: AF, ML phase replicate 2


title: Group A Streptococcus grown in human amniotic fluid, stationary phase, replicate 3

source_name: AF, S phase replicate 3


title: R_aetherivorans-sediment-rep1-technical_rep1

description: This is the first of three biological replicates of the uncontaminated sediment treatment. These data are derived from the first technical replicate.


title: Group A Streptococcus grown in human amniotic fluid, mid log phase, replicate 1

source_name: AF, ML phase replicate 1


title: Group A Streptococcus grown in human amniotic fluid, late log phase, replicate 1

source_name: AF, LL phase replicate 1


title: Group A Streptococcus grown in THY, S phase replicate 3

source_name: THY, S phase replicate 3

value: THY laboratory medium


title: Group A Streptococcus grown in THY, S phase replicate 2

source_name: THY, S phase replicate 2


title: Group A Streptococcus grown in THY, S phase replicate 1

source_name: THY, S phase replicate 1


title: Group A Streptococcus grown in THY, LL phase replicate 1

source_name: THY, LL phase replicate1


title: R_aetherivorans-sediment-rep3-technical_rep1

description: This is the third of three biological replicates of the uncontaminated sediment treatment. These data are derived from the first technical replicate.


title: Group A Streptococcus grown in THY, ML phase replicate 3

source_name: THY, ML phase replicate 3


title: Group A Streptococcus grown in THY, LL phase replicate 2

source_name: THY, LL phase replicate 2


title: Group A Streptococcus grown in THY, ML phase replicate 1

source_name: THY, ML phase replicate1


title: Group A Streptococcus grown in human amniotic fluid, mid log phase, replicate 3

source_name: AF, ML phase replicate 3


title: 3.2.NDV.16

status: Public on Mar 01 2010

city: New Haven

first: Uri

last: Hershberg

state: CT

address: 300 George st

institute: Yale School of Medicine

description: NDV infected monocyte-derived conventional DCs

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus2 Gene Chip Arrays by Mount Sinai Microarray Shared Resource Facility.

data_processing: Raw Affymetrix microarray data were normalized using gcRMA. This analysis was performed using the BioConductor software package in R.

source_name: dendritic cell, NDV, 16 hours post infection, donor 2, sample 2

label_protocol: Good quality RNA was reverse transcribed using T7-oligo(dT)24 to yield double stranded cDNA. cRNA was transcribed and biotinylated from cDNA templates

growth_protocol: Monocyte-derived conventional DCs were obtained from human blood donors following a standard protocol (Hu et al. 2007). Briefly, human monocytes from buffy coats were isolated by Ficoll density gradient centrifugation (Histopaque, Sigma Aldrich) and CD14+ monocytes were immunomagnetically purified by using a MACS CD14 isolation kit (Miltenyi Biotech.). CD14+ Monocytes (0.7x106 cells/ml) were later differentiated into immature cDCs after 5-6 day incubation in DC growth media (RPMI Medium 1640 (Gibco), 10% fetal calf serum (Hyclone), 2 mM of L-glutamine, 100 units/ml penicillin, 100 mg/ml streptomycin (Pen/Strep) (Invitrogen), 500 units/ml hGM-CSF (Preprotech) and 1000 units/ml hIL-4 (Preprotech)) at 37ºC.

extract_protocol: Total RNA was purified from 2.5x10^6 DCs per time sample using RNeasyMicro (Qiagen) with DNase treatment. RNA was eluted from columns using water and quantified by spectrophotometry. Quality control of RNAs was performed using the Agilent Bioanalyzer.

treatment_protocol: Total RNA from cells of 3 different donors were infected with Newcastle disease virus (NDV) strain rNDV/B1, at multiplity of infection (MOI) of 0.5 orwith  contro. Cells were then harvested at : 0, 1, 2, 6, 10 and 18 hour for control and 1, 2, 4, 6, 8, 10, 12, 14, 16 and 18 hours for NDV infection.

value: Monocyte-derived conventional dendritic cells

tag: donor

tag: sample

tag: infection condition

value: NDV

tag: hours post infection


title: R_aetherivorans-sediment-rep1-technical_rep2

description: This is the first of three biological replicates of the uncontaminated sediment treatment. These data are derived from the second technical replicate.

source_name: Wild-type Rhodococcus aetherivorans I24


title: 3.2.NDV.18

scan_protocol: Fragmented cRNA was hybridized to Affymetrix HU133plus2 Gene Chip Arrays by Mount Sinai Microarray Shared Resource Facility.

source_name: dendritic cell, NDV, 18 hours post infection, donor 2, sample 2


title: 3.2.NDV.14

source_name: dendritic cell, NDV, 14 hours post infection, donor 2, sample 2


title: Group A Streptococcus grown in THY, LL phase replicate 3

source_name: THY, LL phase replicate 3


title: 3.2.NDV.6

source_name: dendritic cell, NDV, 6 hours post infection, donor 2, sample 2


title: 3.2.NDV.12

source_name: dendritic cell, NDV, 12 hours post infection, donor 2, sample 2


title: 3.1.NDV.8

source_name: dendritic cell, NDV, 8 hours post infection, donor 2, sample 1


title: 3.2.AF.6

description: Control (allantoic fluid only)  infected monocyte-derived conventional DCs

