title: control uninephrectomy

city: Louisville

first: Shirong

last: Zheng

state: KY

address: 570 S Preston St.

department: Pediatrics

institute: University of Louisville

description: FVB-uni: uninephrectomy treatment in nondiabetic mice.

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

scan_protocol: Arrays were scanned using a GCS 3000 7G scanner and GCOS software (Affymetrix, Santa Clara, CA).

data_processing: To identify genes altered by diabetes, two comparisons of signal intensity were made, OVE-uni versus FVB-uni (designated as UNI ratio) and OVE-sham versus FVB-sham (designated as SHAM ratio).  The ratio of normalized signal intensity was determined for each probe set on the chip.  Genes with a two-fold or greater change in signal were uploaded to Ingenuity software (Ingenuity Pathway Analysis, Redwood City, CA) for canonical pathway analysis.

source_name: pooled RNA from 4 FVB-uni mice

label_protocol: 3' IVT Express Kit was used for biotin labeling.

growth_protocol: OVE diabetic mice on the FVB background were bred in our animal facility and had free access to standard rodent chow and water throughout the study.

extract_protocol: RNA was extracted from frozen kidney using TriZol reagent. RNA was pooled from 4 mice in each group (OVE-uni, OVE-sham, FVB-uni, FVB-sham).  A 100ng aliquot of RNA from the pooled sample was used for probe preparation.

treatment_protocol: Uninephrectomy was applied to OVE26 mice and their littermates at the age of 2 months.  All mice were sacrificed under anesthesia at 4.5 months of age, which was 10 weeks after surgery. Kidneys were harvested under anesthesia and perfused with phosphate-buffered saline.  Half of the kidney from each animal was snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

tag: strain/background

value: FVB/NJ

value: control

value: kidney

value: 4.5 months

tag: disease

value: nondiabetic

tag: surgery

value: uninephrectomy

tag: time after surgery

value: 10 weeks


title: control sham

status: Public on Apr 15 2011

type: RNA

country: USA

description: FVB-sham: sham surgery treatment in nondiabetic mice.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: pooled RNA from 4 FVB-sham mice

tag: genotype

tag: tissue

tag: gender

value: female

tag: age

value: sham


title: Moderate rep10 (OHN)

city: Mount Desert

first: Gareth

middle: Rhys

last: Howell

address: 600 Main Street

institute: The Jackson Laboratory

description: ONH L120287

hyb_protocol: Hybridization and post-hybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix).

scan_protocol: The arrays were scanned with a GeneChipTM  Scanner 3000 laser confocal slide scanner

data_processing: The images were quantified using GeneChipTM Operating Software (GCOS) v1.2.  Probe level data were imported into the R statistical software environment (http://www.r-project.org) and expression values for each probe set on the array were summarized using the Robust MultiChip Average (RMA) method with quantile normalization in the R/affy package

source_name: ONH moderate glaucoma

label_protocol: Biotin-labeled cDNA was synthesized separately from 20ng of each total RNA sample per the manufacturer’s protocols (Ovation™ Biotin System (NuGEN, San Carlos, CA). 2.5 μg of each biotin-labeled and fragmented cDNA sample was then hybridized onto Mouse Genome 430 v2.0 GeneChip™ arrays (Affymetrix, Santa Clara, CA).

growth_protocol: All mice were housed in a 14 h light to 10 h dark cycle

extract_protocol: For tissue harvesting, mice were anesthetized and the left eye was dissected free, and the cornea and lens removed. The optic nerve was cut close to the back of the eye. The optic nerve head was excised using a sharpened 1mm glass capillary centered over the optic nerve and immediately placed in RNAlater® (Qiagen). A small portion of central retina as well as a small portion of choroid and sclera are included in this tissue. This tissue is substantially enriched for the glial lamina. The retina (containing no optic nerve head) was then dissected free from the back of the eye and placed in a separate vial containing RNAlater (Ambion, Austin TX) and stored at 4oC until required. The process was repeated for the right eye. Dissection of each eye was completed in ≤5 minutes (10 minutes per mouse)

tag: phenotype

value: moderate glaucoma

tag: strain

value: optic nerve head

value: 10.5 months


title: Severe rep3 (OHN)

description: ONH R113657

source_name: ONH severe glaucoma

value: severe glaucoma


title: Moderate rep3 (OHN)

description: ONH L113657


title: Moderate rep5 (OHN)

description: ONH R115837


title: Moderate rep2 (OHN)

description: ONH L112876


title: diabetes sham

description: OVE-sham: sham surgery treatment in diabetic mice.

source_name: pooled RNA from 4 OVE-sham mice

value: OVE26 transgenic

value: diabetic


title: No or early 2 rep11 (OHN)

description: ONH L115843

source_name: ONH no or early glaucoma

value: no or early glaucoma


title: diabetes uninephrectomy

description: OVE-uni: uninephrectomy treatment in diabetic mice.

source_name: pooled RNA from 4 OVE-uni mice


title: MC_Val_G5

type: genomic

city: Lucknow

first: Natesan

last: Manickam

state: Uttar Pradesh

address: Mahatma Gandhi Marg

department: Department Environmental Biotechnology Division

country: India

institute: Indian Institute of Toxicology Research

description: E. coli DH5α, E.coli BL21, E.coli K12 NCTC50192

hyb_protocol: 1.25 micrograms of cy3 labeled samples were hybridized.  Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 24 hours

scan_protocol: The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C

data_processing: Images were quantified using Agilent Feature Extraction Software (10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities.

molecule: genomic DNA

organism:
Escherichia coli K-12
Sphingomonas sp. NM05
Escherichia coli BL21
Escherichia coli DH5[alpha]

source_name: Genomic DNA of mixed culture containing only non-degraders in equal ratio

label_protocol: The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). DNA of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3  dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields

growth_protocol: The Sphingomonas sp. strain NM-05 used in the study is a known degrader of γ-hexachlorocyclohexane (γ-HCH) and has been isolated from the vicinity of an industry India Pesticide Limited, Chinhat industrial area, Lucknow which is involved in manufacturing chlorinated pesticides for last 25 years. The strain was harvested in mineral salt medium with 0.34mM γ-HCH as sole source of carbon and energy. The strain Bordetella sp. strain IITR-02 used in this study has been isolated from the vicinity of the industry India Pesticide Limited, Chinhat, Lucknow and is found to be a degrader of 1,2-, 1,4-dichloro and 1,2,3- and 1,2,4-trichlorobenzene. The strain was harvested in mineral salt medium with 3.2mM of 1,2,4-trichlorobenzene as sole source of carbon and energy. The bacterium Rhodococcus sp. strain RHA1 which is a known degrader of polychlorinated biphenyls, substituted phenols, benzoates and phthalates was grown on 0.2% biphenyl and 20mM of benzoate as carbon sources. The strain Escherichia coli DH5α and Escherichia coli BL21 were grown in Luria-Bertani medium and strain Escherichia coli K12  was grown in nutrient broth to an OD560nm of 0.4 at 37 degree centigrade with continuous shaking.

extract_protocol: The genomic DNA from pure and mixed bacterial cultures was isolated using the Wizard genomic DNA isolation kit (Promega corporation, Madison, USA) as per manufacturer's instructions. The concentration of DNA was analyzed by Nanodrop spectrophotometer (Nanodrop Technologies Inc, Rockland, USA), and quality was determined by analysis on DNA 12000 kit (Caliper Sciences, USA) using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

tag: isolation source

value: Mixed culture


title: MC_Val_G4

description: Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1,Bordetella sp. strain IITR-02

organism:
Rhodococcus jostii RHA1
Sphingomonas sp. NM05
Bordetella sp. IITR-02

source_name: Genomic DNA of mixed culture containing only degraders in equal ratio


title: MC_Val_G6

source_name: Genomic DNA of mixed culture containing NM-05 cells in double ratio than other degraders (NM-05:IITR-02:RHA1 in 2:1:1 ratio)


title: MC_Val_G7

source_name: Genomic DNA of mixed culture containing IITR-02 cells in double ratio than other degraders (NM-05:IITR-02:RHA1 in 1:2:1 ratio)


title: MC_Val_G8

source_name: Genomic DNA of mixed culture containing RHA1 cells in double ratio than other degraders (NM-05:IITR-02:RHA1 in 1:1:2 ratio)


title: Neurons_W45_Rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 45 minutes of TTX washout after 48 hours of TTX treatment

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using the Rosetta Resolver® system (version 7.2) (Rosetta Biosoftware, Kirkland, WA).

organism: Rattus norvegicus

source_name: Dissociated neuronal culture

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Neuronal cultures were prepared by dissociating the cortices of pre-natal rat pups and neurons were maintained in Neurobasal media supplementd with B27 or NS21. Cells were used in the window of 11-15 days in culture.

extract_protocol: Total RNA was extracted using the Rneasy kit (Qiagen) using manufacterurer's protocol. DNA contamination was eliminated by digesting the samples on column using RNAse-free DNAse (Qiagen). RNA was quantified using the Nanodrop-1000 spectrophotometer.

