title: Florida_46h_30C_rep2

description: biological replicate

source_name: common reference

value: Florida

value: raised at 30°C

value: 46 hours after fertilization


title: Mexico_24h_28C_rep2

status: Public on Jun 23 2010

type: RNA

city: University Park

first: Nicholas

last: Polato

state: PA

address: 208 Mueller Lab

department: Biology

country: USA

institute: Penn State University

description: technical replicate

hyb_protocol: Dye coupled cDNAs were mixed together in a hybridization buffer consisting of 0.25% SDS, 25 mM HEPES, and 3× SSC. Hybridization mixtures were boiled at 99°C for 2 minutes then allowed to cool at room temperature for 5 minutes. Cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific, NH) and slides were incubated overnight at 63°C in a custom hybridization chamber.  The hybridized microarray slides were washed twice in 0.6× SSC and 0.01% SDS, rinsed in 0.06× SSC, and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B slide scanner (MDS).

data_processing: Spot intensities were extracted and background was subtracted using GenePix Pro 6.0.  GPR files were read into the Bioconductor package LIMMA (Smyth 2005) for further analysis. Normalization was performed using print-tip specific LOWESS to normalize within arrays and the quantile normalization method (Yang and Thorne 2003) to normalize between arrays.

molecule: total RNA

organism: Orbicella faveolata

label_protocol: 1 μg of total RNA was amplified with the MessageAmp II aRNA Kit (Ambion, TX). To prime the reverse transcription (RT) reaction 3 μg of aRNA was incubated with 2 μL of 5 μg/μL random nonamers for 10 minutes at 70°C. RT was carried out for 2 hours at 50°C using a master mix with a 4:1 ratio of aminoallyl-dUTP to TTP. Products of the RT reaction were hydrolyzed by incubating the cDNA in 10 μL of 0.5M EDTA and 10 μL of 1M NaOH for 15 minutes at 65°C. Following hydrolysis, RT products were purified using MinElute columns (Qiagen, CA). Dye coupling reactions were performed using Cy3 and Cy5 dyes (GE Healthcare, PA) diluted in 18 μL of dimethyl sulphoxide. The coupling reactions were run in the dark for 2 hours at room temperature. A final cleanup was performed using the MinElute Cleanup Kit, and dye coupling was confirmed on a NanoDrop spectrophotometer.

growth_protocol: Gametes from multiple parent colonies of M. faveolata were collected during mass spawning events in Puerto Morelos, Mexico (20°52’28.77”N, 86°51’04.53”W) and Key Largo, Florida  (25°6’42.66”N, 80°18’18.72”W). Sperm and eggs were pooled and incubated for two hours to allow for fertilization. Sperm concentration ranged from 2.3*10^11 to 6*10^11. Fertilized eggs were washed and transferred to temperature controlled aquaria consisting of small plastic containers suspended in polycarbonate bins containing filtered sea water. To prevent fouling, water was circulated with an aquarium pump and changed daily with filtered sea water pretreated to the target temperature.

extract_protocol: Total RNA of coral larvae was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. RNA pellets were cleaned further with RNeasy Mini columns (Qiagen).

treatment_protocol: Two treatment temperatures were chosen to reflect non-stressful and elevated temperatures for each sampling location; 27°C & 30°C in Florida, and 27.5°C & 31.5°C in Mexico.

tag: sample type

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

tag: developmental stage

value: coral larvae

tag: site

value: Mexico

tag: temperature

value: raised at 27.5°C

tag: age

value: 24 hours after fertilization


title: Schiz J2

type: genomic

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

hyb_protocol: Array hybridizations were carried out with 490μl of hybridization mixtures for 40 h at 65℃, then washed for 5 min at room temperature in Oligo aCGH Wash Buffer 1 (Agilent), followed by 1 min at 37℃ in Oligo aCGH Wash Buffer 2 (Agilent).

scan_protocol: The hybridized arrays were scanned using an Agilent G2565BA DNA microarray scanner (Agilent Technologies). The ScanControl Software (Agilent Technologies) was used for image acquisition. In brief, the arrays were imaged at a resolution of 5 μm. Excitation of Cy3 and Cy5 was performed at a wavelength of 532 and 635 nm, respectively. A laser power of 100% was used. Each array was subjected to a series of scans. The signals were digitized into 16 bit/pixel, yielding a maximum detection range from 1 to 65536; i.e., almost five orders of magnitude.

data_processing: After image acquisition, data extraction, normalization and transformation were carried out by using Agilent Feature Extraction Software, version 8.1.1 (Agilent Technologies), procedures listed as follow:  (1) Place Grid, find and measure spots  -define what is the array format of the image to be processed.  (2) Flag outliers  a. Compute population outliers- flag features and local backgrounds as population outliers if the minimum number of replicates is met and the mean signals varies significantly from the distribution.  b. Compute NonUniform outliers- flag features and local backgrounds as NonUniform if the pixel distribution is outside the boundary defined by the three-parameter noise model.  (3)   Compute Background, bias and error              Background subtraction→ signal correction → choose error model   (4) Dye normalization –   a. Use rank consistent probes.  b. Normalization correction methods: Linear method  (5) Compute ratios- the log ratio values are capped to 4 with appropriate signs in positive and negative directions.  Subsequent data analysis was performed with the other custom analytical software, CGH Analytics (version 3.5.14, Agilent Technologies). The Linear smoothing algorithm is used in the Moving Average approach to smooth the data sets with window size of 5 Mb.

molecule: genomic DNA

organism: Homo sapiens

source_name: schizophrenia patient J2

label_protocol: Genomic DNA was completely fragmented with AluI and RsaI (Promega, Madison, WI, USA ), followed by purification with QIAprep Spin Miniprep Kit (Qiagen). All of the digested DNAs were subjected to labeling reactions using Agilent’s Genomic DNA Labeling Kit PLUS per manufacturer’s instructions.

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes with the PureGene DNA Purification Kit (Gentra Systems, Minneapolis, MN, USA) according to the manufacturer’s instructions.

tag: gender

value: male

tag: tissue

value: peripheral blood lymphocytes

tag: disease state

value: Schizophrenia

source_name: equal amounts of DNA extracted from ten healthy men or ten healthy women who live in Taiwan

value: Healthy


title: A137_15_BSA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description:
Biopsy taken from healthy female.
Donor3_BSA

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described n the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using RMA.

label: biotin

source_name: primary myotubes, isolated from M. obliquus internus abdominis, BSA

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix, as per the manufacturer's instructions.

growth_protocol: Satellite cells were isolated from the M. obliquus internus abdominis of 3 healthy female donors. The cells were cultured in DMEM-Glutamax (5.5 mM glucose), 2 % FCS, 2 % Ultroser G, P/S, and amphotericin B. At 70-80 % confluence the growth medium was replaced by DMEM-Glutamax™ supplemented with 2 % FCS, P/S, 1.25 µg/ml amphotericin B, and 25 pM insulin to induce differentiation. The cells were cultured in humidified 5 % CO2 atmosphere at 37 °C, and the medium was changed every 2–3 days.

extract_protocol: Total RNA was prepared from the primary myotubes using Agilent Total RNA isolation kit according to the supplier’s protocol (Agilent Technologies, Santa Clara, CA, USA). RNA was used individually and RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Myoblasts were grown to confluence, allowed to differentiate for 6 days, and then preincubated for 24 h with different fatty acids (oleic acid [OA], palmitic acid [PA], eicosapentaenoic acid [EPA] or linoleic acid [LA], each at 100 µM) or bovine serum albumin [BSA] (40 µM) before RNA isolation.

value: female

value: 35 years

value: musculus obliquus internus abdominis

tag: cell type

value: primary myotubes

tag: fatty acid

value: bovine serum albumin (BSA) control

tag: donor


title: Mexico_24h_28C_rep1

description: technical replicate


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 16 wk HFD no drug Pool #4 (n=3)

city: Seattle

first: Xia

last: Yang

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: Aortic arch gene expression profiling of Apoe knockout mice fed a high fat western diet for 2, 4, and 6 month.

hyb_protocol: Microarrays are incubated at 40C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver? system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

organism: Mus musculus

source_name: Aortic arch, Apoe-/-, HFD, control pool

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: strain

value: aortic arch

tag: genotype

value: Apoe-/-

tag: diet

value: high fat diet (HFD)

tag: timepoint

value: equal amounts of 8, 16, and 24 weeks

value: reference

source_name: Aortic arch, Apoe-/-, HFD, 16 weeks

value: 16 weeks


title: Schiz I1

source_name: schizophrenia patient I1


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 8 wk HFD no drug Pool #2 (n=2)

source_name: Aortic arch, Apoe-/-, HFD, 8 weeks

value: 8 weeks


title: A137_14_EPA

description:
Biopsy taken from healthy female.
Donor3_EPA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, EPA

value: eicosapentaenoic acid (EPA)


title: Schiz H2

source_name: schizophrenia patient H2

value: male


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 8 wk HFD no drug Pool #3* (n=3)


title: Florida_46h_30C_rep1

description: biological replicate

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

value: coral larvae

value: Florida

value: raised at 30°C

value: 46 hours after fertilization


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 16 wk HFD no drug Pool #5 (n=3)