source_name: dendritic cell, control, 6 hours post infection, donor 2, sample 2

value: AF


title: 3.2.NDV.1

source_name: dendritic cell, NDV, 1 hours post infection, donor 2, sample 2


title: 3.1.NDV.4

source_name: dendritic cell, NDV, 4 hours post infection, donor 2, sample 1


title: Group A Streptococcus grown in THY, ML phase replicate 2

source_name: THY, ML phase replicate2


title: 3.2.NDV.10

source_name: dendritic cell, NDV, 10 hours post infection, donor 2, sample 2


title: 3.2.NDV.8

source_name: dendritic cell, NDV, 8 hours post infection, donor 2, sample 2


title: 3.2.NDV.2

source_name: dendritic cell, NDV, 2 hours post infection, donor 2, sample 2


title: 3.2.NDV.4

source_name: dendritic cell, NDV, 4 hours post infection, donor 2, sample 2


title: 3.1.AF.18

source_name: dendritic cell, control, 18 hours post infection, donor 2, sample 1


title: 3.1.NDV.12

source_name: dendritic cell, NDV, 12 hours post infection, donor 2, sample 1


title: 3.2.AF.0

source_name: dendritic cell, control, 0 hours post infection, donor 2, sample 2


title: 3.1.NDV.2

source_name: dendritic cell, NDV, 2 hours post infection, donor 2, sample 1


title: 3.1.NDV.10

source_name: dendritic cell, NDV, 10 hours post infection, donor 2, sample 1


title: 3.2.AF.10

source_name: dendritic cell, control, 10 hours post infection, donor 2, sample 2


title: 3.1.NDV.14

source_name: dendritic cell, NDV, 14 hours post infection, donor 2, sample 1


title: 3.1.NDV.16

source_name: dendritic cell, NDV, 16 hours post infection, donor 2, sample 1


title: 3.1.NDV.6

source_name: dendritic cell, NDV, 6 hours post infection, donor 2, sample 1


title: 3.1.NDV.1

source_name: dendritic cell, NDV, 1 hours post infection, donor 2, sample 1


title: 3.1.NDV.18

source_name: dendritic cell, NDV, 18 hours post infection, donor 2, sample 1


title: 3.1.AF.10

source_name: dendritic cell, control, 10 hours post infection, donor 2, sample 1


title: 3.1.AF.0

source_name: dendritic cell, control, 0 hours post infection, donor 2, sample 1


title: 3.1.AF.6

source_name: dendritic cell, control, 6 hours post infection, donor 2, sample 1


title: 3.1.AF.2

source_name: dendritic cell, control, 2 hours post infection, donor 2, sample 1


title: 2.2.NDV.18

source_name: dendritic cell, NDV, 18 hours post infection, donor 1, sample 2


title: 3.1.AF.1

source_name: dendritic cell, control, 1 hours post infection, donor 2, sample 1


title: 2.2.NDV.16

source_name: dendritic cell, NDV, 16 hours post infection, donor 1, sample 2


title: Sp Gcn5-myc enrichment normal conditions

type: genomic

city: Huddinge

first: Anthony

last: Wright

address: Blickagången 6

country: Sweden

institute: Karolinska Institute

description: This file contains genome-wide signal intensity for Gcn5-myc enrichment under normal conditions in S. pombe. Two experimental samples and two control samples are used for analysis. MAT (see data processing) was used for data processing with the band width setting at 250, max gap at 300 and min probe at 10.

hyb_protocol: Fragmented genomic DNA  was hybridized to Affymetrix GeneChip S. cerevisiae Tilling 1.0R according to  Affymetrix chromatin immunoprecipitation assay protocol. 2005-2006

scan_protocol: According to affymetrix chromatin immunoprecipitation assay protocol. 2005-2006

data_processing:
Model-based analysis of tilling-array (MAT) was used. Johnson WE etc. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA 103 (2006) 12457-12462.
MAT data processing with the band width setting at 250, max gap at 300 and min probe at 10.

molecule: genomic DNA

organism: Saccharomyces cerevisiae/Schizosaccharomyces pombe fusant

source_name: strain Hu2020 (ChIP fraction)

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol: affymetrix chromatin immunoprecipitation assay protocol. 2005-2006

growth_protocol: Yeast cells grow at 25°C in YPD medium to log phase.

extract_protocol: Experimental procedure was essentially according to Johnsson ect, EMBO reports, 2009 (in press)

treatment_protocol: untreated

tag: agent

value: no treatment

tag: time

tag: tag

value: myc

tag: genotype

value: h-, gcn5-myc::KanMX6, leu1-32, ura4-D18, ade6-M210

tag: antibody

value: monoclonal anti-c-Myc

source_name: strain Fy368 (wild type control)


title: Sp Gcn5-myc enrichment KCl stress conditions

description: This file contains genome-wide signal intensity for Gcn5-myc enrichment under KCl stress conditions in S. pombe. Two experimental samples and two control samples are used for analysis. MAT (see data processing) was used for data processing with the band width setting at 250, max gap at 300 and min probe at 10.

treatment_protocol: KCl treatment: cell grown to mid log phase in YES at 25°C, then treated with KCl (final concentration 1M) 60 min