treatment_protocol: Neurons were treated for 48 hours with TTX and then TTX was washed out using regular media (3 washes). Samples were collected either 15 or 45 minutes after TTX washout.

tag: cell type

value: Mature neurons

tag: treatment


title: Neurons_W15_Rep1

description: Gene expression after 15 minutes of TTX washout after 48 hours of TTX treatment


title: Mature Neural Cells Derived from hESC-replicate 1

city: Tehran

first: Vahid

last: Hajihoseini

state: Tehran

address: Banihashem st, resalat ave

department: Systems Biology

country: Iran

institute: Royan Institute

description: Mature Neural Cells Drived from hESC-replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Lumi package in R

organism: Homo sapiens

source_name: Royan H6 hESC

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Mature Neural Cells Drived from hESC


title: Neurons_W45_Rep3

value: Gene expression after 45 minutes of TTX washout after 48 hours of TTX treatment


title: Mature Neural Cells Derived from hESC-replicate 2

description: Mature Neural Cells Drived from hESC-replicate 2


title: Neural ectoderm Derived from human embryonic stem cell-replicate 3

description: Neural ectoderm drived from human embryonic stem cell-replicate 3


title: Mature Neural Cells Derived from hESC-replicate 3

description: Mature Neural Cells Drived from hESC-replicate 3


title: Neurons_W15_Rep3

value: Gene expression after 15 minutes of TTX washout after 48 hours of TTX treatment


title: Neural ectoderm Derived from human embryonic stem cell-replicate 2

description: Neural ectoderm drived from human embryonic stem cell-replicate 2


title: Neurons_W15_Rep2


title: MC_Val_G3

description: Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1,Bordetella sp. strain IITR-02, E. coli DH5α, E.coli BL21, E.coli K12 NCTC50192

organism:
Escherichia coli K-12
Rhodococcus jostii RHA1
Sphingomonas sp. NM05
Escherichia coli BL21
Escherichia coli DH5[alpha]
Bordetella sp. IITR-02

source_name: Genomic DNA of all strains (degraders and non-degraders) isolated individually and mixed in equal ratio (500ng each)


title: Neural ectoderm Derived from human embryonic stem cell-replicate 1

description: Neural ectoderm drived from human embryonic stem cell-replicate 1


title: Neurons_W45_Rep1


title: MC_Val_G2

description: Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1,Bordetella sp. strain IITR-02, E. coli DH5α, E.coli BL21 and E.coli K12 NCTC50192

source_name: Genomic DNA of mixed culture (Degraders and non-degraders in 2:1 ratio)


title: 432 siRNA-Nkx2-3--rep2

city: hershey

first: wei

last: yu

address: 500 university drive

institute: pennsylvania state university

description: SAMPLE 8

hyb_protocol: performed at Genomics Core of the Cleveland Clinic Lerner Research Institute

data_processing:
The raw intensity data in Illumina HumanHT-12 expression beads were exported from BeadStudio software and pre-processed in Bioconductor lumi package. Specially, raw data were transformed using variance-stabilizing transformation (VST) and log2 transformation.
The quantile normalization was performed to normalize transformed microarray data. Bioconductor LIMMA package was used to detect differentially expressed genes. The p-value from moderated t-tests in LIMMA were adjusted by Benjamini and Hochberg's method to control false discovery rate.

source_name: HIMEC

label_protocol: cRNA was labeled  with biotin-UTP using the Illimina Total Preo RNA Amplification Kit (Ambion)

growth_protocol: HIMEC lines were cultured in MCDB131 supplemented with 20% FBS, heparin, ECGS, and antibiotics at 37 0C with  5% co2

extract_protocol: RNA was extracted from HIMEC using the Rneasy mini kit (QIAGEN Sciences)

treatment_protocol: HIMEC were transfected with siRNA-Nkx2-3 using TransPass HUVEC transfection reagent (New England BioLabs)

tag: cell line

value: human intestinal microvascular endothelial cells (HIMEC)

tag: himec subline

tag: transfection


title: MC_Val_G1

source_name: Genomic DNA of mixed culture (Degraders: NM-05, IITR-02, RHA1; Non-degraders: DH5α, BL21 and K12 in equal ratio)


title: Neurons_TTX_Rep2

description: Gene expression after 48 hours of TTX treatment


title: 432 siRNA-Nkx2-3--rep1

description: SAMPLE 7

scan_protocol: performed at Genomics Core of the Cleveland Clinic Lerner Research Institute


title: 432 vector--rep2

description: SAMPLE 6

value: control


title: Neural initiation stage of human embryonic stem cell-replicate 3


title: Neurons_TTX_Rep3

value: Gene expression after 48 hours of TTX treatment


title: Chl_IPL_SD_RP1

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in chloroaromatic contaminated site; aliquot 1; to test the replication of the results

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1 & 10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities.

organism: soil metagenome

source_name: Total soil DNA from areas around IPL, Lucknow aliquot 1

growth_protocol: The Sphingomonas sp. strain NM-05 used in the study is a known degrader of γ-hexachlorocyclohexane (γ-HCH) and has been isolated from the vicinity of an industry India Pesticide Limited, Chinhat industrial area, Lucknow which is involved in manufacturing chlorinated pesticides for last 25 years. The strain was harvested in mineral salt medium with 0.34mM γ-HCH as sole source of carbon and energy. The strain Escherichia coli DH-5α was grown in Luria-Bertani medium to an O.D. of 0.4 at 37 degree centigrade with continuous shaking. The soil/sludge samples were collected in air tight vessels,transported on ice (4○C) to the laboratory and processed immediately for DNA isolation. At each sampling location multiple samples were collected from close (100m) to far (500m) from the industry, along the effluent channel and at the place where effluent channel from the industrial area falls into the river.

extract_protocol: The total DNA to be used as target for microarray hybridization was isolated from soil/ sediment samples using the Mo Bio Power soil DNA kit (Mo Bio Inc., Carlsbad, CA, USA) as per manufacturer’s instructions. Before processing for DNA isolation, the soil/ sediments were mixed thoroughly using a mortar-pestle. One gm of soil/sediment was taken for DNA isolation, and during processing with the kit, lysozyme was added to facilitate the lysis of bacteria. The genomic DNA from pure bacterial cultures was isolated using the Wizard genomic DNA isolation kit (Promega corporation, Madison, USA) as per manufacturer's instructions. The concentration of DNA was analyzed by Nanodrop spectrophotometer (Nanodrop Technologies Inc, Rockland, USA), and quality was determined by analysis on DNA 12000 kit (Caliper Sciences, USA) using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: Soil


title: 432 vector--rep1

description: SAMPLE 5


title: Chl_IPL_SD_RP2

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in chloroaromatic contaminated site; aliquot 2; to test the replication of the results

source_name: Total soil DNA from areas around IPL, Lucknow aliquot 2


title: Neural initiation stage of human embryonic stem cell-replicate 2


title: Neural initiation stage of human embryonic stem cell-replicate 1


title: Neurons_TTX_Rep1


title: 21B siRNA-Nkx2-3--rep2

description: SAMPLE 4


title: gingival epithelial cell RNA_infected_6h_rep2

first: Richard

middle: J

last: Lamont

address: 570 South Preston Street

department: Oral Biology

description: infected 2

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 (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 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: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix. Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193]. A transcript to be listed as detectable must meet at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). 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. t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric. All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: gingival epithelial cell RNA, control, 6 h

label_protocol: The microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3 dye staining.

growth_protocol: Primary epithelial cells were grown to 80% confluence in DermaLife medium (Lifetech) at 37°C in 5% CO2.

extract_protocol: Cells were lysed with TriZOL reagent for RNA extraction. The miRNeasy kit was used.

treatment_protocol: Cells were exposed to P. gingivalis at MOI 100, or uninfected controls, for 6 h.

value: primary gingival epithelial cells

value: Porphyromonas gingivalis infection


title: gingival epithelial cell RNA_infected_6h_rep3

description: infected 3

source_name: gingival epithelial cell RNA, infected, 6 h


title: TGFBR1 inhibitor, biological rep2

city: Prague

first: Vladimir

last: Cermak

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics, Czech Academy of Sciences

description: Gene expression data from chicken embryo dermal fibroblasts treated with TGFBR1 Kinase Inhibitor II.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite (version 6.4) using Affymetrix default annotation and GC-RMA as normalization method.

organism: Gallus gallus

source_name: Chicken embryo dermal myofibroblasts treated with 500 nM TGFBR1 Kinase Inhibitor II

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

growth_protocol: The CEDM cells were obtained from day 10 chicken embryo skin explants and cultured in DMEM supplemented with antibiotics, 4% fetal bovine serum and 2% chicken serum.