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 8 wk HFD no drug Pool #1 (n=3)


title: Florida_46h_27C_rep3

description: biological replicate

value: raised at 27°C


title: Florida_46h_27C_rep2

description: biological replicate


title: A137_12_OA

description:
Biopsy taken from healthy female.
Donor3_OA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, OA

value: female

value: 35 years

value: musculus obliquus internus abdominis

value: primary myotubes

value: oleic acid (OA)


title: A137_09_EPA

description:
Biopsy taken from healthy female.
Donor2_EPA

value: 36 years


title: A137_13_LA

description:
Biopsy taken from healthy female.
Donor3_LA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, LA

value: linoleic acid (LA)


title: A137_10_BSA

description:
Biopsy taken from healthy female.
Donor2_BSA

value: bovine serum albumin (BSA) control


title: Schiz G2

source_name: schizophrenia patient G2

value: peripheral blood lymphocytes

value: Schizophrenia

value: Healthy


title: A137_11_PA

description:
Biopsy taken from healthy female.
Donor3_PA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, PA

value: palmitic acid (PA)


title: Florida_46h_27C_rep1

description: biological replicate

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

value: coral larvae


title: Schiz I2

source_name: schizophrenia patient I2

value: male


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 16 wk HFD no drug Pool #6* (n=3)

value: aortic arch

value: Apoe-/-

value: high fat diet (HFD)

value: equal amounts of 8, 16, and 24 weeks

value: reference

value: 16 weeks


title: Florida_22h_30C_rep3

description: biological replicate

value: Florida

value: raised at 30°C

value: 22 hours after fertilization


title: Schiz H1

source_name: schizophrenia patient H1


title: A137_07_OA

description:
Biopsy taken from healthy female.
Donor2_OA

value: female

value: 36 years

value: musculus obliquus internus abdominis

value: primary myotubes

value: oleic acid (OA)


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 24 wk HFD no drug Pool #11 (n=3)

source_name: Aortic arch, Apoe-/-, HFD, 24 weeks

value: 24 weeks


title: Florida_22h_30C_rep2

description: biological replicate

source_name: common reference

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

value: coral larvae


title: Schiz E2

source_name: schizophrenia patient E2

value: peripheral blood lymphocytes

value: Schizophrenia

value: Healthy


title: A137_05_BSA

description:
Biopsy taken from healthy female.
Donor1_BSA

value: 32 years

value: bovine serum albumin (BSA) control


title: A137_06_PA

description:
Biopsy taken from healthy female.
Donor2_PA

value: palmitic acid (PA)


title: Schiz F2

source_name: schizophrenia patient F2

source_name: equal amounts of DNA extracted from ten healthy men or ten healthy women who live in Taiwan


title: Schiz E1

source_name: schizophrenia patient E1


title: Schiz D1

source_name: schizophrenia patient D1


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 24 wk HFD no drug Pool #10 (n=3)

source_name: Aortic arch, Apoe-/-, HFD, control pool

value: aortic arch

value: Apoe-/-

value: high fat diet (HFD)

value: equal amounts of 8, 16, and 24 weeks

value: reference


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta C57BL/6 Control 16 wk HFD Pool #16 (n=3)

source_name: Aortic arch, control, HFD, 16 weeks

value: wt

value: 16 weeks

value: control


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta ApoE KO 24 wk HFD no drug Pool #12 (n=3)

value: 24 weeks


title: Schiz G1

source_name: schizophrenia patient G1

value: female


title: Florida_22h_30C_rep1

description: biological replicate

value: pooled reference of coral larvae from Mexico raised at three temperatures (27.5°C, 29°C, 31.5°C) at 12, 24, 36, and 48 hours after fertilization

value: coral larvae

value: Florida

value: raised at 30°C

value: 22 hours after fertilization


title: Schiz D2

source_name: schizophrenia patient D2

value: male

value: peripheral blood lymphocytes

value: Schizophrenia

value: Healthy


title: Florida_22h_27C_rep1

description: biological replicate

value: raised at 27°C


title: Florida_22h_27C_rep3

description: biological replicate


title: Florida_22h_27C_rep2

description: biological replicate


title: A137_04_EPA

description:
Biopsy taken from healthy female.
Donor1_EPA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, EPA

value: 32 years

value: musculus obliquus internus abdominis

value: primary myotubes

value: eicosapentaenoic acid (EPA)


title: Pseudomonas aeruginosa strain RM536, dnr mutant, anaerobic, replicate2

status: Public on Jun 22 2010

city: Braunschweig

first: Max

last: Schobert

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universitaet Braunschweig

description: RNA was pooled from three independent cultures prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

hyb_protocol: The GeneChip was hybridized at the Affymetrix core facility at the Helmholtz Centre for Infection Research in Braunschweig for 16 h at 50°C and 60 rpm using an GeneChip Hybridisation oven 640. Washing was done using an Affymetrix Fluidics Station 400.

scan_protocol: Scanning was done at the Affymetrix core facility at the Helmholtz Centre for Infection Research in Braunschweig using an HP GeneArray scanner for quantification with Affymetrix Microarray Suite Version 5.0.

data_processing:
Raw data obtained from the Affymetrix GeneArray Scanner (CEL files) were preprocessed with the Bioconductor software framework. Expression values were computed with the Robust Multichip Average (RMA) method (Irizarry et al. 2003, Irizarry et al. 2003a) from the perfect match intensities, using quantile normalization and median polish as summarization method.

References:
Irizarry, R.A., Hobbs, B., Collin, F., Beazer-Barclay, Y.D., Antonellis, K.J., Scherf, U. and Speed, T.P. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264
Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B. and Speed, T.P. (2003a). Summaries of Affymetrix GeneChip probe level data., Nucleic Acids Res. , 31, e15

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa strain RM536 incubated under anaerobic conditions in AB-medium

label_protocol: cDNA was synthesized from RNA pooled from three independent cultures and subsequently hybridyzed on one GeneChip.  The cDNA synthesis, fragmentation and labeling were performed according to protocols for the Affymetrix Pseudomonas GeneChip® (Santa Clara, California) with the following modification: 0.6 U DNase I were used per µg cDNA for fragmentation to yield the desired cDNA size range of 50 - 200 bases as confirmed by gel electrophoresis. This was verified by separating 200 ng of fragmented cDNA on a 15 % acrylamide gel and staining with SYBRgold (Molecular Probes, Eugene, United States).

growth_protocol: Pseudomonas aeruginosa was grown in a modified AB minimal medium, containing 25 µM FeSO4, 20 mM glucose and 50 mM NaNO3. The 200 ml aerobic cultures were grown in 1 l Erlenmeyer flasks at 37 °C and 300 rpm. The aerobic culture was grown to an OD578 of 0.3 and then 130 ml were transferred to a 135 ml sealed serum flask. Control experiments verified that oxygen tension decreased within 3 - 5 min below the detection limit of an oxygen electrode. The cells were harvested after incubation for additional 2h under anaerobic conditions.

extract_protocol:
25 ml of the culture were cooled down with crushed ice, harvested and subjected to total RNA isolation by a modified hot phenol method (Aiba et al., 1981; von Gabain et al., 1983). The obtained RNA was treated with RNase-free DNase I and further purified by RNeasy columns (Qiagen, Hilden, Germany). The integrity of total RNA as well as the transcription of anaerobic marker genes in the harvested cells was confirmed by Northern Blot analysis.