value: 1M KCl


title: 2.2.NDV.8

source_name: dendritic cell, NDV, 8 hours post infection, donor 1, sample 2

tag: cell type


title: 2.1.NDV.14

source_name: dendritic cell, NDV, 14 hours post infection, donor 1, sample 1


title: 2.1.NDV.8

source_name: dendritic cell, NDV, 8 hours post infection, donor 1, sample 1


title: 2.2.NDV.2

source_name: dendritic cell, NDV, 2 hours post infection, donor 1, sample 2


title: 2.2.NDV.6

source_name: dendritic cell, NDV, 6 hours post infection, donor 1, sample 2


title: 2.2.NDV.14

source_name: dendritic cell, NDV, 14 hours post infection, donor 1, sample 2


title: 2.1.NDV.12

source_name: dendritic cell, NDV, 12 hours post infection, donor 1, sample 1


title: 2.2.NDV.1

source_name: dendritic cell, NDV, 1 hours post infection, donor 1, sample 2


title: 2.2.AF.10

source_name: dendritic cell, control, 10 hours post infection, donor 1, sample 2


title: 2.2.NDV.10

source_name: dendritic cell, NDV, 10 hours post infection, donor 1, sample 2


title: 2.2.AF.18

source_name: dendritic cell, control, 18 hours post infection, donor 1, sample 2


title: 2.1.NDV.4

source_name: dendritic cell, NDV, 4 hours post infection, donor 1, sample 1


title: 2.2.NDV.4

source_name: dendritic cell, NDV, 4 hours post infection, donor 1, sample 2


title: 2.2.NDV.12

source_name: dendritic cell, NDV, 12 hours post infection, donor 1, sample 2


title: 2.1.NDV.10

source_name: dendritic cell, NDV, 10 hours post infection, donor 1, sample 1


title: 2.1.NDV.6

source_name: dendritic cell, NDV, 6 hours post infection, donor 1, sample 1


title: 2.1.AF.10

source_name: dendritic cell, control, 10 hours post infection, donor 1, sample 1


title: 2.1.AF.6

source_name: dendritic cell, control, 6 hours post infection, donor 1, sample 1


title: 2.2.AF.1

source_name: dendritic cell, control, 1 hours post infection, donor 1, sample 2


title: 2.2.AF.6

source_name: dendritic cell, control, 6 hours post infection, donor 1, sample 2


title: 2.2.AF.2

source_name: dendritic cell, control, 2 hours post infection, donor 1, sample 2


title: 2.1.NDV.1

source_name: dendritic cell, NDV, 1 hours post infection, donor 1, sample 1


title: 2.1.NDV.2

source_name: dendritic cell, NDV, 2 hours post infection, donor 1, sample 1


title: 2.1.AF.0

source_name: dendritic cell, control, 0 hours post infection, donor 1, sample 1


title: 2.2.AF.0

source_name: dendritic cell, control, 0 hours post infection, donor 1, sample 2


title: 2.1.NDV.16

source_name: dendritic cell, NDV, 16 hours post infection, donor 1, sample 1


title: 3_10_Control_4h_rep3

city: Freiburg

first: Irmgard

last: Merfort

state: BW

address: Stefan-Meier-Str. 19

department: Department of Pharmaceutical Biology and Biotechnology

country: Germany

institute: University of Freiburg - Institute of Pharmaceutical Science

description: Gene expression data from primary mouse hepatocytes

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

scan_protocol: Affymetrix GeneArray Scanner3001

data_processing: Mouse430V2 Affymetrix CEL data files were uploaded into Expressionist Refiner Array® version 4.5 (Genedata AG, Basel, Switzerland) for data condensation. Oligo hybridization intensities were condensed to probe set expression values using the MAS5 Affymetrix Statistical algorithm according to [60]. Condensed data were normalized using Expressionist Analyst® version 4.5 (Genedata AG, Basel, Switzerland). The mapping from probe-sets to genes was performed using the Phylosopher seqmap tool based on the NCBI mouse genome version 33. Absolute probe set expression values were scaled on the chip level by logarithmic mean normalization (for each chip, the geometric mean of all probe set values was scaled to 10000).

source_name: primary murine hepatocytes cultivated on collagen coated plates

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

extract_protocol: RNA was prepared from cultured hepatocytes with the Qiagen RNEasy plus Kit according to the manufactures instructions. For each sample, 2 million cells were used for RNA isolation and purification. Samples for microarray analysis were subjected to a quality control using an Agilent Bioanalyzer with the Pico RNA-Kit. Only RNA with a RIN better than 8.2 was used for labeling and subsequent hybridization.

value: liver

tag: gender

value: male

value: Control


title: 3_6_IL17_1h_rep3


title: 3_14_TNFa_4h_rep3

value: TNFa


title: 2_10_Control_4h_rep2


title: 3_3_IL1b_1h_rep3


title: 3_12_IL1b_4h_rep3


title: 3_16_TNFa/IL17_4h_rep3


title: 2_7_TNFa/IL17_1h_rep2


title: 2_14_TNFa_4h_rep2


title: 2_3_IL1b_1h_rep2


title: 2_16_TNFa/IL17_4h_rep2


title: 3_5_TNFa_1h_rep3


title: 2_1_Control_1h_rep2


title: 3_1_Control_1h_rep3


title: 2_15_IL17_4h_rep2


title: 3_15_IL17_4h_rep3


title: 3_7_TNFa/IL17_1h_rep3


title: 2_6_IL17_1h_rep2


title: 1_15_IL17_4h_rep1


title: 1_5_TNFa_1h_rep1


title: 2_5_TNFa_1h_rep2


title: 2_12_IL1b_4h_rep2


title: 1_10_Control_4h_rep1


title: 1_7_TNFa/IL17_1h_rep1


title: 1_14_TNFa_4h_rep1


title: 1_6_IL17_1h_rep1


title: 1_16_TNFa/IL17_4h_rep1


title: 1_12_IL1b_4h_rep1


title: MSC_miR335_rep1

city: Madrid

first: Manuel

middle: Angel

last: Gonzalez

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Gene expression in bone marrow-derived MSC transduced with a lentiviral vector encoding miR-335.

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were dried out using a centrifuge.

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software version 9.5.3.1 (Agilent Technologies)

data_processing: Data pre-processing were done using the Bioconductor package Agi4x44PreProcess. The data were background corrected and normalized between arrays in order to compensate for systematic technical differences between chips. We selected the MeanSignal and the BGMedianSignal for the foreground and background signals, respectively, from the collection of signals provided by the Agilent Feature Extraction image analysis software. These signals were used for the background correction and normalization of the data. First, we produced a Background Subtracted Signal using the half option in Agi4x44Preprocess. According to this method, background signal is subtracted from the foreground signal and any intensity which is less than 0.5 is reset to be equal to 0.5 to produce positive corrected intensities. After background correction, data were normalized between arrays using quantile method. An offset equals 50 were added to the intensities before log-transforming, so that the log ratios are shrunk towards zero at the lower intensities. The AFE software attaches to each feature a flag that identifies different quantification errors of the signal. These quantification flags can be used to filter out signals that don’t reach a minimum arbitrary criterion of quality. The data were filtered trying to 1) keeping features within the dynamic range of the scanner and 2) keeping features that are of good quality. To keep features within the dynamic range, for every replicated spot across the whole set of samples, we demanded that at least 75% of the replicated probes in at least one experimental condition had a quantification flag denoting that the signal is within the dynamic range. To keep features of good quality for the analysis, for each replicated spot across the whole set of samples we filtered out those probes  that had more than 25% of the replicates in at least one experimental condition with a flag indicating presence of outliers. The Bioconductor annotation package hgug4112a.db was employed to assign to each Agilent probe ID the corresponding gene accession number code.

source_name: bone marrow mesenchymal stem cells, overexpressing miR335

label_protocol: 1 ug of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP.

growth_protocol: Human bone-marrow and skin biopsies were obtained from healthy donors. Mesenchymal stem cells (from bone marrow) and skin fibroblasts were isolated as described. All cells were cultured in expansion medium (Dulbecco’s modified Eagle’s medium (DMEM), with 4.5 g/l D-glucose supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, and 50 μg/ml gentamicin; all culture reagents from Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was isolated by using the miRNeasy Mini Kit (Qiagen, Valencia, CA), according to manufacturer's instructions.