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

treatment_protocol: The cells were treated with 500 nM TGFBR1 Kinase Inhibitor II (2-(3-(6-Methylpyridin-2-yl)-1H-pyrazol-4-yl)-1,5-naphthyridine) from Calbiochem dissolved in DMSO for 48 hours. The control cells were treated with 0.1% DMSO only.

tag: breed

value: brown Leghorn

value: chicken embryo dermal myofibroblasts (CEDM)

value: TGFBR1 kinase inhibitor II


title: 21B vector--rep2

description: SAMPLE 2


title: ECDH5_GD_RP1

description: Comparative genomic hybridization for pure genomic DNA of strain DH5α (used as biological negative control)

organism: Escherichia coli DH5[alpha]

source_name: Genomic DNA of Escherichia coli DH5α

value: Pure culture


title: Human embryonic stem cell - replicate 3

description: Human embryonic stem cell - replicate 3

value: Human embryonic stem cell


title: 21B siRNA-Nkx2-3--rep1

description: SAMPLE 3


title: 21B vector--rep1

description: SAMPLE 1


title: NM-05_GD_1250_RP1

description: Comparative genomic hybridization for pure genomic DNA of strain NM-05 (used as biological positive control)

organism: Sphingomonas sp. NM05

source_name: Genomic DNA of Sphingomonas sp. strain NM-05


title: gingival epithelial cell RNA_infected_6h_rep1

description: infected 1


title: Human embryonic stem cell - replicate 2

description: Human embryonic stem cell - replicate 2


title: PET_SD_RP1

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in petroleum contaminated site

source_name: Total sludge DNA from areas around Mathura oil refinery

value: Sludge


title: HM_SD_RP1

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in heavy metal contaminated site

source_name: Total soil/ sludge DNA from Jajmau industrial area, Kanpur

value: Soil/sludge


title: DMSO control, biological rep2

description: Gene expression data from chicken embryo dermal fibroblasts treated with DMSO only as a control.

source_name: Chicken embryo dermal myofibroblasts treated with DMSO only

value: DMSO


title: TGFBR1 inhibitor, biological rep3


title: Human_PT0812_SAGM

city: Nagasaki

first: Norisato

last: Mitsutake

address: 1-12-4 Sakamoto

country: Japan

institute: Nagasaki University

hyb_protocol: 12.5 ug of aRNAs were hybridized for 16 hr. GeneChips were then washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: The data was analyzed using Affymetrix GeneChip Command Console and Affymetrix Expression Console.

label_protocol: Biotinylated aRNAs were prepared using Affymetrix recommended protocol. Briefly, cDNA was generated from total RNA (100 ug) and labeled aRNA was transcribed by in vitro transcription.

extract_protocol: Total RNAs were extracted with ISOGEN reagent using standard procedure.

treatment_protocol: PT: primary thyrocytes were plated with DMEM:F12 (1:2) with 3.3% FBS; SAGM: medium was then replaced with SAGM and incubated for about 2 weeks.

value: thyroid

value: primary thyrocytes


title: Human_PT0812_PT


title: Human embryonic stem cell - replicate 1

description: Human embryonic stem cell - replicate 1


title: Human_PT0811_SAGM


title: gingival epithelial cell RNA_control_6h_rep3

description: control 3


title: DMSO control, biological rep3


title: DMSO control, biological rep1


title: TGFBR1 inhibitor, biological rep1


title: CETP_SD_RP1

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in effluent from a CETP

source_name: Total DNA of primary sludge from CETP, Kanpur


title: gingival epithelial cell RNA_control_6h_rep1

description: control 1


title: gingival epithelial cell RNA_control_6h_rep2

description: control 2


title: River bed_SD_RP1

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in Gomti river bed

organism: freshwater sediment metagenome

source_name: Total DNA of Sediment from Gomti river, Lucknow

value: Sediment


title: Human_PT0808_PT


title: Human_PT0811_PT


title: moderately differentiated tumors prostate glands

city: Bonn

first: Andreas

last: Lindstrot

address: Sigmund-Freud-Str. 25

department: Molekular Patholoy

country: Germany

institute: University of Bonn

hyb_protocol: The hybridization was performed according to Agilent 60mer oligo Microarray processing protocol using Agilent gene expression hybridization kit. Briefly Cy3-labeled fragmented cRNA in hybridization buffer was hybridyzed over nigth (17h 65°C ) to Agilent whole human genome oligo Micrarray 4x44k using Agilent recommended hybridization chamber and oven. Finally the microarray was washed once with the agilent gene expression wash buffer 1 for 1 minute at Room temperature followed by a second wash with preheated Agilent gene expression wash buffer 2 (37° for 1 Minutes). The last washing step was performed with acetonitrile

scan_protocol: Flourescence signals of the hydridysed agilent microarray were detected using the Agilent Microarray scanner system.

data_processing: the Agilent feature extraction software FES was used to read out and process the microarray image file. For the determination of differential gene expression FES derived output data files were further analyzed using the Rosetta resolver gene expression data analysis system (Rosetta biosoftware). All samples were labeled with Cy3, the ratio experiments are designated as control vs experiments. The ratios are always calculated by dividing sample signal intensity through control signal intensity.

source_name: prostate glands

label_protocol: For the linear T7 based amplification step, 0.26 - 0.3µg of total RNA sample was used. To produce Cy3-labebeld cRNA, the RNA samples were amplified and labeld using Agilent low RNA input linear Amp Kit (Agilent Technologies) following manufactures protocol.

extract_protocol: The extraction of the laser microdissected glands was performed according to the manual of the Qiagen Rneasy Micro Kit including a recommend DNAse digestion

tag: tumor stage

value: Gleason 6-7a


title: Chl_SD_RP1

description: Comparative genomic hybridization for profiling of biodegradation and 16S rRNA gene in chloroaromatic contaminated site

source_name: Total soil/ sludge DNA from chloroaromatic contaminated site, IPL, Lucknow


title: poorly differentiated tumors prostate glands

value: Gleason 8-9


title: Human_PT0808_SAGM


title: Family17_EnrichedFetalDNA

status: Public on Apr 14 2011

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

description: Hybridized to 250K_Nsp

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

scan_protocol: Each array was washed using Affymetrix Fluidics Station 640, and scanned using the GeneChip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

data_processing: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.

source_name: Enriched Fetal DNA

label_protocol: DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, and biotinylated according to the manufacturer's recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).

extract_protocol: Biopsied trophectoderm and arrested whole embryo samples underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).

value: enriched fetal DNA from maternal plasma

tag: family


title: Family17_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: Family17_CryopreservedEmbryo_12

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_7

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_10

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_11

description: Hybridized to 250K_Nsp


title: Family16_Buccal_gDNA_1

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: Family17_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Family17_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: Family17_Buccal_gDNA_1

description: Hybridized to 250K_Nsp


title: Family16_TransferredEmbryo_3

description: Hybridized to 250K_Nsp


title: Family16_WholeEmbryo_3

description: Hybridized to 250K_Nsp

source_name: Whole Embryo

value: whole embryo


title: Family16_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: Family17_CryopreservedEmbryo_8

description: Hybridized to 250K_Nsp


title: Family16_EnrichedFetalDNA

description: Hybridized to 250K_Nsp


title: Family16_TransferredEmbryo_2

description: Hybridized to 250K_Nsp


title: Family17_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: Family16_WholeEmbryo_4

description: Hybridized to 250K_Nsp


title: Family17_maternal_gDNA

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: Family16_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_9

description: Hybridized to 250K_Nsp


title: Family17_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: Family16_Buccal_gDNA_2

description: Hybridized to 250K_Nsp


title: Family16_paternal_gDNA

description: Hybridized to 250K_Nsp


title: Family16_WholeEmbryo_1

description: Hybridized to 250K_Nsp


title: Family17_CryopreservedEmbryo_6

description: Hybridized to 250K_Nsp


title: Family16_WholeEmbryo_2

description: Hybridized to 250K_Nsp


title: Family15_Buccal_gDNA_1

description: Hybridized to 250K_Nsp


title: Family15_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred embryo


title: Family15_CryopreservedEmbryo_8

description: Hybridized to 250K_Nsp


title: Family14_Buccal_gDNA_1

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_7

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_9

description: Hybridized to 250K_Nsp


title: Family14_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: Family15_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: Family15_paternal_gDNA

description: Hybridized to 250K_Nsp


title: Family15_maternal_gDNA

description: Hybridized to 250K_Nsp


title: Family14_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: SGBS hypoxia 16h, biological rep3

city: Feldkirch

first: Heinz

last: Drexel

address: Carinagasse 47

country: Austria

institute: VIVIT

hyb_protocol: Following RNA purification, 20 μg of cRNA were fragmented at 95°C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to the ‘Human Genome U133 2.0’ arrays (Affymetrix).

scan_protocol: The arrays were stained and washed in an Affymetrix fluidic station 450. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.

data_processing: Microarray data analysis was performed in R (http://www.r-project.org) using packages from the Bioconductor project (PMID 15461798). GeneChip raw expression values were normalized and summarized using the GC robust multi-array average (GCRMA) method.