References:
Aiba, H., S. Adhya & B. de Crombrugghe, (1981) Evidence for two gal promoters in intact Escherichia coli. J Biol Chem 256: 11905-11910.
von Gabain, A., J. G. Belasco, J. L. Schottel, A. C. Chang & S. N. Cohen, (1983) Decay of mRNA in Escherichia coli: investigation of the fate of specific segments of transcripts. Proc Natl Acad Sci U S A 80: 653-657.

tag: mutation

value: dnr deletion

tag: condition

value: anaerobic


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta C57BL/6 Control 16 wk HFD Pool #17 (n=3)

value: aortic arch

value: Apoe-/-

value: high fat diet (HFD)

value: equal amounts of 8, 16, and 24 weeks

tag: sample type

value: reference

value: wt

value: 16 weeks

value: control


title: Study 2: LFWD Control Pool vs. LFWD 4 Month

description: Aortic arch gene expression profiling of Ldlr knockout mice fed a low fat western diet for 1, 2, 3, and 4 month.

source_name: Aortic arch, Ldlr-/- huCETP, LFWD, control pool

tag: study 2

value: LFWD Control Pool

value: Ldlr-/- with human cholesteryl ester transfer protein (CETP) transgene

value: low fat, cholesterol-containing Western diet (LFWD)

value: equal amounts of 4, 8, 12, and 16 weeks

source_name: Aortic arch, Ldlr-/- huCETP, LFWD, 4 months


title: A137_02_OA

description:
Biopsy taken from healthy female.
Donor1_OA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, OA

value: female

value: 32 years

value: musculus obliquus internus abdominis

value: oleic acid (OA)


title: Schiz C2

source_name: schizophrenia patient C2

value: male

value: peripheral blood lymphocytes

value: Schizophrenia

value: Healthy


title: Pseudomonas aeruginosa, PAO1, anaerobic, replicate2

source_name: Pseudomonas aeruginosa PAO1 incubated under anaerobic conditions in AB-medium

value: wild type

value: anaerobic


title: Pseudomonas aeruginosa strain PAO6261, anr mutant, anaerobic, replicate2

source_name: Pseudomonas aeruginosa strain PAO6261 incubated under anaerobic conditions in AB-medium

value: anr deletion


title: Pseudomonas aeruginosa, PAO1, aerobic, replicate1

source_name: Pseudomonas aeruginosa PAO1 grown under aerobic conditions in AB-medium

growth_protocol:
Pseudomonas aeruginosa was grown in a modified AB minimal medium, containing 25 µM FeSO4, 20 mM glucose and 50 mM NaNO3. The 200 ml aerobic cultures were grown in 1 l Erlenmeyer flasks at 37 oC and 300 rpm. Cells were harvested in the early exponential phase at an OD578 of 0.3.
AB minimal medium described in: Clark, D. J. & O. Maaløe. (1967) DNA replication and the division cycle in Escherichia coli. J Mol Biol 23: 99-112.

value: aerobic


title: Schiz B2

source_name: schizophrenia patient B2


title: Schiz C1

source_name: schizophrenia patient C1

source_name: equal amounts of DNA extracted from ten healthy men or ten healthy women who live in Taiwan


title: A137_03_LA

description:
Biopsy taken from healthy female.
Donor1_LA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, LA

value: primary myotubes

value: linoleic acid (LA)


title: A137_01_PA

description:
Biopsy taken from healthy female.
Donor1_PA

source_name: primary myotubes, isolated from M. obliquus internus abdominis, PA

value: palmitic acid (PA)


title: Study 2: LFWD Control Pool vs. LFWD 2 Month

value: LFWD Control Pool

value: aortic arch

value: Ldlr-/- with human cholesteryl ester transfer protein (CETP) transgene

value: low fat, cholesterol-containing Western diet (LFWD)

value: reference

source_name: Aortic arch, Ldlr-/- huCETP, LFWD, 2 months

value: 8 weeks


title: Schiz B1

source_name: schizophrenia patient B1

value: female


title: Aorta ApoE KO 8wk, 16wk, 24wk HFD Vehicle Pool (n=21) vs. Aorta C57BL/6 Control 16 wk HFD Pool #18 (n=3)

source_name: Aortic arch, Apoe-/-, HFD, control pool

value: Apoe-/-

value: high fat diet (HFD)

value: equal amounts of 8, 16, and 24 weeks

source_name: Aortic arch, control, HFD, 16 weeks

value: wt

value: 16 weeks

value: control


title: Study 2: LFWD Control Pool vs. LFWD 3 Month

value: equal amounts of 4, 8, 12, and 16 weeks

source_name: Aortic arch, Ldlr-/- huCETP, LFWD, 3 months

value: 12 weeks


title: Pseudomonas aeruginosa, PAO1, aerobic, replicate2

value: wild type

value: aerobic


title: Study 2: LFWD Control Pool vs. LFWD 1 Month

source_name: Aortic arch, Ldlr-/- huCETP, LFWD, control pool

value: LFWD Control Pool

source_name: Aortic arch, Ldlr-/- huCETP, LFWD, 1 month

value: 4 weeks


title: Pseudomonas aeruginosa, PAO1, anaerobic, replicate1

value: anaerobic


title: Pseudomonas aeruginosa strain RM536, dnr mutant, anaerobic, replicate1

source_name: Pseudomonas aeruginosa strain RM536 incubated under anaerobic conditions in AB-medium

value: dnr deletion


title: Expression Profile of Proliferative Human Cytotrophoblasts Grown on Fibronectin: Replicate 2

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 East Hancock, CS Mott Center

institute: Wayne State University

description: mRNA from proliferative cytotrophoblast cells grown on fibronectin.

hyb_protocol: Hybridization to Illumina Sentrix Expression BeadChip, staining and washing were carried out as described (Illumina, Wallingford).

scan_protocol: Scanning procedures were carried out as described by Illumina, Wallingford.

data_processing: The data were analyzed with Illumina Beat Studio using Cubic Spline normalization

label: Biotin

molecule: polyA RNA

source_name: Proliferative Cytotrophoblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA (Whole-Genome Gene Expression with IntelliHyb Seal System  Illumina).

growth_protocol: HTR-8/SVneo cells, maintained at passage 38-45, were cultured in mass at the Cell Culture Facility of the Cleveland Clinic (Cleveland OH, USA) in 1:1 Ham’s F12:DMEM medium containing 10% fetal bovine serum and antibiotics (penicillin and streptomycin). Cells were grown to confluence at 37ºC in a humidified 5%CO2/95% air incubator. Prior to assessing invasion, the adherent HTR-8/SVneo cells were harvested trypsin/EDTA then transferred to roller bottles coated with either 10 µg/ml fibronectin (diluted with sterile PBS), or Matrigel ™, diluted 1:10 with sterile PBS. The cells were then rinsed free of serum then cultured on Matrigel ™ or fibronectin for 24 hours in serum free 1:1 Ham’s F12: DMEM medium supplemented with 5mg/ml BSA.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen Inc., Valencia, CA,
USA).  The resulting RNA was then amplified and labeled by in vitro
transcription using the Illumina RNA amplification system (Ambion, Austin,
TX, USA).  A 750 ng aliquot of the in vtro transcribed prove was used for
hybridization to Illumina Sentrix Human-8 v2 Expression BeadChip arrays.
The array analysis was carried out in duplicate were performed for
HTR-8/SVneo cells grown either on Matrigel T or fibronectin, for a total of
four isolations.

value: proliferative cytotrophoblast

tag: cell line

value: mRNA from proliferative human cytotrophoblast cells obtained from HTR-8/SVneo cell line


title: FOXP3Genome_hs18_5

city: Adelaide

middle: Martin

last: Pederson

state: SA

address: North Terrace

department: Biological Sciences

country: Australia

institute: University of Adelaide

description: FOXP3 ChIP Biological Rep 1-2, chip E

hyb_protocol: Approximately 9 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven and washed with Fluidics station 450 protocol FS450_0001

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
All analysis was performed with NCBI build 36/hg18 of the human genome. The model-based analysis of tiling array (MAT) algorithm (Johnson WE et al 2006; PNAS 103(33), 1257-12462) was used to find regions of FOXP3 binding. Matched total input DNA were used as control samples.
FOXP3 ChIP in primary human natural T regulatory cells, using Total Input DNA as control, 2 biological replicates.  The supplementary 'Treg.ab.Hs.Tiling2.0.FDR0.5.bed' file contains 8305 high quality binding FOXP3 binding regions.

source_name: FOXP3 ChIP DNA from expanded Human T regulatory cells

label_protocol: Samples (~9μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

growth_protocol: Cord blood CD4+ CD25+ (nTreg) cells were isolated from MNC using a Dynabeads Regulatory CD4+CD25+ T cell kit (Invitrogen). The purity for each cell type was routinely greater than 90% by two colour flow cytometry for CD4 and CD25 expression. Ex vivo expansion of isolated T cell populations (1x106 cells/well in a 24 well plate) were performed in X-Vivo 15 media (Lonza) supplemented with 20mM HEPES-, pH 7.4, 5% heat inactivated pooled human serum (Lonza), 2mM l-glutamine and 500U/ml recombinant human interleukin-2 (rhIL2; R&D research) in the presence of Dynabeads CD3/CD28 T cell expander beads (Invitrogen; Cat# 111-41D) at a bead to cell ratio of 3:1. Cells were expanded for 8 days in the presence of Dynabeads prior to magnetic removal of the beads and culture in X-Vivo 15 media supplemented as above except with 100U/ml rhIL2.