treatment_protocol: Cells grown in expansion medium.

value: bone marrow

value: cultured mesenchymal stem cells (hMSC)

tag: condition

value: overexpressing miR335


title: 1_1_Control_1h_rep1


title: MSC_miR335_rep3


title: 1_3_IL1b_1h_rep1


title: MSC_control_rep1

description: Gene expression in bone marrow-derived MSC transduced with a lentiviral vector encoding a control miRNA.

source_name: bone marrow mesenchymal stem cells, control

value: control vector


title: MSC_control_rep2


title: MSC_miR335_rep2


title: Time couse B, 75 minutes

city: Seattle

first: John

last: Aitchison

state: WA

institute: Institute for Systems Biology

hyb_protocol: Agilent Yeast ChIP-on-chip protocol version 9.2

scan_protocol: Scanned using a PerkinElmer ScanArray Express, with PMT adjusted to 10 points higher than the level where no spots are saturated

data_processing: Image analysis was performed with Agilent Feature Extraction, converted to GenePix Result (GPR) format and analyzed using Agilent ChIP Analytics

organism: Saccharomyces cerevisiae

source_name: IP from 75 minutes after cell cycle  release

label_protocol: Labeling was performed per manufacturers instructions

growth_protocol: S. cerevisiae strains are from the W303 background and grown in YPD in a 10 L Bioflo 410 fermenter (New Brunswick Scientific) to a density of ~7x106/mL at 30C

extract_protocol: Time points were collected in two separate experiments – a) every 15 min after release from the G1 block from 0 min – 105 min and b) every 5 min beginning 20 min after block (through S-phase) from 20 -50 min.  For each time-point to be used for ChIP, a 750 mL sample was cross-linked by incubation in 1% formaldehyde at room temperature for 20 min

treatment_protocol: alpha-factor was added to a final concentration of 50 nM, and the cells were incubated for another 3 hours prior to release

value: W303 background, PSF2-Protein A tagged

source_name: Whole cell extract from 75 minutes after cell cycle  release


title: MSC_control_rep3


title: Time couse B, 105 minutes

source_name: IP from 105 minutes after cell cycle  release

source_name: Whole cell extract from 105 minutes after cell cycle  release


title: Time couse A, 25 minutes

source_name: Whole cell extract from 25 minutes after cell cycle  release

source_name: IP from 25 minutes after cell cycle  release


title: Time couse A, 35 minutes

source_name: Whole cell extract from 35 minutes after cell cycle  release

source_name: IP from 35 minutes after cell cycle  release


title: Time couse A, 45 minutes

source_name: Whole cell extract from 45 minutes after cell cycle  release

source_name: IP from 45 minutes after cell cycle  release


title: Time couse A, 40 minutes

source_name: Whole cell extract from 40 minutes after cell cycle  release

source_name: IP from 40 minutes after cell cycle  release


title: Time couse B, 30 minutes

source_name: IP from 30 minutes after cell cycle  release

source_name: Whole cell extract from 30 minutes after cell cycle  release


title: Time couse B, 60 minutes

source_name: IP from 60 minutes after cell cycle  release

source_name: Whole cell extract from 60 minutes after cell cycle  release


title: Time couse B, 90 minutes

source_name: IP from 90 minutes after cell cycle  release

source_name: Whole cell extract from 90 minutes after cell cycle  release


title: Time couse A, 30 minutes


title: Time couse B, 45 minutes


title: Time couse A, 50 minutes

source_name: Whole cell extract from 50 minutes after cell cycle  release

source_name: IP from 50 minutes after cell cycle  release


title: Time couse A, 20 minutes

source_name: Whole cell extract from 20 minutes after cell cycle  release

source_name: IP from 20 minutes after cell cycle  release


title: Time couse B, 0 minutes

source_name: IP from 0 minutes after cell cycle  release

source_name: Whole cell extract from 0 minutes after cell cycle  release


title: Reference HapMap sample NA12812_C10

city: Turku

first: Elisa

middle: Maarit

last: Närvä

address: Tykistönkatu 6

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: Hybridized in Finnish DNA Microarray Centre

hyb_protocol: accordingly manufactures protocol

scan_protocol: accordingly manufactures protocol

data_processing: For detecting copy number variation in the samples, we utilized Affymetrix Genotyping Console 3.0.1 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples for copy number variation (CNV), Loss of heterozygosity (LOH) and Single nucleotide polymorphism (SNP).

label: TdT

source_name: Reference HapMap sample NA12812_C10

label_protocol: accordingly manufactures protocol

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: cell samples were harvested in each collaborative laboratorion, washed with PBS and sent as a frozen cell pellet to analysis laboratory. Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen)