source_name: human SGBS mature adipocytes, hypoxia,16h

label_protocol: 500 ng total RNA was processed to generate a biotinylated hybridization target using the ‘One Cycle cDNA Synthesis’ kit and the ‘One Cycle Target Labelling’ kit (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols. In brief, total RNA was reverse-transcribed into cDNA using an anchored oligo-dTT7-Primer, converted into double-stranded cDNA and purified with the ‘Affymetrix Sample Clean-up’ kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by T7 polymerase-mediated in vitro transcription including a modified nucleotide for subsequent biotinylation.

extract_protocol: Total RNA was prepared from control and treated SGBS cells, in triplicate experiments, with the ‘RNeasy Lipid Tissue’ kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany), followed by purification of the RNA with the ‘RNeasy Mini’ kit (Qiagen).

treatment_protocol: Hypoxia for 0, 3, 6 and 16 hours, respectively.

value: adipose

value: mature adipocytes

tag: disease state

value: Simpson-Golabi-Behmel syndrome (SGBS)

tag: condition

value: hypoxia

tag: time

value: 16 hrs


title: Family15_CryopreservedEmbryo_6

description: Hybridized to 250K_Nsp

tag: tissue


title: SGBS hypoxia 6h, biological rep3

source_name: human SGBS mature adipocytes, hypoxia, 6h

value: 6 hrs


title: Family13_TransferredEmbryo_2

description: Hybridized to 250K_Nsp


title: Family14_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: Family14_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: Family14_TransferredEmbryo_2

description: Hybridized to 250K_Nsp


title: Family14_EnrichedFetalDNA

description: Hybridized to 250K_Nsp


title: Family14_maternal_gDNA

description: Hybridized to 250K_Nsp


title: Family13_EnrichedFetalDNA

description: Hybridized to 250K_Nsp


title: Family14_Buccal_gDNA_2

description: Hybridized to 250K_Nsp


title: Family15_Buccal_gDNA_2

description: Hybridized to 250K_Nsp


title: Family13_Buccal_gDNA

description: Hybridized to 250K_Nsp


title: Family15_EnrichedFetalDNA

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp


title: Family15_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp


title: SGBS hypoxia 3h, biological rep3

source_name: human SGBS mature adipocytes, hypoxia, 3h

value: 3 hrs


title: Family14_paternal_gDNA

description: Hybridized to 250K_Nsp


title: SGBS control, biological rep3

source_name: human SGBS mature adipocytes, control

value: normoxia


title: Family13_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: SGBS hypoxia 6h, biological rep2


title: NHDF Dex A

city: Stanford

first: Patrick

middle: O

last: Brown

state: CA

address: Beckman Center b439

department: Department of biochemistry

institute: Stanford university school of medicine

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60867.gif
Figure in article: 2

hyb_protocol: not provided

scan_protocol: scanner model: GenePix 4000A

data_processing: Rubins 2003 - Data filtering and analysis; Array images were scanned using an Axon Scanner 4000A (Axon Instruments, Union City, CA), and image analysis was performed using GenePix Pro version 3.0.6.89 (Axon Instruments, Union City, CA). Grids were manually aligned and features were found using the software feature extraction. Features were visually inspected for blemishes and removed from downstream analysis. Data were uploaded to the Stanford Microarray Database (http://genome-www5.stanford.edu/) and normalized using regression correlation. Data were expressed as the log2 ratio of fluorescence intensities of the sample and the reference, for each element on the array. Data were filtered to exclude elements that did not have a regression correlation of Cy5 to Cy3 signal over the pixels spanning the array element of ??0.6 and intensity/background ratio of ??2.5 in at least 80% of the arrays. For each gene, the expression levels over the timecourse for each monkey were ??time-zerotransformed?? by subtracting the average of the pre-infection baseline expression level from that animal so that the values of each timepoint represent changes relative to the uninfected samples. The genes whose expression varied from the uninfected baseline by at least 3 fold in at least 3 samples were selected for further analysis. The data were hierarchically clustered using the Cluster program (http://rana.lbl.gov/EisenSoftware.htm) and displayed using TreeView (http://rana.lbl.gov/EisenSoftware.htm).; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Kate,,Rubins

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: NHDF Dex A

label_protocol: Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA  1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul:    mRNA 3-4ug  pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL  2. Heat to 65oC for 10 min and cool on ice.   3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture  5X first-strand buffer 6.0uL  0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL   4. Incubate at 42oC for 1 hr.   5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr.   6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min.   7. Neutralize by addition of 15uL of 0.1N HCl.  8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column.  Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon.  9. WASH 1: Spin 7-8 min. at 14,000g (=RCF).  Remove flow through and save to a separate tube.  10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube.  11.  WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL  polyA RNA (Sigma, #P9403) 2 uL 10ug/uL  tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane.  Make sure not to dry the membrane completely!  12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Kate,,Rubins

extract_protocol:
Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases.  Keep the samples cold or on ice as much as possible to prevent RNA degradation.   Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment.  2. Add 1mL of Trizol to the frozen PBMC pellet.   3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes.  4. Vortex and transfer to 1.5ml microfuge tubes if not already in them.  5. Add 0.2 mls chloroform per 1 ml Trizol.  Vortex or shake vigorously and incubate at room temp. for 2-3 minutes.  6. Centrifuge at 12,000g for 15 minutes at 4C.  7. Transfer the aqueous phase to a fresh tube.  (The volume will be about 60% of the volume of Trizol.)  Note:  If isolating DNA, save the organic phase.  Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low.  8. Add 0.5 mLs of isopropanol per 1 ml Trizol used.  Incubate at room temp. for 10 minutes.   9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C.    10. The RNA pellet will be visible at the bottom of the tube.  Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  11. WASH 1: Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  13. WASH 2:  Wash the pellet with 1 ml 70% EtOH.  Centrifuge at top speed 14,000g for 5-7 minutes.  14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube.  15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes).  Do not overdry!  16. Resuspend the pellet in 20uls of DEPC H2O.  Store at ?80C.  17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Kate,,Rubins
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug  Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water  70oC for 10 min in a thermocycler with lid on, but not clamped down.   Centrifuge briefly.   Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly.  Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes.   Add to the master mix: Amount Reagent 1uL Reverse Transcriptase  Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting.   42oC for 2 hours in thermocycler with lid on, but not clamped down.   Centrifuge briefly, place on ice, and immediately proceed to next step  SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  16oC for 2 hours in thermocycler with lid completely off.    DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min.  Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through.  Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol.  Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column.   Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g.   Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat.   Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC.  IN VITRO TRANSCRIPTION  Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 6 hours in hybridization oven.  Add to each reaction: Amount Reagent 2uL DNaseI  Gently pipette or flick to mix, and then centrifuge briefly.  37oC for 30min in hybridization oven   aRNA PURIFICATION  Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes.  Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min.  Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL.   Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing.  Apply entire sample to the equilibrated filter cartridge.  Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube.  Add 650uL aRNA Wash Buffer to each filter.   Centrifuge for 1 minute at 10,000 x g.   Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube.  Elute aRNA by adding 50uL preheated (50oC) water to center of column.  Incubate at room temperature for 2 min.  Centrifuge for 1 minute at 10,000 x g.  Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g.   Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Kate,,Rubins

tag: infection

tag: compound based treatment

value: Dexamethasone

value: Primary Human Dermal Fibroblast


title: Family13_CryopreservedEmbryo_7

description: Hybridized to 250K_Nsp


title: SGBS hypoxia 16h, biological rep2


title: MPX 12 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63908.gif
Figure in article: 1

scan_protocol: scanner model: GenePix 4200A

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

value: Stratagene Universal Human Reference RNA

source_name: MPX 12 HeLa cells infected with MPX in vitro 5.5.05

value: Monkeypox Virus

value: HeLa


title: SGBS control, biological rep2


title: NHDF 0hr D

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60860.gif
Figure in article: 2

source_name: NHDF 0hr D

value: 0 h


title: SGBS hypoxia 6h, biological rep1


title: SGBS hypoxia 16h, biological rep1


title: NHDF 0hr C

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60859.gif
Figure in article: 2

source_name: NHDF 0hr C


title: SGBS hypoxia 3h, biological rep2


title: Family13_CryopreservedEmbryo_6

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: Family13_CryopreservedEmbryo_5

description: Hybridized to 250K_Nsp


title: Mock 12 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63897.gif
Figure in article: 1

source_name: Mock 12 HeLa cells Mock Infected in vitro 5.5.05

value: Mock infection


title: NHDF 24hr IFNa B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60862.gif
Figure in article: 2

source_name: NHDF 24hr IFNa B

value: Interferon-alpha


title: NHDF Dex B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60868.gif
Figure in article: 2

source_name: NHDF Dex B


title: Killed MPX 24 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63903.gif
Figure in article: 1

source_name: Killed MPX 24 HeLa cells infected with Mock in vitro 5.5.05

value: killed Monkeypox Virus


title: NHDF 0hr B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60852.gif
Figure in article: 2

source_name: NHDF 0hr B


title: Mock 2 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63895.gif
Figure in article: 1

source_name: Mock 2 HeLa cells Mock Infected in vitro 5.5.05

value: 2 h


title: NHDF p[IC] B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60864.gif
Figure in article: 2

source_name: NHDF p[IC] B

value: polyinosinic-polycytidylic acid


title: SGBS hypoxia 3h, biological rep1

value: adipose

value: mature adipocytes

value: Simpson-Golabi-Behmel syndrome (SGBS)

value: hypoxia


title: Killed MPX 1 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63899.gif
Figure in article: 1

source_name: Killed MPX 1 HeLa cells infected with Killed MPX in vitro 5.5.05

value: 1 h


title: MPX 6 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63907.gif
Figure in article: 1

source_name: MPX 6 HeLa cells infected with MPX in vitro 5.5.05

value: 6 h


title: NHDF I+P A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60857.gif
Figure in article: 2

source_name: NHDF I+P A

value: Ionomycin + PMA

value: Primary Human Dermal Fibroblast


title: NHDF TNFa A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60855.gif
Figure in article: 2