extract_protocol: Cells were treated for 10 minutes in 1% formaldehyde solution (50 mM HEPES KOH, pH 7.5, 100mM NaCl, 1mM EDTA, 0.5mM EGTA and 11% formaldehyde). Cell lysis, chromatin immunoprecipitation (ChIP) and DNA isolation steps for human FOXP3 ChIP-on-chip experiments were carried out essentially as described in (Lee et al. 2006; Nature Protocols, 1(2), 3599-3606), using 5x107 cells per immunoprecipitation with either a rabbit anti-Foxp3 IgG (Novus Biochem) or ChIP grade control rabbit IgG Sera (Abcam). Chromatin shearing conditions was performed with a Misonix S-4000 ultrasonic processor (Misonix) with a microtip. Total input chromatin was also purified from an aliquot (100μl) of crosslinked material and the concentration determined using a Nanodrop UV spectrophotometer (Thermo Scientific). Amplification of immunoprecipitated and input chromatin (10ng) for labelling and hybridisation to Affymetrix Human Tiling 2.0R arrays was by whole genome amplification (WGA; Sigma GenomePlex WGA kit) (O'Geen et al. 2006; Biotechniques 41(5) 577-580 ) adapted for Affymetrix labelling systems by the inclusion of 0.11mM dUTP in the amplification reaction. Amplified material was purified using a PCR clean up kit (QIAGEN). Labelling and hybridisation of amplified material was carried out at the Biomolecular Resource Facility (John Curtin School of Medical Research, Australian National University).

treatment_protocol: Expanded cord blood Treg cells were cultured overnight prior to re-stimulation (2hours) with 1mM Ionomycin (Sigma) before Formaldehyde cross-linking.

value: cord blood

value: CD4+CD25+ natural T regulatory cells (nTreg)

tag: antibody

value: Rabbit polyclonal anti-human FOXP3 IgG (Novus Biologicals)

source_name: Input DNA from expanded Human T regulatory cells

tag: cells


title: FOXP3Genome_hs18_7

description: FOXP3 ChIP Biological Rep 1-2, chip G


title: Expression Profile of Proliferative Human Cytotrophoblasts Grown on Fibronectin: Replicate 1


title: Expression Profile of Invasive Human Cytotrophoblasts Grown on Matrigel: Replicate 1

description: mRNA from invasive cytotrophoblast cells grown on matrigel.

data_processing: The data were analyzed with Illumina Beat Studio using Cubic Spline Normalization

source_name: Invasive Cytotrophoblasts

value: invasive cytotrophoblast

value: mRNA from invasive human cytotrophoblast cells obtained from HTR-8/SVneo cell line


title: Expression Profile of Invasive Human Cytotrophoblasts Grown on Matrigel: Replicate 2


title: Schiz A2

source_name: schizophrenia patient A2

tag: gender

value: female

value: peripheral blood lymphocytes

value: Schizophrenia

value: Healthy


title: A137_08_LA

description:
Biopsy taken from healthy female.
Donor2_LA

tag: age

value: 36 years

tag: tissue

value: musculus obliquus internus abdominis

value: primary myotubes

value: linoleic acid (LA)


title: n248-1N

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description: 3D cultured genetically engineered human esophageal cells

hyb_protocol: The fragmented cRNA was hybridised to HGU133 arrays at 45 °C in a hybridization oven for 16 hr)

scan_protocol: Chip scanning was done with an Affymetrix Gene Array Scanner G2500A.

data_processing: The analysis was normalized using the LVS (least-variant set) method. Reference: PMID 18318917.  The software used for the microarray analysis is the SAS/STAT software version 9.1 of the SAS system for PC.

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted from laser-capture microdissected organotypic cultures using the Arcturus PicoPure kit

tag: engineered escc

value: non-invading

tag: p53 mutation

tag: egfr overexpression

value: no

tag: htert over-expression

value: yes


title: Macrophage No Stim 2

city: Davis

first: William

last: Hu

state: CA

address: 451 Health Science Dr.

department: Medical Microbiology & Immunology

institute: UC Davis

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: After scanning, fluorescence data were processed by the GeneChip operating system (version 1.1, Affymetrix). Background correction, normalization, generation of expression values, and analysis of differential gene expression were performed using dChip analysis software (DNA-Chip analyzer (dChip), version 1.3, Harvard University) in compliance with minimal information about microarray experiment (MIAME) guidelines (www.ncbi.nlm.nih.gov).

source_name: Macrophage

label_protocol: cDNA were synthesized (Superscript Choice System, Invitrogen) utilizing an oligo(dT)24 primer. Biotinylated cRNA was synthesized using a BioArray HighYield RNA transcription labeling kit (ENZO Diagnostics) and purified through RNeasy nucleic acid columns. cRNA quality was evaluated by hybridization to Test3 GeneChips (Affymetrix), and only samples whose 3:5 ratios were less than three were utilized for subsequent hybridization to HuGene U95-AV2 GeneChips (Affymetrix).

extract_protocol: Total cellular RNA was extracted (RNeasy kit, Qiagen)

treatment_protocol: No Treatment

tag: cell type

value: Macrophage

tag: stress

value: unstimulated


title: n273-2N

tag: egfr over-expression


title: n273-1N


title: pig skeletal muscle at d21, biological rep1

city: chongqing

first: shi

last: ping

address: beibei

department: school of life science

country: China

institute: southwest university

description: Gene expression data from pig skeletal muscle at 21 days after birth.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450(Affymetrix,P/N 00-0079).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000(Affymetrix,P/N 00-00212).

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

organism: Sus scrofa

source_name: Pig skeletal muscle at 21 days after birth

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

growth_protocol: Tissue samples were stored in liquid nitrogen.

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

value: skeletal muscle

value: post-natal day 21


title: Macrophage Stimulated 1

treatment_protocol: S. Typhimurium Flagellin Stimulated

value: stimulated with Flagellin


title: n175-2N


title: pig skeletal muscle at d14, biological rep1

description: Gene expression data from pig skeletal muscle at 14 days after birth.

source_name: Pig skeletal muscle at 14 days after birth

value: post-natal day 14


title: pig skeletal muscle at d14, biological rep3


title: n248-2N


title: pig skeletal muscle at d21, biological rep3


title: pig skeletal muscle at d21, biological rep2


title: pig skeletal muscle at d14, biological rep2


title: n175-1N


title: R248-3N


title: Macrophage No Stim 1


title: pig skeletal muscle at d7, biological rep3

description: Gene expression data from pig skeletal muscle at 7 days after birth.

source_name: Pig skeletal muscle at 7 days after birth

value: post-natal day 7


title: pig skeletal muscle at d7, biological rep2


title: R248-3I

value: invading (invasive)


title: E273-3I


title: n143-1N


title: n143-2N


title: pig skeletal muscle at d7, biological rep1


title: Matrix Association of Invasive Human Cytotrophoblasts Grown on Matrigel: Replicate 2

description: Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy.  The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood.  The aim of this experiment was to characterize the matrix association of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behaviors, and to correlate  nuclear matrix attachment and cell phenotype.

hyb_protocol: Hybridized at NimbleGen facilities as per NimbleGen protocol

scan_protocol: Scanned at NimbleGen facilities as per NimbleGen protocol

data_processing: Dual channel array data was q spline normalized using the NimbleGen data analysis suite. Normalized signal ratios were analyzed for enrichment in either the loop or matrix fraction.

source_name: Loop Associated DNA from Human Cytotrophoblasts

label_protocol: Labeling was conducted by the array manufacturer at NimbleGen's facilities

growth_protocol: HTR-8/SVneo cells, maintained at passage 38-45, were cultured in mass at the Cell Culture Facility of the Cleveland Clinic (Cleveland OH, USA) in 1:1 Ham’s F12:DMEM medium containing 10% fetal bovine serum and antibiotics (penicillin and streptomycin).  Cells were grown to confluence at 37ºC in a humidified 5%CO2/95% air incubator.  Prior to assessing invasion, the adherent HTR-8/SVneo cells were harvested trypsin/EDTA then transferred to roller bottles coated with either 10 µg/ml fibronectin (diluted with sterile PBS), or Matrigel ™, diluted 1:10 with sterile PBS.  The cells were then rinsed free of serum then cultured on Matrigel ™ or fibronectin for 24 hours in serum free 1:1 Ham’s F12: DMEM medium supplemented with 5mg/ml BSA.