value: reference HapMap

tag: cell line


title: Reference HapMap sample NA12763_A06

source_name: Reference HapMap sample NA12763_A06

value: female


title: Reference HapMap sample NA12751_C7

source_name: Reference HapMap sample NA12751_C7


title: Reference HapMap sample NA12801_B09_2

source_name: Reference HapMap sample NA12801_B09_2


title: Reference HapMap sample NA12801_A03

source_name: Reference HapMap sample NA12801_A03


title: Reference HapMap sample NA12801_C09_2

source_name: Reference HapMap sample NA12801_C09_2


title: Reference HapMap sample NA12801_C3

source_name: Reference HapMap sample NA12801_C3


title: Reference HapMap sample NA11832_B08

source_name: Reference HapMap sample NA11832_B08


title: Reference HapMap sample NA12740_C6

source_name: Reference HapMap sample NA12740_C6


title: Reference HapMap sample NA12249_B10

source_name: Reference HapMap sample NA12249_B10


title: Reference HapMap sample NA12249_C5

source_name: Reference HapMap sample NA12249_C5


title: Reference HapMap sample NA12751_C7_2

source_name: Reference HapMap sample NA12751_C7_2


title: Reference HapMap sample NA12249_B07

source_name: Reference HapMap sample NA12249_B07


title: Reference HapMap sample NA12753_A01

source_name: Reference HapMap sample NA12753_A01


title: Reference HapMap sample NA10831_B06

source_name: Reference HapMap sample NA10831_B06


title: Reference HapMap sample NA11832_C2

source_name: Reference HapMap sample NA11832_C2


title: Reference HapMap sample NA12144_A08

source_name: Reference HapMap sample NA12144_A08


title: Reference HapMap sample NA07357_D09_2

source_name: Reference HapMap sample NA07357_D09_2


title: Reference HapMap sample NA12145_A05

source_name: Reference HapMap sample NA12145_A05


title: Reference HapMap sample NA10855_D06

source_name: Reference HapMap sample NA10855_D06


title: Reference HapMap sample NA11831_C8_2

source_name: Reference HapMap sample NA11831_C8_2


title: Reference HapMap sample NA12750_D08

source_name: Reference HapMap sample NA12750_D08


title: Reference HapMap sample NA10835_D05

source_name: Reference HapMap sample NA10835_D05


title: Reference HapMap sample NA10846_A09

source_name: Reference HapMap sample NA10846_A09


title: Reference HapMap sample NA11832_A10

source_name: Reference HapMap sample NA11832_A10


title: Reference HapMap sample NA11832_D07

source_name: Reference HapMap sample NA11832_D07


title: human embryonic stem cell line HS237 p135

value: human embryonic stem cell


title: Reference HapMap sample NA11831_C8

source_name: Reference HapMap sample NA11831_C8


title: Reference HapMap sample NA12248_D02

source_name: Reference HapMap sample NA12248_D02


title: Reference HapMap sample NA07357_C1

source_name: Reference HapMap sample NA07357_C1


title: Reference HapMap sample NA07357_B03

source_name: Reference HapMap sample NA07357_B03


title: Reference HapMap sample NA07357_A07

source_name: Reference HapMap sample NA07357_A07


title: Reference HapMap sample NA07022_A04

source_name: Reference HapMap sample NA07022_A04


title: Reference HapMap sample NA07345_C4

source_name: Reference HapMap sample NA07345_C4


title: Reference HapMap sample NA06993_D04

source_name: Reference HapMap sample NA06993_D04


title: human embryonic stem cell line FES75 p19

value: FES75 p19


title: human embryonic stem cell line FES61 p48

value: FES61 p48


title: Reference HapMap sample NA06993_B01

source_name: Reference HapMap sample NA06993_B01


title: Reference HapMap sample NA07056_A02

source_name: Reference HapMap sample NA07056_A02


title: human embryonic stem cell line FES22 p41

value: FES22 p41


title: Reference HapMap sample NA06991_D01

source_name: Reference HapMap sample NA06991_D01


title: human embryonic stem cell line HS306 p35


title: Reference HapMap sample NA06993_C11

source_name: Reference HapMap sample NA06993_C11


title: human embryonic stem cell line H9 p34

source_name: human embryonic stem cell line H9 p34


title: human embryonic stem cell line HS293 p60


title: human embryonic stem cell line I6 p50

source_name: human embryonic stem cell line I6 p50


title: human embryonic stem cell line H9 p25

source_name: human embryonic stem cell line H9 p25


title: human embryonic stem cell line HS401 p53


title: Reference HapMap sample NA06985_D10

source_name: Reference HapMap sample NA06985_D10


title: human embryonic stem cell line CCTL-14 p38

value: CCTL-14 p38


title: Sc Gcn5-myc enrichment KCl stress conditions

description: This file contains genome-wide signal intensity for Gcn5-myc enrichment under KCl stress conditions in S. cerevisiae. Two experimental samples and two control samples are used for analysis. MAT (see data processing) was used for data processing with the band width setting at 250, max gap at 300 and min probe at 10.

source_name: strain BQS1350 (ChIP fraction)

value: 1M KCl

value: myc

value: By4742 Gcn5-MYC13-KanMX6

value: monoclonal anti-c-Myc

source_name: strain By4742 (wild type control)

value: no treatment

value: MATα, his3-1, leu2-0, lys2-0, ura3-0


title: human embryonic stem cell line I3 p41

source_name: human embryonic stem cell line I3 p41


title: Sc Gcn5-myc enrichment normal conditions

description: This file contains genome-wide signal intensity for Gcn5-myc enrichment under normal conditions in S. cerevisiae. Two experimental samples and two control samples are used for analysis. MAT (see data processing) was used for data processing with the band width setting at 250, max gap at 300 and min probe at 10.


title: Virginoparae-Females-rep3

city: Rennes

first: Stephanie

last: Jaubert

address: domaine de la Motte

country: France

institute: INRA

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA or other control RNAs and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 µL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: For each chip and each probe, the average signal value and its standard deviation were quantified. Data were analyzed by first subtracting the background, then integrating all the signals corresponding for the same probe for one given chip. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3x(background standard deviation) and spot CV < 0.5. CV. When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level. Then normalization the signals from all arrays were performed using a LOWESS filter (Locally-weighted Regression). Results obtained in the different reproductive morphs were compared by comparing the ratio of the two sets of detected signals (log2) and p-values of the t-test were calculated. Differentially detected signals were those with p-value<0.05.

organism: Acyrthosiphon pisum

source_name: Adult females

label_protocol: An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments (LC-Sciences).

growth_protocol: The LSR1 clone of the pea aphid Acyrthosiphon pisum was reared and maintained as clonal individuals (parthenogenesis) on the plant Vicia fabae at 18°C under a 16h photoperiod for long-day condition (parthenogenesis). Sexual individuals and sexuparae were produced by rearing the pea aphid at 18°C under a 12h photoperiod (short-day condition).

extract_protocol: Total RNAs were extracted from 10 adult females 48h after the final moult. Three independent samples were analysed for each reproductive morph. Total RNAs were extracted using miRNeasy purification kit (QIAGEN) according to manufacturer’s instructions. Quality of RNAs was checked with the Bioanalyser (Agilent). The assay started from 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 bases) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.

tag: reproduction mode

value: Virginoparae

tag: tissue

value: whole organism


title: human embryonic stem cell line FES21 p51

value: FES21 p51

value: male


title: Sexuparae-Females-rep3

treatment_protocol: Sexual individuals and sexuparae were produced by rearing the pea aphid at 18°C under a 12h photoperiod (short-day condition).

tag: strain

value: Sexuparae


title: Sexuparae-Females-rep2

value: female


title: Virginoparae-Females-rep2


title: Oviparae-Females-rep3

value: Oviparae


title: Oviparae-Females-rep2


title: Virginoparae-Females-rep1


title: Sexuparae-Females-rep1


title: Oviparae-Females-rep1


title: human embryonic stem cell line I3.2 p55

source_name: human embryonic stem cell line I3.2 p55

value: human embryonic stem cell


title: human embryonic stem cell line CCTL-14 p49

value: CCTL-14 p49


title: human embryonic stem cell line CCTL-10 p33

value: CCTL-10 p33


title: MSC_osteodiff_rep2

description: miRNA expression in bone marrow-derived MSC after 9 days of osteogenic induction.