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02

source_name: NHDF TNFa A

value: TNF-alpha


title: NHDF 24hr Mock B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60861.gif
Figure in article: 2

value: Stratagene Universal Human Reference RNA

source_name: NHDF 24hr Mock B

value: PBS


title: Killed MPX 6 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63901.gif
Figure in article: 1

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC

source_name: Killed MPX 6 HeLa cells infected with Killed MPX in vitro 5.5.05

value: HeLa


title: Family13_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp

value: cryopreserved embryo


title: Family13_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp


title: NHDF LPS B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60866.gif
Figure in article: 2

source_name: NHDF LPS B

value: LPS


title: HUES-9_P33

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

description: Blastocyst-derived ES cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: sample type

value: Embryonic stem cells

value: normal

value: HUES


title: HUES-8_P24

description: Blastocyst-derived ES cells

value: Male


title: Family13_CryopreservedEmbryo_4

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo


title: 201B7_P18

description: Fibroblast-derived iPS cells established by Dr Yamanaka

value: inducible pluripotent stem cells


title: Family13_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: SGBS control, biological rep1

source_name: human SGBS mature adipocytes, control

value: adipose

tag: cell type

value: mature adipocytes

value: Simpson-Golabi-Behmel syndrome (SGBS)

value: normoxia


title: HUES-6_P25

description: Blastocyst-derived ES cells


title: Family12_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: Family13_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: HUES-3_P29

description: Blastocyst-derived ES cells


title: NHDF LPS A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60858.gif
Figure in article: 2

value: Stratagene Universal Human Reference RNA

source_name: NHDF LPS A

value: Primary Human Dermal Fibroblast


title: Family13_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: NHDF 0hr A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60851.gif
Figure in article: 2

source_name: NHDF 0hr A

value: 0 h


title: Mock 0a HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63893.gif
Figure in article: 1

source_name: Mock 0 HeLa cells Mock Infected in vitro 5.5.05

value: Pre infection

value: HeLa


title: Killed MPX 2 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63900.gif
Figure in article: 1

source_name: Killed MPX 2 HeLa cells infected with Killed MPX in vitro 5.5.05

value: 2 h

value: killed Monkeypox Virus


title: Killed MPX 12 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63902.gif
Figure in article: 1

source_name: Killed MPX 12 HeLa cells infected with Killed MPX in vitro 5.5.05


title: HUES-2_P21

description: Blastocyst-derived ES cells

value: Embryonic stem cells

value: normal

value: HUES


title: NHDF 24hr Mock A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60853.gif
Figure in article: 2

source_name: NHDF 24hr Mock A

value: PBS


title: Mock 1 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63894.gif
Figure in article: 1

source_name: Mock 1 HeLa cells Mock Infected in vitro 5.5.05

value: 1 h

value: Mock infection


title: NHDF I+P B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60865.gif
Figure in article: 2

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02

source_name: NHDF I+P B

value: Ionomycin + PMA


title: Family12_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: Mock 0b HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63904.gif
Figure in article: 1

source_name: Stratagene UHR, 1 round of amp(Ambion MessageAmp) 8/9/05, spiked in MPX/VAC


title: Family12_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: NHDF p[IC] A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60856.gif
Figure in article: 2

source_name: NHDF p[IC] A

value: polyinosinic-polycytidylic acid


title: NHDF TNFa B

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60863.gif
Figure in article: 2

value: Stratagene Universal Human Reference RNA

source_name: NHDF TNFa B

value: TNF-alpha


title: Family12_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: UtE-iPS-11_P31

description: UtE1104-derived iPS cells

value: Female

value: inducible pluripotent stem cells


title: 0hr 1a in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50435.gif
Figure in article: 1

scan_protocol: scanner model: GenePix 4000B

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

source_name: 0hr 1a in vitro monocyte pox timecourse

value: 0 h

value: Primary Human Macrophage


title: UtE-iPS-11_P13

description: UtE1104-derived iPS cells


title: UtE-iPS-11_P18

description: UtE1104-derived iPS cells


title: UtE-iPS-11_P39

description: UtE1104-derived iPS cells


title: Family12_WholeEmbryo_4

description: Hybridized to 250K_Nsp

source_name: Whole Embryo

value: whole embryo


title: NHDF 24hr IFNa A

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60854.gif
Figure in article: 2

source_name: NHDF 24hr IFNa A

value: Interferon-alpha

value: Primary Human Dermal Fibroblast


title: UtE-iPS-7_P9

description: UtE1104-derived iPS cells

value: normal


title: 0hr 2a-2 in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50442.gif
Figure in article: 1


title: VAC-WR 24hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50465.gif
Figure in article: 1

value: Vaccinia WR


title: UtE-iPS-6_P22

description: UtE1104-derived iPS cells


title: VAC 4 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55151.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: VAC 4 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04

value: 4 h


title: MPX 9hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50483.gif
Figure in article: 1

value: 9 h

value: Monkeypox Virus


title: MPX 2 HeLa

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63906.gif
Figure in article: 1

source_name: MPX 2 HeLa cells infected with MPX in vitro 5.5.05

value: 2 h

value: HeLa


title: Killed MPX 0.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50471.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

value: killed Monkeypox Virus


title: UtE-iPS-4_P30

description: UtE1104-derived iPS cells


title: MPX 4hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50481.gif
Figure in article: 1


title: UtE-iPS-4_P8

description: UtE1104-derived iPS cells


title: Family12_WholeEmbryo_2

description: Hybridized to 250K_Nsp


title: VAC-WR 2hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50456.gif
Figure in article: 1


title: Family12_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: VAC 12 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55153.gif
Figure in article: 1

source_name: VAC 12 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04


title: UtE1104

description: Endometrium-derived cells

value: Female

value: Endometrium


title: PAE-iPS-5_P34

description: PAE551-derived iPS cells

value: Male

value: inducible pluripotent stem cells


title: PAE-iPS-11_P8

description: PAE551-derived iPS cells


title: g-MPX 0hr Pool b Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55117.gif
Figure in article: 1

source_name: g-MPX 0hr Pool Primary Human Macrophages infected with Killed Monkeypox in vitro 7.29.04

value: 0 h

value: Primary Human Macrophage


title: MPX 24 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55166.gif
Figure in article: 1

source_name: MPX 24 hr Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04


title: Family12_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: PAE-iPS-5_P18

description: PAE551-derived iPS cells

value: normal


title: PAE-iPS-5_P31

description: PAE551-derived iPS cells


title: PAE-iPS-4_P8

description: PAE551-derived iPS cells


title: Family12_WholeEmbryo_3

description: Hybridized to 250K_Nsp

value: whole embryo


title: Family11_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: VAC 2 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55204.gif
Figure in article: 1

source_name: VAC 2 hr Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04

value: Vaccinia WR

value: Primary Human Dermal Fibroblast


title: Family11_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

value: enriched fetal DNA from maternal plasma


title: 0hr 3b in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50444.gif
Figure in article: 1

source_name: 0hr 3b in vitro monocyte pox timecourse

value: Mock infection


title: Family11_Buccal_gDNA

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: Family11_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: g-MPX 4 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55188.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: g-MPX 4 hr Primary Human Skin FibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 4 h

value: killed Monkeypox Virus


title: MPX 1hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50488.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

value: 1 h

value: Monkeypox Virus


title: PAE-iPS-1_P31

description: PAE551-derived iPS cells

value: Male

value: inducible pluripotent stem cells


title: VAC 0 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55201.gif
Figure in article: 1

source_name: VAC 0 hr Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04

value: 0 h


title: Family10_Buccal_gDNA

description: Hybridized to 250K_Nsp


title: PAE-iPS-1_P26

description: PAE551-derived iPS cells


title: Family11_WholeEmbryo

description: Hybridized to 250K_Nsp

source_name: Whole Embryo


title: g-MPX 12 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55146.gif
Figure in article: 1

source_name: g-MPX 12 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: Primary Human Macrophage


title: Family11_paternal_gDNA

description: Hybridized to 250K_Nsp

value: paternal blood


title: BKV6

type: other

city: Livermore

first: Kevin

last: McLoughlin

address: PO Box 808

department: Global Security

institute: Lawrence Livermore National Laboratory

description: data used in Table 3 and Figure 4

hyb_protocol: Hybridization was performed at NimbleGen Systems-Iceland, Reykjavik, Iceland, or in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 6 µg of labelled DNA was used for hybridization. Hybridization was performed in a NimbleGen Hybridization system using the NimbleGen Hybridization kit (Roche NimbleGen).