extract_protocol: After extraction for 5 minutes in 2 M NaCl the halo structures were gently washed with REact® 3 restriction buffer (Invitrogen, Carlsbad, CA, USA) for 20 minutes at room temperature then centrifuged at 1000 x g at 4ºC three times  to remove any residual non-nuclear matrix proteins.  After the third wash, the DNA loops were separated from the matrix bound DNA by restriction digestion with 400 U of EcoRI (Invitrogen) at 37˚C for 3 hours.  After the restriction digest, the DNA was centrifuged at 16,000 X g for five minutes at 4ºC to pellet the nuclear matrix bound portion of the DNA.  The supernatant, containing the loop-associated DNA, was then moved to a clean tube.  The nuclear matrix bound DNA was washed 2 additional times with React ® 3 (Invitrogen) buffer to minimize loop contamination of the matrix-bound DNA.  The remaining residual proteins were removed from both the loop and matrix associated DNA by overnight digestion with 50 μg/mL proteinase K buffered with 50 mM Tris-HCl buffer, pH 8.0, with 50mM NaCl, 25 mM EDTA and 0.5% SDS.  DNA from each fraction was then purified using the Quantum-Prep Matrix kit (BioRad, Hercules, CA, USA), and then resuspended in nuclease-free deionized water and stored at   -20ºC.

value: invasive cytotrophoblast

value: DNA not found to be associated with the nuclear matrix in invasive human cytotrophoblast cells obtained from HTR-8/SVneo cell line

source_name: Matrix Associated DNA from Human Cytotrophoblasts

value: DNA associated with the nuclear matrix in invasive human cytotrophoblast cells obtained from HTR-8/SVneo cell line


title: Matrix Association of Invasive Human Cytotrophoblasts Grown on Matrigel: Replicate 1


title: Matrix Association of Proliferative Human Cytotrophoblasts Grown on Fibronectin: Replicate 2

value: proliferative cytotrophoblast

value: DNA not found to be associated with the nuclear matrix in proliferative (non-invasive) human cytotrophoblast cells obtained from HTR-8/SVneo cell line

value: DNA associated with the nuclear matrix in proliferative (non-invasive) human cytotrophoblast cells obtained from HTR-8/SVneo cell line


title: E273-2N

value: non-invading


title: pig skeletal muscle at d0, biological rep3

description: Gene expression data from pig skeletal muscle within 24 hours after birth.

source_name: Pig skeletal muscle within 24 hours after birth

value: post-natal day 0


title: pig skeletal muscle at d0, biological rep2


title: E248-1I

value: yes


title: Epuro-2N


title: pig skeletal muscle at d0, biological rep1


title: E248-2I


title: CD4T_S3_TGF(+)

city: Shinjyuku-ku

first: Tomohito

last: Takimoto

state: Tokyo

address: 35 Shinanomachi

department: Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

description: Gene expression data from Smad3-deficient CD4+ T cells cultured with TGF-b for 24hr.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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 GeneChip Operating Software 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Murine purified Smad3-deficient CD4+ T cells stimulated with TGF-b for 24hr

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: FACS-sorted CD4+CD25-CD44loCD62Lhi T cells (3 x 10^6 cells) were stimulated with plate-bound anti-CD3e (1ug/ml), soluble anti-CD28 (1ug/ml), anti-IFN-g (10ug/ml), anti-IL-4 (10ug/ml) and recombinant murine IL-2 (10ng/ml) in the absence or presence of 2ng/ml of TGF-b for 24 hr.

tag: strain

value: CD4+ T cells

tag: genome/variation

tag: treatment group

value: with TGF-b for 24hr


title: Epuro-3N


title: CD4T_S23h_TGF(+)

description: Gene expression data from Smad2-deficient/Smad3-hetero CD4+ T cells cultured with TGF-b for 24hr.

source_name: Murine purified Smad2-deficient/Smad3-hetero CD4+ T cells stimulated with TGF-b for 24hr

value: Smad2del/del, Smad3+/-


title: Epuro-1N


title: E273-1I


title: CD4T_WT_TGF(+)

description: Gene expression data from wild-type CD4+ T cells cultured with TGF-b for 24hr.

source_name: Murine purified wild-type CD4+ T cells stimulated with TGF-b for 24hr

value: wild-type


title: E273-3N


title: CD4T_WT_TGF(-)

description: Gene expression data from wild-type CD4+ T cells cultured without TGF-b for 24hr.

source_name: Murine purified wild-type CD4+ T cells stimulated without TGF-b for 24hr

value: without TGF-b for 24hr


title: CD4T_S2_TGF(-)

description: Gene expression data from Smad2-deficient CD4+ T cells cultured without TGF-b for 24hr.

source_name: Murine purified Smad2-deficient CD4+ T cells stimulated without TGF-b for 24hr


title: CD4T_S3_TGF(-)

description: Gene expression data from Smad3-deficient CD4+ T cells cultured without TGF-b for 24hr.

source_name: Murine purified Smad3-deficient CD4+ T cells stimulated without TGF-b for 24hr


title: CD4T_S23h_TGF(-)

description: Gene expression data from Smad2-deficient/Smad3-hetero CD4+ T cells cultured without TGF-b for 24hr.

source_name: Murine purified Smad2-deficient/Smad3-hetero CD4+ T cells stimulated without TGF-b for 24hr


title: E248-2N


title: E273-2I


title: Stimulated CD4+ CD25+ Cells, Expansion 88

description: Stimulated, Cord Blood Derived, CD4+ CD25+ Regulatory T Cells

hyb_protocol: Hybridisation to Affymetrix Human Exon 1.0ST arrays was carried out according to the manufacturers protocols

data_processing: Gene-Level expression estimates were obtained using Robust Multichip Analysis (RMA) and the statistical software R.

source_name: CD4+ CD25+ Treg Cells, Stimulated

label_protocol: Labelling was carried out according to the manufacturers protocols

growth_protocol: Expansion was carried out at a ratio of 3 beads/cell in the presence of 1000units/ml of recombinant human IL2 for 8 days, followed by 3 days of culture without beads.

extract_protocol: Total RNA, including small molecular weight RNA, was isolated using QIAshredder and a miRNeasy mini kit (QIAGEN).

treatment_protocol: Resting cells were rested for 60 hours after expansion. Stimulated cells were treated with Ionomycin for 2hrs prior to RNA extraction.

value: Cord Blood

value: CD4+ CD25+ Regulatory T Cells (Treg)

tag: treatment

value: Stimulated


title: CD4T_S2_TGF(+)

description: Gene expression data from Smad2-deficient CD4+ T cells cultured with TGF-b for 24hr.

source_name: Murine purified Smad2-deficient CD4+ T cells stimulated with TGF-b for 24hr


title: E248-1N


title: Pseudomonas aeruginosa strain PAO6261, anr mutant, anaerobic, replicate1

description: RNA was pooled from three independent cultures prior to cDNA synthesis. cDNA from three independent cultures was hybridized to one microarray.

source_name: Pseudomonas aeruginosa strain PAO6261 incubated under anaerobic conditions in AB-medium

tag: mutation

value: anr deletion

tag: condition

value: anaerobic


title: E175-3N


title: Stimulated CD4+ CD25+ Cells, Expansion 87


title: E175-1N


title: Stimulated CD4+ CD25- Cells, Expansion 88

description: Stimulated, Cord Blood Derived, CD4+ CD25- T Cells

source_name: CD4+ CD25- Th Cells, Stimulated

value: CD4+ CD25- Thelper Cells


title: E175-1I

description: 3D cultured genetically engineered human esophageal cells

value: invading (invasive)


title: E143-3N


title: Stimulated CD4+ CD25+ Cells, Expansion 43


title: Matrix Association of Proliferative Human Cytotrophoblasts Grown on Fibronectin: Replicate 1

tag: sample type

value: DNA not found to be associated with the nuclear matrix in proliferative (non-invasive) human cytotrophoblast cells obtained from HTR-8/SVneo cell line

value: proliferative cytotrophoblast

tag: cell line


title: Resting CD4+ CD25+ Cells, Expansion 43

description: Resting, Cord Blood Derived, CD4+ CD25+ Regulatory T Cells

source_name: CD4+ CD25+ Treg Cells, Resting

value: Resting


title: FOXP3Genome_hs18_3

description: FOXP3 ChIP Biological Rep 1-2, chip C

source_name: FOXP3 ChIP DNA from expanded Human T regulatory cells

value: cord blood

value: CD4+CD25+ natural T regulatory cells (nTreg)

tag: antibody

value: Rabbit polyclonal anti-human FOXP3 IgG (Novus Biologicals)