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized to Human miRNA V2 Microarray 8x15K (G4470B, Agilent Technologies) for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies). Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 9.5.3.1.

data_processing: Data pre-processing and differential expression analysis were done using the Bioconductor package AgiMicroRna. The Total Gene Signal provided by the Agilent Feature Extracion image analysis software was used for the data analysis. Data were normalized between arrays using the quantile method. The image analysis software attach to each feature a flag that identifies different quantification errors of the signal that can be used to filter out the microRNAs that do not reach a minimum of quality. This filtering was done after the normalization of the Total Gene Signal. We kept for the analysis those microRNA genes flagged by Agilent Feature Extraction software as detected (gIsGeneDetected=1) in at least one experimental condition. Basically, the gIsGeneDetected filtering removes microRNAs that are not expressed in any experimental condition.

source_name: bone marrow mesenchymal stem cells, osteogenic induction

label_protocol: miRNA Microarray System Protocol (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

treatment_protocol: Cells grown in osteogenic medium (expansion medium plus 10 mM β-glycerophosphate, 0.1 μM dexamethasone, 0.2 mM ascorbic acid).

value: bone marrow

value: cultured mesenchymal stem cells (hMSC)

value: osteogenic induction


title: MSC_osteodiff_rep1


title: MSC_undiff_rep2

description: miRNA expression in undifferentiated bone marrow-derived MSC.

source_name: bone marrow mesenchymal stem cells, undifferentiated

value: undifferentiated


title: MSC_adipodiff_rep1

description: miRNA expression in bone marrow-derived MSC after 9 days of adipogenic induction.

source_name: bone marrow mesenchymal stem cells, adipogenic induction

treatment_protocol: Cells grown in adipogenic medium (expansion medium plus 0.01 μM dexamethasone, 0.5 mM IBMX, 60 μM indomethacin).

value: adipogenic induction


title: MSC_adipodiff_rep2


title: MSC_undiff_rep1


title: Fib_rep4

description: miRNA expression in skin fibroblasts.

source_name: skin fibroblasts

value: skin

value: cultured fibroblasts


title: Fib_rep2

description: miRNA expression in skin fibroblasts.


title: Fib_rep3

description: miRNA expression in skin fibroblasts.


title: MSC_rep4

description: miRNA expression in bone marrow-derived MSC.


title: MSC_rep3


title: human embryonic stem cell line FES29 p37

value: FES29 p37


title: Fib_rep1

description: miRNA expression in skin fibroblasts.


title: MSC_rep2


title: MSC_rep1


title: 6H_IFNAR_Mock_D7-93

city: San Francisco

first: Sajeev

last: Batra

state: CA

institute: UCSF

hyb_protocol: Labeled sample was hybridized to the MEEBO array in 3x SSC at 63C for 42 hours.

scan_protocol: MEEBO arrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using the bundled GenePix 6.0 software.

data_processing: Spot analysis was performed with GenePix v6.0, data was stored and normalized in Nomad2 database.

source_name: aRNA from BMDM from 6H_IFNAR_Mock_D7-93

label_protocol: Total RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy5.

extract_protocol: Qiagen RNeasy RNA Isolation kit

tag: age

value: 8 w

value: bone marrow derived macrophages

tag: genome/variation

source_name: amplified mouse custom pooled reference RNA

label_protocol: Total RNA extracted from the samples was amplified using Amino Allyl MessageAmp II aRNA kit from Ambion. The amplified material was then coupled to Cy3.

value: wild type


title: 8H_IFNAR_7B_con_D7-98

source_name: aRNA from BMDM from 8H_IFNAR_7B_con_D7-98


title: 2H_IFNAR_Mock_D7-92

source_name: aRNA from BMDM from 2H_IFNAR_Mock_D7-92


title: 6H_IFNAR_7B_con_D7-96

source_name: aRNA from BMDM from 6H_IFNAR_7B_con_D7-96


title: Schizosaccharomyces Pombe wild type strain KCl treatment, replicate 4

description: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min compared to non-treated sample at 25C.

hyb_protocol: See reference:  Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

scan_protocol: Slides were scanned using Bio-rad Vers-Array ChipReader.

data_processing: Scanned slides were quantified with Imagene 4.2 software. Quantified data were loaded to GeneSpring software and normalized by lowess normalization.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min.

growth_protocol: Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.

tag: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min at 25C.

growth_protocol: Strain was grown on YEA medium at 25C to log phase.

treatment_protocol: Schizosaccharomyces Pombe wild type strain Fy368 was grown in rich medium at 25C.

tag: Schizosaccharomyces Pombe wild type strain Fy368 was grown in rich medium at 25C as control.


title: Schizosaccharomyces Pombe wild type strain KCl treatment, replicate 3

description: Schizosaccharomyces Pombe wild type strain Fy368 treated with 1M KCl for 60min was compared to non-treated sample at 25C.

label_protocol: See reference:  Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: Strain was grown on YEA medium at 25C to log phase then treated with 1M KCl for 60min.

growth_protocol: Strain was grown on YEA medium at 25C to log phase in rich medium.


title: 6H_WT_7B_con_D7-90

source_name: aRNA from BMDM from 6H_WT_7B_con_D7-90


title: Saccharomyces cerevisiae wild type KCl treatment replicate 1

description: Saccharomyces cerevisiae strain By4741 treated with 1M KCl for 60min compared to non-treated sample.