scan_protocol: Microarrays were scanned  at NimbleGen Systems-Iceland, Reykjavik, Iceland, or in-house at SSI, Denmark.

data_processing: Data was analyzed using NimbleScan software and custom software developed at Lawrence Livermore National Laboratory, CA, USA and  described in 'Gardner et al. A Micobial Detection Array (MDA) for Viral and Bacterial Detection. BMC Genomics 2010 Nov 25;11:668'. Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Probes were classified as detected if the intensity exceeded a threshold equal to the 99th percentile of intensities for negative control probes, except for the RSV+ tracheal aspirate-sample that was analyzed using the 95th percentile.

molecule: other

label_protocol: Labelling was performed at NimbleGen Systems-Iceland, Reykjavik, Iceland, or in-house at SSI, Denmark, according to manufacturer’s protocol (Gene expression analysis, Roche NimbleGen). Briefly, 1 µg of heat-denatured WTA-amplified sample was labelled using nick translation with Cy3-labeled random nonamer primers (TriLink Biotechnologies) and Klenow fragment (exo-) (NEB) at 37 ºC for 2 hours. Labelled DNA was iso-propanol precipitated and the pellet washed, dried, reconstituted and quantitated.

extract_protocol: Five- to two-hundred microliters of clinical sample was centrifuged at 17,000 g for 10 minutes. The supernatant was filtered through a 0.22 µm Ultrafree MC spin filter (Millipore) at 2000 g for 2 minutes and DNase treated (6 U DNaseI Amplification grade, Invitrogen) for 1½ hours at room temperature while shaken in a Thermomixer (AH Diagnostics). The viral nucleic acid (NA) was extracted using the PureLink Viral RNA/DNA kit (Invitrogen), without the addition of carrier RNA. The extracted viral NA was eluted with 20-30 µl DNase/RNase-free sterile water, and stored at -20 ºC or immediately used. To be able to amplify both DNA virus and RNA virus samples with the same protocol, we used the described Whole Transcriptome Amplification (WTA) method (Berthet et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Molecular Biology 2008, 9:77) by using the QuantiTect WTA kit (Qiagen) according to manufacturer’s protocol, except for the reverse transcription step that was replaced by the Superscript VILO kit (Invitrogen). The WTA protocol includes 3 sequential reactions: firstly a reverse transcription reaction to generate cDNA, secondly a ligation of generated cDNA into larger transcriptomes and thirdly a Repli-g amplification of the generated transcriptomes. Neither of the two first reactions (cDNA synthesis and ligation) had any adverse effects when performed on a DNA-virus. Briefly, 14 µl of extracted viral NA was put into a 20 µl-VILO reaction and incubated at 42 ºC for 1 hour. The Superscript enzyme was inactivated at 95 ºC for 5 minutes, 10 µl of the VILO cDNA reaction was added to 10 µl of ligation mix and incubated at 22 ºC for 2 hours. Thirty microliters of amplification mix containing Phi29 polymerase and random primers was then added and amplification performed at 30 ºC for 8 hours. The reaction was terminated by incubation at 95 ºC for 5 minutes. Amplified material was purified using QIAamp DNA mini kit (Qiagen) using a modified protocol (www.qiagen.com), and checked for purity and concentration using a NanoDrop spectrophotometer (Thermo Scientific) and agarose gel electrophoresis. The DNA was then stored at -80 ºC or immediately used for microarray analysis.

tag: isolation source

value: urine

tag: extracted molecule

value: viral DNA/RNA

tag: confirmed content

value: BK polyomavirus


title: g-MPX 2 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55143.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: g-MPX 2 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 2 h


title: PAE-iPS-1_P8

description: PAE551-derived iPS cells

value: normal

tag: cell line


title: Family11_maternal_gDNA

description: Hybridized to 250K_Nsp

value: maternal blood


title: g-MPX 0 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55174.gif
Figure in article: 1

source_name: g-MPX 0 hr Primary Human SkinFibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: Primary Human Dermal Fibroblast


title: Family12_WholeEmbryo_1

description: Hybridized to 250K_Nsp

value: whole embryo


title: Family10_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: PAE551

description: Placental artery endothelial cells

value: Placental artery


title: BKV5

description: data used in Table 3 and Figure 4


title: MPX 24 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55216.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: MPX 24 hr Primary Human Skin Fibroblasts S100 infected with Ebola-Zaire in vitro 7.29.04


title: Mock 48hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50448.gif
Figure in article: 1

value: Mock infection


title: Edom-iPS-3_P29

description: Edom22-derived iPS cells

value: Female


title: NegCtrl

description: data used in Table 2

value: water

value: total DNA/RNA


title: BKV3

description: data used in Table 3 and Figure 4


title: VAC-NY 1hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50460.gif
Figure in article: 1

value: 1 h

value: Vaccinia NY

value: Primary Human Macrophage


title: Family10_WholeEmbryo_2

description: Hybridized to 250K_Nsp


title: BKV4

description: data used in Table 3 and Figure 4

value: urine

value: viral DNA/RNA


title: Edom-iPS-2_P31

description: Edom22-derived iPS cells

value: inducible pluripotent stem cells


title: Family10_TransferredEmbryo

description: Hybridized to 250K_Nsp

value: transferred embryo


title: Edom-iPS-2_P42

description: Edom22-derived iPS cells

value: normal


title: Edom-iPS-2_P22

description: Edom22-derived iPS cells


title: Family10_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

value: cryopreserved embryo


title: MPX 12 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55164.gif
Figure in article: 1

source_name: MPX 12 hr Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04

value: Monkeypox Virus


title: MPX 0 Pool FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55210.gif
Figure in article: 1

source_name: MPX 0 Pool Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04

value: 0 h

value: Primary Human Dermal Fibroblast


title: HEV-A+

description: data used in Table 2

value: faeces

value: Human Enterovirus A


title: Family10_WholeEmbryo_1

description: Hybridized to 250K_Nsp

value: whole embryo


title: RSV+

description: data used in Table 2

value: Human Respiratory Syncytial virus


title: MPX 0.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50486.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA


title: Edom-iPS-1_P23

description: Edom22-derived iPS cells

value: Female


title: HCV+2

description: data used in Table 2

value: serum

value: Hepatitis C virus


title: Edom22

description: Menstrual blood-derived cells

value: Menstrual blood


title: AM-iPS-13_P5

description: AM936EP-derived iPS cells


title: HCV+1

description: data used in Table 2

value: viral DNA/RNA


title: Dengue1+

description: data used in Table 2

value: Dengue virus type 1


title: AM-iPS-20_P10

description: AM936EP-derived iPS cells

value: inducible pluripotent stem cells


title: Sapo+

description: data used in Table 2

value: Sapovirus


title: MPX 0 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55155.gif
Figure in article: 1

source_name: MPX 0 hr Primary Human Macrophages infected with Monkeypox-Zaire in vitro 7.29.04

value: Primary Human Macrophage


title: AM-iPS-8_P29

description: AM936EP-derived iPS cells

value: normal


title: Family10_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: VAC-NY 1.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50462.gif
Figure in article: 1

value: Vaccinia NY


title: AM-iPS-8_P20

description: AM936EP-derived iPS cells


title: VAC 0 Pool FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55202.gif
Figure in article: 1

source_name: VAC 0 Pool Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04

value: 0 h

value: Vaccinia WR

value: Primary Human Dermal Fibroblast


title: AstroSapo+

description: data used in Table 2

value: faeces

value: Astrovirus & Sapovirus


title: RotaA+

description: data used in Table 2

value: Rotavirus A


title: Killed MPX 2hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50474.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

value: 2 h

value: killed Monkeypox Virus


title: VAC 24 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55208.gif
Figure in article: 1

source_name: VAC 24 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04


title: JCV+

description: data used in Table 2

value: viral DNA/RNA

value: JC polyomavirus


title: AM-iPS-8_P6

description: AM936EP-derived iPS cells

value: Female

value: inducible pluripotent stem cells


title: BKV+

description: data used in Table 2

value: urine

value: BK polyomavirus


title: Family9_TransferredEmbryo_2

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: AM-iPS-5_P7

description: AM936EP-derived iPS cells

value: normal


title: HPV16-53-6-61+

description: data used in Table 2

value: Human Papillomavirus 16,53,6 & 61


title: AM-iPS-3_P5

description: AM936EP-derived iPS cells


title: Family9_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

value: enriched fetal DNA from maternal plasma


title: VAC 0 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55148.gif
Figure in article: 1