source_name: Input DNA from expanded Human T regulatory cells

tag: cells


title: Resting CD4+ CD25+ Cells, Expansion 86

tag: tissue


title: E143-1I

tag: engineered escc

tag: p53 mutation

value: yes


title: Stimulated CD4+ CD25+ Cells, Expansion 41


title: FOXP3Genome_hs18_4

description: FOXP3 ChIP Biological Rep 1-2, chip D


title: Stimulated CD4+ CD25- Cells, Expansion 87


title: E143-3I

tag: htert over-expression


title: E143-2N

value: non-invading


title: E143-2I


title: Resting CD4+ CD25+ Cells, Expansion 87

tag: cell type


title: Resting CD4+ CD25- Cells, Expansion 88

description: Resting, Cord Blood Derived, CD4+ CD25- T Cells

source_name: CD4+ CD25- Th Cells, Resting


title: Resting CD4+ CD25+ Cells, Expansion 88


title: Stimulated CD4+ CD25+ Cells, Expansion 86


title: E175-2N


title: Stimulated CD4+ CD25- Cells, Expansion 86


title: Resting CD4+ CD25- Cells, Expansion 87


title: E143-1N


title: E273-1N


title: Resting CD4+ CD25- Cells, Expansion 86


title: E175-2I


title: E175-3I


title: Stimulated CD4+ CD25- Cells, Expansion 43


title: Stimulated CD4+ CD25- Cells, Expansion 41


city: Amherst

first: Ashley

middle: Edwin

last: Franks

state: MA

address: University of Massachusetts at Amherst, Dept. of Microbiology, Morrill IV North

department: Microbiology

institute: University of Massachusetts Amherst

description: Inner portion of current producing biofilm separated by microtoming

hyb_protocol: Affymetrix prokaryotic protocol (p69Affy, p75 Adobe)

data_processing: by ArrayStar (DNASTAR Inc) using the Robust Multichip Average (RMA) algorithm, average of 3 replicates

organism: Geobacter sulfurreducens

source_name: Inner Portion of G. sulfurreduccens current producing biofilm

growth_protocol: G. sulfurreducens was growing in a microbial fuel cell to maximum power

extract_protocol: RNA was extracted from the biofilm sections with an acetone extraction method as previously described (Holmes, D. E., K. P. Nevin, et al. (2004).  In situ expression of Geobacteraceae nifD in subsurface sediments. Appl. Environ. Microbiol. 70: 7251-9.

treatment_protocol: Biofilm treated with RNAse protect and spatially separated into inner and outer layers

value: wildtype PCA

tag: biofilm


description: Outer portion of current producing biofilm separated by microtoming

scan_protocol: Affymetrix prokaryotic protocol (p69Affy, p75 Adobe)

source_name: Outer Portion of G. sulfurreduccens current producing biofilm


title: DvH_240min._6500_ppm_Nitrate_set285

type: mixed

city: Berkeley

first: Adam

middle: P.

last: Arkin

address: 1 Cyclotron Road

department: Physical Biosciences Division

institute: Virtual Institute for Microbial Stress and Survival

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with 6500 ppm Nitrate.  Treatment time point = 240 min.

hyb_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P. Wall, J. D. and Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72:4370-4381.

scan_protocol: ImaGene software

data_processing: For a given time point (control or treatment), three microarray slides corresponding to three biological replicates were used. To estimate the average log (base 2) expression levels from replicate arrays, log expression levels from each array were normalized globally. This was calculated as follows. First, the net signal of each spot was calculated by subtracting out the background and adding a pseudosignal of 100 to enforce a positive value. If the resulting net signal was still less than 50, a value of 50 was used. Next, the expression level for each spot was calculated from the ratio of the two channels (mRNA over genomic DNA). Finally, the mean expression level and standard deviation of each spot were estimated, requiring n > 1, where n is the number of scorable replicates. To estimate the differential gene expression between the control and treatment conditions, normalized log ratios were calculated.  Each log ratio was calculated as log2(treatment)  log2(control). This log ratio was normalized using LOWESS (locally weighted scatterplot smoothing) on the difference versus the sum of the log expression level (12). Since sector-based artifacts were detected, each log ratio was further normalized by subtracting the median of all spots within each sector. The final normalized log ratio (log2R) was calculated from the average ratio of spots for each gene. To assess the significance of the normalized log ratio, a Z score was calculated by the following equation (0.25 is a pseudovariance term): Z = log2(treatment/control)/(0.25 + variance). The final normalized log ratio (log2R) was calculated from the average ratio of spots for each gene. To assess the significance of the normalized log ratio, a Z score was calculated by the following equation (0.25 is a pseudovariance term): Z = log2(treatment/control)/(0.25 + variance).

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 240min. 6500 ppm Nitrate

growth_protocol: Inoculate 200 ml of log-phase inoculum culture to 2000 ml of defined PIPES buffered medium LS4D. Grow culture in six 2L glass bottles placed in the anaerobic chamber at 30oC till OD of ~0.3. Three bottles will be the control(Ph 7.0, sterile water added) and the other three bottles will be the varibles (105 mM sodium nitrate). Harvest 50 ml of cells from each of the six bottles at 30, 60, 120, 240 and 480 min after treatment. All sampling occur in the anaerobic chamber. Samples were chilled and pumped through stainless steel tubing in ice-water into centrifuge bottlessurrounded by ice. Harvested biomass was centrifuged at 11,000  g for 10 min at 4oC.  Cell pellets were washed in 50ml anoxic 10mM phosphate buffered saline and centrifuged as above.  Cell pellets were immediately frozen in liquid N2 and stored at -80oC until RNA isolation.

extract_protocol: RNA extraction, purification, and labeling were performed independently on each cell sample. Total cellular RNA was isolated using TRIzol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer's protocol. RNA extracts were purified according to the RNeasy Mini Kit (QIAGEN, Valencia, CA) instructions, and on-column DNase digestion was performed with an RNase-free DNase set (QIAGEN, Valencia, CA) to remove genomic DNA contamination, according to the manufacturer's procedure.

treatment_protocol: 240min. 6500 ppm Nitrate.

value: Hildenborough

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, genomic DNA.

extract_protocol: Genomic DNA was extracted from D. vulgaris cultures at stationary phase using a standard protocol detailed elsewhere and labeled with the fluorophore Cy3-dUTP (Amersham Biosciences, Piscataway, NJ). The efficiency of labeling was routinely monitored by measuring the absorbance at 260 nm (for DNA concentration), 550 nm (for Cy3), or 650 nm (for Cy5).


title: FOXP3Genome_hs18_2

description: FOXP3 ChIP Biological Rep 1-2, chip B


title: DvH_30min._6500_ppm_Nitrate_set281

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with 6500 ppm Nitrate.  Treatment time point = 30 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 30min. 6500 ppm Nitrate

label_protocol: He, Q., Huang, K. H., He, Z., Alm, E. J., Fields, M. W., Hazen, T. C., Arkin, A. P. Wall, J. D. and Zhou, J. 2006. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Appl. Environ. Microbiol. 72:4370-4381.

treatment_protocol: 30min. 6500 ppm Nitrate.


title: DvH_60min._6500_ppm_Nitrate_set282

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with 6500 ppm Nitrate.  Treatment time point = 60 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 60min. 6500 ppm Nitrate

treatment_protocol: 60min. 6500 ppm Nitrate.


title: stroma_MDS_n4

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

department: Biochemistry

country: Brazil

institute: Universidade de Sao Paulo

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

scan_protocol: Slides were scanned immediately after washing on the GenePix Scanner (G2505B). Scan resolution 5um.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized among the samples by quantile using Spotfire DecisionSite® for Microarray Analysis (TIBCO Software Inc, Somerville, MA, USA).

label: Cy3, Cy5

source_name: MDS Patient4,stroma,Male,70y

label_protocol: For each individual sample, 150 ng total RNA was amplified and labeled with Cy3 or Cy5 using the Agilent Low RNA Input Fluorescent Linear Amplification Kit PLUS, two-Color (Agilent Technologies) according to the manufacturer’s recommendations. Labeled cRNA was hybridized using Gene Expression Hybridization Kit (Agilent).

growth_protocol: BM mononuclear cells (BMMNCs) were isolated by density-gradient centrifugation through Ficoll-Paque Plus (GE Healthcare, Uppsala, Sweden), labeled with CD34 MicroBeads, and CD34+ cells were isolated using MACS magnetic cell separation columns (Miltenyi Biotec, Mönchengladbach, Germany) according to the manufacturer’s instructions. The purity of CD34+ cells was at least 85% as determined by fluorescence-activated cell sorting (FACS), using anti-CD34 antibody (Caltag Laboratories, Burlingame, CA). The mononuclear cells without CD34+, were plated onto Iscove’s Dulbeccos (IMDM)  (Sigma, St Louis, MO, USA) supplemented with 10% fetal bovine serum and 10% horse serum. Supernatant with non-adherent cells was removed weekly and replaced with fresh medium. When the monolayer was established (90% confluence) cells were trypsinized and plated under the same conditions. After three re-platings, a homogeneous cell population was obtained and the stromal cells were evaluated by FACS for the absence of CD34, CD45 and CD68 antigens.