hyb_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

source_name: Saccharomyces cerevisiae strain By4741 treated with 1M KCl for 60min.

growth_protocol: Strain was grown on YPD medium at 25C to log phase then treated with 1M KCl for 60min.

treatment_protocol: Saccharomyces cerevisiae strain By4741 treated with 1M KCl for 60min at 25C.

source_name: Saccharomyces cerevisiae strain By4741

growth_protocol: Strain was grown on YPD medium at 25C to log phase.

treatment_protocol: Saccharomyces cerevisiae strain By4741 was grown in rich medium at 25C.

tag: Saccharomyces cerevisiae strain By4741 was grown in rich medium at 25C as control.


title: Saccharomyces cerevisiae gcn5 mutant KCl treatment replicate 1

description: Saccharomyces cerevisiae gcn5 mutant strain 7285 treated with 1M KCl for 60min compared to wild type parental strain By4741 treated with similar condition.

source_name: Saccharomyces cerevisiae gcn5 mutant strain 7285 treated with 1M KCl for 60min.

treatment_protocol: Saccharomyces cerevisiae gcn5 mutant strain 7285 treated with 1M KCl for 60min at 25C.

source_name: Saccharomyces cerevisiae wild type strain By4741 treated with 1M KCl for 60min.

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: Saccharomyces cerevisiae wild type strain By4741 treated with 1M KCl for 60min at 25C as control.


title: 8H_WT_7B_con_D7-91

source_name: aRNA from BMDM from 8H_WT_7B_con_D7-91


title: Saccharomyces cerevisiae gcn5 mutant replicate 1

description: Saccharomyces cerevisiae gcn5 mutant strain 7285 was compared to wild type parental strain By4741 in rich medium at 25C.

source_name: Saccharomyces cerevisiae gcn5 mutant strain 7285.

treatment_protocol: Saccharomyces cerevisiae gcn5 mutant strain 7285 was grown in rich medium at 25C.

extract_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: Saccharomyces cerevisiae wild type strain By4741 was grown in rich medium at 25C.

tag: Saccharomyces cerevisiae wild type strain By4741 was grown in rich medium at 25C as control.


title: Saccharomyces cerevisiae gcn5 mutant KCl treatment replicate 2

description: Saccharomyces cerevisiae gcn5 mutant strain 17285 treated with 1M KCl for 60min compared to wild type parental strain By4742 treated with similar condition.

source_name: Saccharomyces cerevisiae gcn5 mutant strain 17285 treated with 1M KCl for 60min.

label_protocol: See reference: Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004)

treatment_protocol: Saccharomyces cerevisiae gcn5 mutant strain 17285 treated with 1M KCl for 60min at 25C.

source_name: Saccharomyces cerevisiae wild type strain By4742 treated with 1M KCl for 60min.

treatment_protocol: Saccharomyces cerevisiae wild type strain By4742 treated with 1M KCl for 60min at 25C as control.


title: 4H_IFNAR_7B_con_D7-95

source_name: aRNA from BMDM from 4H_IFNAR_7B_con_D7-95


title: Saccharomyces cerevisiae gcn5 mutant replicate 2

description: Saccharomyces cerevisiae gcn5 mutant strain 17285 was compared to wild type parental strain By4742 in rich medium at 25C.

source_name: Saccharomyces cerevisiae gcn5 mutant strain 17285.

extract_protocol: See reference:  Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004)

treatment_protocol: Saccharomyces cerevisiae gcn5 mutant strain 17285 was grown in rich medium at 25C.

treatment_protocol: Saccharomyces cerevisiae wild type strain By4742 was grown in rich medium at 25C.

tag: Saccharomyces cerevisiae wild type strain By4742 was grown in rich medium at 25C as control.


title: human embryonic stem cell line H7 s6 teratoma p125

value: H7 s6 teratoma p125


title: human embryonic stem cells H9 p25

description: Hybridized in Finnish DNA microarray Centre

hyb_protocol: accordingly to the manufacturer's instructions (Affymetrix)

data_processing: Probe values were directly linked to  Ensembl genes (build 49) using alternative CDF-files provided by brainarray (http://brainarray.mbni.med.umich.edu/), version 11. R package aroma.affymetrix  was used in analyzing the gene values of the expression and RMA for pre-processing the Exon array values.

source_name: human embryonic stem cells

growth_protocol: standard for human embryonic stem cells

extract_protocol: RNA was isolated from cell pellets using Rneasy Kit (Qiagen). To eliminate genomic DNA from the samples Dnase I (Qiagen) digestion in column was included.

value: female


title: 4H_WT_7B_con_D7-89

source_name: aRNA from BMDM from 4H_WT_7B_con_D7-89

source_name: amplified mouse custom pooled reference RNA


title: human embryonic stem cell line H1 p61

source_name: human embryonic stem cell line H1 p61

value: male


title: human embryonic stem cell line H7 p91

source_name: human embryonic stem cell line H7 p91

value: human embryonic stem cell


title: human embryonic stem cells H7 s6 p132

scan_protocol: accordingly to the manufacturer's instructions (Affymetrix)


title: 6h_SM1_con_D4-187

source_name: aRNA from BMDM from 6h_SM1_con_D4-187


title: human embryonic stem cell line CCTL-12 p143


title: human embryonic stem cells H7 s6 p237

label_protocol: accordingly to the manufacturer's instructions (Affymetrix)


title: 2H_WT_7B_con_D7-88

source_name: aRNA from BMDM from 2H_WT_7B_con_D7-88


title: 6H_WT_Mock_D7-87

source_name: aRNA from BMDM from 6H_WT_Mock_D7-87


title: 9h_SM1_con

source_name: aRNA from BMDM from 9h_SM1_con


title: 2H_WT_Mock_D7-86

source_name: aRNA from BMDM from 2H_WT_Mock_D7-86


title: 3h_SM1_con_D4-186

source_name: aRNA from BMDM from 3h_SM1_con_D4-186


title: human embryonic stem cells H7 s14 p38


title: 9h_Ub_con_D4-182

source_name: aRNA from BMDM from 9h_Ub_con_D4-182


title: Saccharomyces cerevisiae wild type KCl treatment replicate 2

description: Saccharomyces cerevisiae strain By4742 treated with 1M KCl for 60min compared to non-treated sample.