source_name: VAC 0 hr Primary Human Macrophages infected with Vaccinia WR in vitro 7.29.04

value: 0 h

value: Vaccinia WR

value: Primary Human Macrophage


title: Mock 24hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50446.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

value: Mock infection


title: AM-iPS-6_P7

description: AM936EP-derived iPS cells


title: HPV16+

description: data used in Table 2

value: Human Papillomavirus 16


title: Family9_Buccal_gDNA_1

description: Hybridized to 250K_Nsp

source_name: Buccal gDNA

value: bucca


title: Family9_WholeEmbryo_7

description: Hybridized to 250K_Nsp

source_name: Whole Embryo

value: whole embryo


title: AM936EP

description: Amnion-derived cells

value: Amnion


title: Family9_WholeEmbryo_8

description: Hybridized to 250K_Nsp


title: HSV2+

description: data used in Table 2

value: viral DNA/RNA

value: Human Herpesvirus 2 (Herpes simplexvirus 2)


title: Family9_TransferredEmbryo_1

description: Hybridized to 250K_Nsp


title: Family9_WholeEmbryo_6

description: Hybridized to 250K_Nsp


title: VAC-NY 12hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50468.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

value: Vaccinia NY


title: MEFs, 3

city: Berlin

first: Torben

last: Redmer

address: Robert-Roessle Str. 10

department: Signaling in embryonic stem cells

institute: Max-Delbrueck-Center (MDC)

description: replicate 3

data_processing: The data were normalised using quantile normalisation. Data shown in the table matrix comprise 9871 genes with a detection p-value of p<0.05.

source_name: MEFs from E12.5 murine embryos

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit

growth_protocol: cells were plated on gelatin-coated plates and grown for 4 days in presence of LIF

extract_protocol: RNA was extracted with Trizol reagent and DNase I digested followed by a clean-up step using RNeasy MinElute Cleanup Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells were not treated and kept under undifferentiated conditions in presence of LIF

tag: strain


title: Family9_WholeEmbryo_5

description: Hybridized to 250K_Nsp


title: HSV1+

description: data used in Table 2

value: Human Herpesvirus 1 (Herpes simplexvirus 1)


title: MRC-iPS-91_P36

description: MRC5-derived iPS cells

value: Male

value: inducible pluripotent stem cells


title: MEFs, 2

description: replicate 2


title: Family9_WholeEmbryo_2

description: Hybridized to 250K_Nsp


title: MRC-iPS-25_P37

description: MRC5-derived iPS cells

value: normal


title: MRC-iPS-75_P4

description: MRC5-derived iPS cells


title: Family9_WholeEmbryo_4

description: Hybridized to 250K_Nsp


title: MEFs, 1

description: replicate 1


title: Family9_CryopreservedEmbryo_3

description: Hybridized to 250K_Nsp

value: cryopreserved embryo


title: ESKM-iPSCs, +LIF, 3

description: replicate 3

source_name: iPS cells from induction of MEFs with ESKM


title: Family9_WholeEmbryo_1

description: Hybridized to 250K_Nsp


title: Family9_WholeEmbryo_3

description: Hybridized to 250K_Nsp


title: Family9_CryopreservedEmbryo_2

description: Hybridized to 250K_Nsp


title: Family9_Buccal_gDNA_2

description: Hybridized to 250K_Nsp


title: MRC-iPS-25_P17

description: MRC5-derived iPS cells


title: ESKM-iPSCs, +LIF, 2

description: replicate 2


title: MRC-iPS-25_P30

description: MRC5-derived iPS cells


title: g-MPX 2 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55184.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: g-MPX 2 hr Primary Human Skin FibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 2 h

value: killed Monkeypox Virus

value: Primary Human Dermal Fibroblast


title: genomic DNA from MRC-iPS-11_P4

description: MRC5-derived iPS cells


title: g-MPX 0 Pool FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55177.gif
Figure in article: 1

source_name: g-MPX 0 Pool Primary HumanSkinFibroblastsS100 infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: 0 h


title: ESKM-iPSCs, +LIF, 1

description: replicate 1


title: VAC 8 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55206.gif
Figure in article: 1

source_name: VAC 8 hr Primary Human Skin Fibroblasts S100 infected with Vaccinia WR in vitro 7.29.04

value: 8 h

value: Vaccinia WR


title: MPX 0 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55209.gif
Figure in article: 1

source_name: MPX 0 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04

value: Monkeypox Virus


title: OSKM-iPSCs, +LIF, 3

description: replicate 3

source_name: iPS cells from induction of MEFs with OSKM


title: genomic DNA from MRC-iPS-19_4

description: MRC5-derived iPS cells


title: The expression of microRNAs in placentae with severe pre-eclampsia, P4_Cy5

city: Beijing

first: Jianqing

last: Zhao

address: 18 Life Science Parkway

country: China

institute: Capitalbio. Crop

description: the microRNA expression difference in human placentae tissue with severe pre-eclampsia

hyb_protocol: standard Capitalbio Methods

scan_protocol: CapitalBio manual

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy.

source_name: human placentae tissue with severe pre-eclampsia.

label_protocol: We use the T4 RNA ligase labeling method, in which about 4 microgram of LMW-RNA is labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy5-3' (CU-Cy5, Dharmacon) with 2 units of T4 RNA ligase (NEB). The labeled RNA is precipitated using the sodium acetate-ethanol method and hybridized overnight. The array is washed twice before the scanning.

extract_protocol: total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions, and the low-molecular-weight RNA (LMW-RNA) be isolated using the PEG solution precipitation method.

value: placentae

tag: phenotype

value: severe pre-eclampsia

source_name: human normal placentae tissue.

label_protocol: We use the T4 RNA ligase labeling method, in which about 4 microgram of LMW-RNA is labeled with 500 ng of 5'-phosphate-cytidyl-uridyl-cy3-3' (CU-Cy3, Dharmacon) with 2 units of T4 RNA ligase (NEB). The labeled RNA is precipitated using the sodium acetate-ethanol method and hybridized overnight. The array is washed twice before the scanning.


title: Family9_CryopreservedEmbryo_1

description: Hybridized to 250K_Nsp

source_name: Cryopreserved Embryo

tag: family


title: Family8_Buccal_gDNA

description: Hybridized to 250K_Nsp

value: bucca


title: OSKM-iPSCs, +LIF, 2

description: replicate 2


title: g-MPX 8 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55145.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: g-MPX 8 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04

value: Primary Human Macrophage


title: The expression of microRNAs in placentae with severe pre-eclampsia, P4_Cy3


title: g-MPX 24 hr Mf 7.29

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55147.gif
Figure in article: 1

source_name: g-MPX 24 hr Primary Human Macrophages infected with Killed Monkeypox-Zaire in vitro 7.29.04


title: Family9_maternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Maternal gDNA

value: maternal blood


title: genomic DNA from MRC5

description: Fetal lung fibroblast cell line, MRC5

value: Male

value: Fetal lung fibroblast

tag: disease state


title: Mock 12hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50459.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX

value: Mock infection


title: The expression of microRNAs in placentae with severe pre-eclampsia, P3_Cy5

value: normal


title: VAC-WR 12hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50463.gif
Figure in article: 1


title: Family9_paternal_gDNA

description: Hybridized to 250K_Nsp

source_name: Paternal gDNA

value: paternal blood


title: OSKM-iPSCs, +LIF, 1

description: replicate 1


title: VAC-WR 0.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50450.gif
Figure in article: 1


title: mESCs, +LIF, 3

description: replicate 3

source_name: mES cells


title: The expression of microRNAs in placentae with severe pre-eclampsia, P3_Cy3


title: mESCs, +LIF, 2

description: replicate 2


title: The expression of microRNAs in placentae with severe pre-eclampsia, P2_Cy5


title: Family8_EnrichedFetalDNA

description: Hybridized to 250K_Nsp

source_name: Enriched Fetal DNA

value: enriched fetal DNA from maternal plasma


title: mESCs, +LIF, 1

description: replicate 1


title: The expression of microRNAs in placentae with severe pre-eclampsia, P2_Cy3


title: Family8_TransferredEmbryo

description: Hybridized to 250K_Nsp

source_name: Transferred Embryo

value: transferred embryo


title: The expression of microRNAs in placentae with severe pre-eclampsia, P1_Cy5


title: MPX 2 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55212.gif
Figure in article: 1

source_name: Stratagene UHR RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX/VAC 8/26/04

source_name: MPX 2 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04

value: 2 h

value: Primary Human Dermal Fibroblast


title: The expression of microRNAs in placentae with severe pre-eclampsia, P1_Cy3


title: Hth_wing

city: Cambridge

first: Siew Woh

last: Choo

address: Downing Street

department: Department of Genetics

country: United Kingdom

institute: University of Cambridge

description: Results file: Hth_wing_LgRto.sgr

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Chips were scanned on an Affymetrix GeneChip Scanner according to the manufacturer’s recommendations.