extract_protocol: Total RNA was extracted with RNAspin Mini RNA Isolation Kit (GE Healthcare, Freiburg, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: subject type

value: MDS

value: stroma

tag: age (yrs)

tag: gender

value: male


title: stroma_MDS_n6

source_name: MDS Patient6,stroma,Male,56y


title: Resting CD4+ CD25- Cells, Expansion 43

value: Cord Blood


title: DvH_120min._6500_ppm_Nitrate_set288

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with 6500 ppm Nitrate.  Treatment time point = 120 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 120min. 6500 ppm Nitrate

treatment_protocol: 120min. 6500 ppm Nitrate.

tag: strain


title: stroma_donor_n7

value: Donor

value: female


title: DvH_240min._6500_ppm_Nitrate_set269


title: DvH_120min._6500_ppm_Nitrate_set283


title: CD34+_MDS_n4

source_name: MDS Patient4,CD34+,Male,70y


title: stroma_MDS_n5

source_name: MDS Patient5,stroma,Female,69y


title: stroma_donor_n8


title: DvH_0min._6500_ppm_Nitrate_set284

description: This sample is one of a series of samples used to investigate the stress response pathways of Desulfovibrio vulgaris Hildenborough treated with Nitrate. This sample was treated with 6500 ppm Nitrate.  Treatment time point = 0 min.

source_name: Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough, 0min. 6500 ppm Nitrate

treatment_protocol: 0min. 6500 ppm Nitrate.

treatment_protocol: 0min. 6500 ppm


title: FOXP3Genome_hs18_6

description: FOXP3 ChIP Biological Rep 1-2, chip F


title: CD34+_MDS_n3

source_name: MDS Patient3,CD34+,Male,62y


title: FOXP3Genome_hs18_1

description: FOXP3 ChIP Biological Rep 1-2, chip A


title: DvH_60min._6500_ppm_Nitrate_set287


title: DvH_30min._6500_ppm_Nitrate_set286


title: stroma_donor_n6


title: CD34+_donor_n4

source_name: Donor4, CD34+,healthy,female, 30y


title: CD34+_MDS_n1

source_name: MDS Patient1,CD34+,Female,72y


title: CD34+_donor_n1

source_name: Donor1,CD34+, healthy, female, 18y


title: CD34+_donor_n2

source_name: Donor2,CD34+, healthy, female, 35y


title: CD34+_donor_n3

source_name: Donor3, CD34+, healthy, female, 54y


title: stroma_donor_n5


title: AB - 2 - mAdbID:98294

status: Public on Jun 21 2010

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 98294

hyb_protocol: Sample Hybridization Protocol Other: The samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.19;; 3.48 Temperature: 33.96

data_processing:
miRNA Data Processing
Calculation Method: The raw signal intensities were imported into BRRArray Tools. signal intensity were background-intensity subtracted. Data are further normalized by median value over entire array.

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: EBV-infected lymphocytes (reference)

label_protocol:
Hy3 Labeling Protocol
Other: 2 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.

extract_protocol:
Trizol Extraction Protocol
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.

value: Lymphoblastoid cells transfected with Epstein-Barr virus (EBV)

source_name: adult peripheral erythroid cells

label_protocol:
Hy5 Labeling Protocol
Other: 2 µg total RNA was directly labeled with miRCURY™ LNA Array Power Labeling Kit (Exiqon, Woburn, MA) according to manufacture’s procedure.

value: peripheral blood

tag: developmental stage

value: adult

value: erythroid cells


title: AB - 1 - mAdbID:98293

description: mAdb experiment ID: 98293

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.19;; 3.46 Temperature: 33.83


title: AB - 4 - mAdbID:98296

description: mAdb experiment ID: 98296

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.19;; 3.49 Temperature: 34.11


title: AB - 3 - mAdbID:98295

description: mAdb experiment ID: 98295

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.19;; 3.47 Temperature: 34.05


title: CB - 3 - mAdbID:98291

description: mAdb experiment ID: 98291

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.17;; 3.46 Temperature: 32.64

source_name: umbilical cord erythroid

value: umbilical cord blood

value: fetus


title: CB - 1 - mAdbID:98289

description: mAdb experiment ID: 98289

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.17;; 3.42 Temperature: 33.01


title: CD34+_MDS_n2

source_name: MDS Patient2,CD34+,Male,78y


title: CB - 4 - mAdbID:98292

description: mAdb experiment ID: 98292

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.17;; 3.44 Temperature: 32.8


title: CB - 2 - mAdbID:98290

description: mAdb experiment ID: 98290

scan_protocol: Creator: GenePix Pro 4.0.1.23 Scanner: GenePix 4000B [84945] ScanPower: 10;; 33 LaserPower: 3.19;; 3.46 Temperature: 33.68


title: Pre-otic domain replicate 4

city: Salt Lake City

first: Christian

middle: N.

last: Paxton

state: UT

department: Neurobiology and Anatomy

institute: Christian

description: Biological replicate 4 of 4. Pre-otic domain compared to Control tissue.

hyb_protocol: Labeled cRNA samples were fragmented, combined with Agilent Hi-RPM Hyb Buffer and applied to microarray enclosed in  Agilent SureHyb Hybridization chambers.  Following incubation, the microarray slide was washed sequentially, dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner at 5 µm resolution.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

organism: Gallus gallus

source_name: Pre-otic domain stg 6-7 chick embryo

label_protocol: The Agilent Two-Color Low RNA Input Linear Amplification Kit was used to generate fluorescently (Cy3/Cy5) labeled cRNA for two-color microarray hybridizations, according to the manufacturer's protocol. Two rounds of linear amplification were included for Nano amounts of RNA, with labeling on the 2nd round.

growth_protocol: Fertilized eggs were acquired and incubated in humidified chambers at 38 degrees Celsius for 23-4.

extract_protocol: Total RNA from each pooled sample was isolated using TRIzol (Invitrogen, Carlsbad, CA) according to the Manufacturer's protocol. RNA was cleaned using Qiagen Rneasy Micro kit (Qiagen, Valencia, CA) according to manufacturer's directions.

treatment_protocol: The pre-otic and rostral control domains were microdissected in saline using a sharpened tungsten needle. The first somite was used to mark the caudal boundary of the pre-otic domain. Test and control samples from the same pooled embyros were matched.

tag: stage

value: Hamburger-Hamilton 6-7

value: Early embryonic chick

source_name: Rostral Control domain stg 6-7 chick embryo


title: Pre-otic domain replicate 3

description: Biological replicate 3 of 4. Pre-otic domain compared to Control tissue.


title: Pre-otic domain replicate 2

description: Biological replicate 2 of 4. Pre-otic domain compared to Control tissue.


title: Pre-otic domain replicate 1

description: Biological replicate 1 of 4. Pre-otic domain compared to Control tissue.


title: Lean WT_10mpk_AM251_eWAT_12

city: Rahway

first: Olivia

last: Fong

state: NJ

department: Molecular Profiling

institute: Merck & Co.

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_eWAT_12

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45°C with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were processed using the Rosetta Resolver® system. The software performs error modeling using the data loaded and processed into the Resolver system. The Resolver system applies the RMA algorithm to combine replicates of the same sequence in an array.  Affymetrix's MAS-5 method is applied to calculate a P-value for such sequences.  The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds of a P-value below which, genes are considered to be significantly expressed.  Errors for the RMA-computed sequences are fitted using methodology developed by Rosetta using the guidelines set in Weng et al. (2006) Bioinformatics 22:1111-1121.  The Resolver system also combines multiple arrays using an averaging process.  The P-values for the combined results are also the combination of individual probe-level P-values (geometric means).  Ratios and their P-values are computed as described in section 2.2 of Weng et al. (2006).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

source_name: eWAT

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.