source_name: Saccharomyces cerevisiae strain By4742 treated with 1M KCl for 60min.

extract_protocol: See reference:  Xue, Y. et al. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 21, 25-39 (2004).

treatment_protocol: Saccharomyces cerevisiae strain By4742 treated with 1M KCl for 60min at 25C.

source_name: Saccharomyces cerevisiae strain By4742

treatment_protocol: Saccharomyces cerevisiae strain By4742 was grown in rich medium at 25C.

tag: Saccharomyces cerevisiae strain By4742 was grown in rich medium at 25C as control.


title: human embryonic stem cells FES61 p48

value: FES61 p48


title: human embryonic stem cells FES75 p19

value: FES75 p19


title: human embryonic stem cell line H7 s6 p230


title: 6h_Ub_con_D4-184

source_name: aRNA from BMDM from 6h_Ub_con_D4-184


title: human embryonic stem cell line H7s14 p30


title: human embryonic stem cell line H7s14 p38


title: human embryonic stem cell line H7 s6 p132


title: human embryonic stem cell line HS293 p26


title: human embryonic stem cell line H7 s6 p237


title: human embryonic stem cells FES21 p51

value: FES21 p51


title: Stimulated (H2O2) vs Control 60 min_repl3

city: Tromsø

first: Erik

last: Hjerde

address: Breivika

department: Department of chemistry

country: Norway

institute: University of Tromsø

description: Technical replicate 3 of 3 at 60 min

hyb_protocol: Samples were hybridised to the microarrays at 42 ºC on a TECAN HS4800 hybridisation station, and microarray slides were subsequently washed, once in 0.1×SSC/0.1% SDS for 5 min at 42 ºC, then once in 0.1×SSC/0.1% SDS for 11 min at room temperature, and finally four times in 0.1×SSC for 1 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Axon Instruments Inc.) Images were quantified using the GenePix v6.1 software

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. J-Express Pro v2.7 (Dysvik and Jonassen 2001) software was used.

organism: Aliivibrio salmonicida LFI1238

source_name: Aliivibrio salmonicida LFI1238 stimulated (H2O2)

label_protocol: cDNA was generated and labelled with Cy3 and Cy5 by using 15 µg RNA, the Aminoallyl cDNA labeling kit (Ambion), and the CyDye™ Post-Labeling Reactive Dye Pack (GE Healthcare).

extract_protocol: Total RNA extracted using RNA-isol reagent (Fischer scientific). DNA was removed using the DNA-free kit (Ambion). Any traces of DNase were removed with the RNeasy Minelute Cleanup kit (Qiagen)

tag: sample type

value: Stimulated (H2O2) LFI1238 after 60 minutes

source_name: Aliivibrio salmonicida LFI1238 control

value: Control LFI1238 after 60 minutes


title: 6h_Mock_D4-178

source_name: aRNA from BMDM from 6h_Mock_D4-178


title: t0_un

source_name: aRNA from BMDM from t0_un


title: Stimulated (H2O2) vs Control 60 min_repl1

description: Technical replicate 1 of 3 at 60 min


title: Stimulated (H2O2) vs Control 60 min_repl2

description: Technical replicate 2 of 3 at 60 min


title: 3h_Ub_con_D4-183

source_name: aRNA from BMDM from 3h_Ub_con_D4-183

source_name: amplified mouse custom pooled reference RNA


title: 9h_7B_Yeast_D4-185

source_name: aRNA from BMDM from 9h_7B_Yeast_D4-185


title: 3h_Mock

source_name: aRNA from BMDM from 3h_Mock


title: Stimulated (H2O2) vs Control 30 min_repl3

description: Technical replicate 3 of 3 at 30 min

value: Stimulated (H2O2) LFI1238 after 30 minutes

value: Control LFI1238 after 30 minutes


title: human embryonic stem cell line H7 s6 teratoma p127

value: H7 s6 teratoma p127


title: Stimulated (H2O2) vs Control 30 min_repl2

description: Technical replicate 2 of 3 at 30 min


title: Stimulated (H2O2) vs Control 15 min_repl2

description: Technical replicate 2 of 3 at 15 min

value: Stimulated (H2O2) LFI1238 after 15 minutes

value: Control LFI1238 after 15 minutes


title: 3h_7B_Yeast_D4-180

source_name: aRNA from BMDM from 3h_7B_Yeast_D4-180

value: 8 w


title: Stimulated (H2O2) vs Control 30 min_repl1

description: Technical replicate 1 of 3 at 30 min


title: human embryonic stem cells FES22 p41

source_name: human embryonic stem cells

value: FES22 p41


title: Stimulated (H2O2) vs Control 15 min_repl3

description: Technical replicate 3 of 3 at 15 min


title: 6h_7B_Yeast_D4-181

source_name: aRNA from BMDM from 6h_7B_Yeast_D4-181

value: bone marrow derived macrophages

value: wild type


title: 9h_Mock_D4-179

source_name: aRNA from BMDM from 9h_Mock_D4-179


title: HLA B8

city: Houston

first: Filemon

last: Tan

state: TX

address: 6431 Fannin

department: Internal Medicine-Rheumatology

institute: UT Houston Medical School

description: Illumina humanRef-8

hyb_protocol: Illumina standard protocol

scan_protocol: Data accquired using Illumina Beadstation 500

data_processing: Background subtraction; rank invariant normalization

label: Biotin/Strepavidin Cy-3

source_name: Human umbilical vein endothelial cells

label_protocol: Illumina standard protocol

growth_protocol: Cells were cultured on collagen-coated 6-well plate in EBM medium supplemented with 10% fetal bovine serum, endothelial cell growth supplement mix at 37C under 5% CO2 in air

extract_protocol: RNA was extracted using Tri Reagent protocol and then was purified with the RNeasy Mini-kit (Qiagen)

value: HUVEC


title: HLA B35

description: Illumina humanRef-8


title: human embryonic stem cell line H7 s6 p128

value: female


title: human embryonic stem cells FES29 p37

value: human embryonic stem cell

value: FES29 p37

value: male