data_processing: Affymetrix CEL files were processed using TiMAT (http://bdtnp.lbl.gov/TiMAT/TiMAT2).  All analyses were based on Release 5 of Drosophila melanogaster genome.  Normalisation was subsequently performed with CelProcessor using default parameters. The log (base2) binding ratios were calculated by comparing specific IPs and control IPs (log (mean specific IP/mean control IP)).  These ratios were then smoothed using a sliding window (675 bp) of trimmed means.  The .sgr files, containing information about the enrichment signals were generated by ScanChip.  The binding peaks were determined by the peak finding algorithm provided in the TiMAT package.

label: TdT

organism: Drosophila melanogaster

source_name: Hth ChIP DNA from 3rd instar wing discs

label_protocol: For the embryo samples, in order to obtain sufficient DNA (7.5 ug) for microarray analysis, 10-20 ng of ChIP and control DNA samples were amplified using Ligation-mediated PCR as described previously (Sandmann et al. 2007, Nature Protocols 1: p2839 - 2855).  For wing or haltere disc chromatin, 0.6 ng was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich).  The amplified DNAs were then purified, fragmented, TdT labeled and hybridized to the Affymetrix Drosophila genome Tiling Array 2.0 according to Affymetrix Chromatin Immunoprecipitation Assay Protocol (http://www.affymetrix.com/support/technical/manuals.affx).

growth_protocol: Embryo collections were performed at 25 ºC and L3 larvae were raised at 25 ºC.

extract_protocol:
Chromatin from 0-16h (after egg laying) old embryos was isolated as described previously (Birch-Machin et al. 2005, Genome Biol. 2005, 6(7): R63).  For the preparation of chromatin from T2 wing and T3 haltere imaginal discs, approximately 150 discs were used.  Chromatin preparation and ChIP were performed as described previously (Birch-Machin et al. 2005, Genome Biol. 2005, 6(7): R63; Adryan et al. 2007, Genome Biol. 8:R167). For the ChIP-array analysis, we assayed ChIP enrichment comparing the specific signal derived from immunoprecipitation of chromatin from a YFP-protein trap line with anti-GFP/YFP antibody versus the control signal from chromatin from the isogenic wild-type progenitor immunoprecipitated with the same anti-GFP/YFP antibody.

Antibody reference:  rabbit anti-GFP antibody (Benton R, Palacios IM, St Johnston D (2002) Drosophila 14-3-3/PAR-5 is an essential mediator of PAR-1 function in axis formation. Dev Cell 3: 659-671.)

treatment_protocol: Chromatin from embryos aged between 0 to 16 h after egg laying was purified as described previously (Birch-Machin et al. 2005, Genome Biol. 2005, 6(7): R63; Adryan et al. 2007, Genome Biol. 8:R167). For the preparation of chromatin from T2 and T3 imaginal discs (haltere, third leg, and wing) late 3rd instar larvae were dissected in PBS. Dissected discs were washed with PBS, fixed in PBS/1.5% formaldehyde for 20 min and washed with PBS. Batches of material were snap-frozen in liquid N2 and stored at -80 ºC.

value: ChIP fraction

tag: genotype/variation

value: Hth-YFP (CPTI-000378) protein trap line

tag: developmental stage

value: 3rd larval instar

value: wing discs

tag: antibody

value: anti-GFP/YFP

source_name: control ChIP DNA (w1118) from 3rd instar wing discs

value: control

value: wild type


title: Colonic Mucosa G

city: Los Angeles

first: KwangHo

last: Lee

address: 1441 Eastlake Ave NOR 6418

department: Biochemistry and Molecular Biology

institute: The University of Southern California

description: Replicate 1 of 4224

hyb_protocol: The biotinylated cRNA was hybridized to the BeadChips per standard Illumina hybridization protocol.

scan_protocol: The hybridized chips were stained and scanned using the Illumina HD BeadArray following the standard Illumina protocol.

data_processing: Scanned image and bead-level data processing were performed using the Illumina BeadStudio software. The summarized data for each bead type were then processed using Partek® Genomics Suite 6.5 software (St. Louis, MO, USA).

source_name: Total RNA from colonic mucosa

label_protocol: Biotinylated, amplified cRNA was prepared from total RNA using the Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was isolated using the Trizol reagent according to the manufacturer’s protocol. The quality of the RNA samples was assessed using the Bio-Rad Experion RNA StdSens analysis kit.

tag: tissue

value: Colonic Mucosa

tag: genotype

value: Dnmt1LO/LO, TgVillacIGY

tag: age

value: 157 days

value: Mixed (129Sv/B6/D2)

tag: mouse id


title: Family8_WholeEmbryo_10

description: Hybridized to 250K_Nsp

source_name: Whole Embryo

value: whole embryo


title: Family8_WholeEmbryo_11

description: Hybridized to 250K_Nsp


title: Colonic Mucosa F

description: Replicate 2 of 4223

tag: gender

value: Male


title: Colonic Mucosa H

description: Replicate 2 of 4224


title: MPX 8 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55214.gif
Figure in article: 1

tag: reference

value: Stratagene Universal Human Reference RNA

source_name: MPX 8 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04

tag: time

value: 8 h

tag: infection

value: Monkeypox Virus

tag: cell type


title: VAC-WR 1hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50452.gif
Figure in article: 1

value: 1 h

value: Vaccinia WR

value: Primary Human Macrophage


title: Hth_haltere

description: Results file: Hth_haltere_LgRto.sgr

source_name: Hth ChIP DNA from 3rd instar haltere discs

tag: sample type

value: ChIP fraction

value: Hth-YFP (CPTI-000378) protein trap line

value: 3rd larval instar

value: haltere discs

source_name: control ChIP DNA (w1118) from 3rd instar haltere discs


title: Colonic Mucosa E

description: Replicate 1 of 4223

tag: strain


title: Family8_WholeEmbryo_9

description: Hybridized to 250K_Nsp


title: Colonic Mucosa D

description: Replicate 2 of 4222


title: Hth_embryo

description: Results file: Hth_emb_LgRto.sgr

source_name: Hth ChIP DNA from 0-16h embryos

value: 0-16h AEL embryo

value: whole body

value: anti-GFP/YFP

source_name: control ChIP DNA (w1118)) from 0-16h embryos

value: control

value: wild type


title: 0hr 2a-1 in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50441.gif
Figure in article: 1

value: 0 h

value: Mock infection


title: Ubx_haltere

description: Results file: Ubx_haltere_LgRto.sgr

source_name: Ubx ChIP DNA from 3rd instar haltere discs

value: Ubx-YFP (CPTI-000601) protein trap line


title: VAC-WR 48hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50478.gif
Figure in article: 1

source_name: Stratagene Universal Human Reference RNA, 1 round of amp(Ambion MessageAmp), 6/27/02, spiked in MPX


title: Colonic Mucosa C

description: Replicate 1 of 4222

value: Colonic Mucosa

value: Male

value: 157 days

value: Mixed (129Sv/B6/D2)


title: Family8_WholeEmbryo_7

description: Hybridized to 250K_Nsp

value: whole embryo


title: Colonic Mucosa B

description: Replicate 2 of 4221


title: Ubx_embryo

description: Results file: Ubx_emb_LgRto.sgr

source_name: Ubx ChIP DNA from 0-16h embryos

value: ChIP fraction

source_name: control ChIP DNA (w1118) from 0-16h embryos


title: MPX 1 hr FibroS100

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/55211.gif
Figure in article: 1

value: Stratagene Universal Human Reference RNA

source_name: MPX 1 hr Primary Human Skin Fibroblasts S100 infected with Monkeypox-Zaire in vitro 7.29.04

value: 1 h

value: Monkeypox Virus

value: Primary Human Dermal Fibroblast


title: Family8_WholeEmbryo_5

description: Hybridized to 250K_Nsp


title: Colonic Mucosa A

description: Replicate 1 of 4221


title: Blood_30weeks_female_4

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

description:
SC20_031
gene expression analysis performed on a whole blood (PAXgene) preparation from a 30-weeks-old female miniature pig.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-020109 Porcine Gene Expression Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. Features flagged with not positive and significant or flagged with not above significant were considered as unexpressed genes. The quantile normalization method was used in our microarray analysis.

organism: Sus scrofa

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

extract_protocol: Whole blood RNA was extracted using the PAXgene RNA Isolation kit from whole blood preserved in Paxgene tubes (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Paxgene tube conservation at -80ºC

value: whole blood

value: female


title: Family8_WholeEmbryo_4

description: Hybridized to 250K_Nsp


title: VAC-NY 0.5hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50457.gif
Figure in article: 1

value: Vaccinia NY

value: Primary Human Macrophage


title: VAC-NY 4hr in vitro monocyte pox timecourse

description:
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50466.gif
Figure in article: 1

value: 4 h


title: Family8_WholeEmbryo_6

description: Hybridized to 250K_Nsp