tag: diet

value: lean (regular chow)

tag: genotype/variation

value: wild-type

tag: treatment

value: 10mpk AM251

value: epididymal white adipose tissue (eWAT)


title: Lean WT Vehicle_eWAT_sample4

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_eWAT_sample4

value: vehicle


title: Lean_CB1R-/-_KO_vehicle_eWAT_15

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_eWAT_15


title: Lean WT Vehicle_eWAT_sample3

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_eWAT_sample3


title: Lean_CB1R-/-_KO_10mpk_AM251_eWAT_23

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_eWAT_23


title: Lean WT_10mpk_AM251_eWAT_14

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_eWAT_14


title: Lean WT Vehicle_eWAT_sample1

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_eWAT_sample1


title: Lean WT_10mpk_AM251_eWAT_11

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_eWAT_11


title: DIO WT Vehicle_eWAT_sample6

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT Vehicle_eWAT_sample6

value: high fat


title: DIO WT_10mpk_AM251_eWAT_37

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_eWAT_37


title: DIO WT_10mpk_AM251_eWAT_33

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_eWAT_33


title: Lean_CB1R-/-_KO_vehicle_eWAT_16

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_eWAT_16


title: Lean_CB1R-/-_KO_vehicle_eWAT_19

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_eWAT_19


title: DIO WT_10mpk_AM251_eWAT_36

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_eWAT_36


title: Lean WT_10mpk_AM251_eWAT_13

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_eWAT_13


title: Lean_CB1R-/-_KO_10mpk_AM251_eWAT_21

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_eWAT_21


title: Lean WT Vehicle_eWAT_sample5

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_eWAT_sample5


title: Lean WT_10mpk_AM251_eWAT_10

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_eWAT_10


title: Lean_CB1R-/-_KO_vehicle_eWAT_17

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_eWAT_17


title: Lean_CB1R-/-_KO_10mpk_AM251_eWAT_20

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_eWAT_20


title: DIO WT_10mpk_AM251_eWAT_34

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_eWAT_34


title: DIO WT_10mpk_AM251_eWAT_35

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_eWAT_35


title: Lean_CB1R-/-_KO_vehicle_eWAT_18

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_eWAT_18


title: DIO WT Vehicle_eWAT_sample4

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT Vehicle_eWAT_sample4


title: DIO WT Vehicle_eWAT_sample5

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT Vehicle_eWAT_sample5


title: Lean WT Vehicle_eWAT_sample2

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_eWAT_sample2


title: DIO WT Vehicle_eWAT_sample3

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT Vehicle_eWAT_sample3


title: DIO WT Vehicle_eWAT_sample1

description: DIO WT Vehicle eWAT (n=5) Virtual Pool vs. DIO WT Vehicle_eWAT_sample1


title: DIO_CB1R-/-_KO_vehicle_eWAT_44

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_eWAT_44


title: DIO_CB1R-/-_KO_vehicle_eWAT_43

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_eWAT_43


title: DIO_CB1R-/-_KO_vehicle_eWAT_42

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_eWAT_42


title: DIO_CB1R-/-_KO_10mpk_AM251_eWAT_50

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_eWAT_50


title: DIO_CB1R-/-_KO_10mpk_AM251_eWAT_46

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_eWAT_46


title: DIO_CB1R-/-_KO_10mpk_AM251_eWAT_48

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_eWAT_48


title: Lean WT Vehicle_Liver_sample5

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_Liver_sample5

source_name: liver

value: liver


title: DIO_CB1R-/-_KO_10mpk_AM251_eWAT_45

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_eWAT_45


title: Lean WT_10mpk_AM251_Liver_12

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_Liver_12


title: Lean WT Vehicle_Liver_sample2

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_Liver_sample2


title: Lean WT_10mpk_AM251_Liver_10

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_Liver_10


title: Lean WT_10mpk_AM251_Liver_11

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_Liver_11


title: Lean_CB1R-/-_KO_vehicle_Liver_15

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_Liver_15


title: Lean WT Vehicle_Liver_sample3

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_Liver_sample3


title: Lean_CB1R-/-_KO_10mpk_AM251_Liver_22

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_Liver_22


title: Lean_CB1R-/-_KO_10mpk_AM251_Liver_23

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_Liver_23


title: Lean WT Vehicle_Liver_sample1

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_Liver_sample1


title: Lean_CB1R-/-_KO_10mpk_AM251_Liver_24

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_Liver_24


title: Lean_CB1R-/-_KO_vehicle_Liver_18

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_Liver_18


title: DIO WT_10mpk_AM251_Liver_38

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_Liver_38


title: DIO WT_10mpk_AM251_Liver_39

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_Liver_39


title: Lean WT Vehicle_Liver_sample4

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT Vehicle_Liver_sample4


title: Lean_CB1R-/-_KO_10mpk_AM251_Liver_20

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_Liver_20


title: Lean_CB1R-/-_KO_10mpk_AM251_Liver_21

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_10mpk_AM251_Liver_21


title: Lean_CB1R-/-_KO_vehicle_Liver_16

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_Liver_16


title: Lean_CB1R-/-_KO_vehicle_Liver_19

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_Liver_19


title: Lean_CB1R-/-_KO_vehicle_Liver_17

description: Lean CB1R-/- KO (n=5) Virtual Pool vs. Lean_CB1R-/-_KO_vehicle_Liver_17


title: DIO WT_10mpk_AM251_Liver_35

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_Liver_35


title: DIO WT_10mpk_AM251_Liver_37

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_Liver_37


title: DIO WT_10mpk_AM251_Liver_33

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT_10mpk_AM251_Liver_33


title: DIO WT Vehicle_Liver_sample3

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT Vehicle_Liver_sample3


title: DIO WT Vehicle_Liver_sample4

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT Vehicle_Liver_sample4


title: DIO_CB1R-/-_KO_vehicle_Liver_41

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_Liver_41


title: DIO WT Vehicle_Liver_sample5

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT Vehicle_Liver_sample5


title: DIO WT Vehicle_Liver_sample1

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT Vehicle_Liver_sample1


title: DIO_CB1R-/-_KO_10mpk_AM251_Liver_48

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_Liver_48


title: DIO_CB1R-/-_KO_vehicle_Liver_44

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_Liver_44


title: DIO WT Vehicle_Liver_sample2

description: DIO WT Vehicle Liver (n=5) Virtual Pool vs. DIO WT Vehicle_Liver_sample2


title: DIO_CB1R-/-_KO_vehicle_Liver_40

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_Liver_40


title: DIO_CB1R-/-_KO_10mpk_AM251_Liver_49

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_Liver_49


title: DIO_CB1R-/-_KO_vehicle_Liver_42

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_Liver_42


title: hypoxic culture-2

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

hyb_protocol: Labeled cDNA was hybridized to GeneChip CauloHi1 according to GeneChip Expression analysis technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: After hybridization for 16 hours at 50°C, arrays were washed using protocol PRO-GE-W52-V3 and stained on a GeneChipFluidics Station (Affymetrix)  according to the Genechip Expression analysis technical manual. The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: CEL intensity files were generated by GCOS (Gene Chip Operating Software ) v. 1.4.  Intensity values were normalized to a mean target value of 500 in GCOS.

organism: Caulobacter vibrioides

source_name: Caulobacter (hypoxic)

label_protocol: Ten μg of each total RNA was processed to produce single-strand cDNA and RNA was removed using 1N NaOH.  cDNA was column purified, fragmented using DNAseI (GE Life Sciences, Piscataway, NJ), and end labeled using GeneChip labeling reagent (Affymetrix, P/N 900542).

growth_protocol: All batches of cells were intially grown to 0.5 OD in a heavily aerated and pH controlled (pH=7) New Brunswick bioreactor in PYE medium.

extract_protocol: Trizol RNA extraction, followed by DNAseI treatment.  RNA was re-extracted using acid phenol, alcohol precipitated, and resuspended in deionized water.

treatment_protocol: Two of the four cell batches were subjected to hypoxia at 0.5 OD by sparging the bioreactor with 100% nitrogen gas while maintain robust stirring of the culture.  After 20 minutes at 0% dissolved oxygen (as measured by a dissolved oxygen probe), cells were harvested for RNA isolation.  Aerated cells were simply harvested at 0.5 OD for RNA isolation (without nitrogen sparge).

tag: stress

value: hypoxia


title: DIO_CB1R-/-_KO_10mpk_AM251_Liver_45

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_Liver_45


title: ammonium_vs_nitrate_3

hyb_protocol: Paired Cy3 and Cy5 labeled cDNA from the treated and untreated samples were hybridized onto spotted DNA oligo arrays using a protocol previously described (Hottes A, Meewan M, Yang D, Arana N, Romero P, et al.  2004. Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. J Bacteriol 186: 1448–1461.)

scan_protocol: After hybridization and washing, the arrays were scanned with a GenePix 4000B scanner (Axon Instruments). Scanned spots were converted to ratios (red/green) with GenePix Pro 5.0 software.

data_processing: Expression ratio data for the biological replicates were normalized by median centering and analyzed using the Significance Analysis for Microarrays (SAM) package.

label_protocol: Cy3 or Cy5-labeled cDNA was generated from 20 µg of total RNA by reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using 1 µg of random hexamer primers (Invitrogen, Carlsbad, CA).

growth_protocol: four independent cultures of Caulobacter crecentus were grown in each of two medium conditions: M2(nitrate)glucose and M2(ammonium)glucose.  Cultures in each medium type were grown to OD660=0.3 and RNA was isolated from each.

extract_protocol: Trizol RNA extraction, followed by DNAseI treatment.  RNA was re-extracted using acid phenol, alcohol precipitated, and resuspended in dionized water.

treatment_protocol: measuring steady-state transcriptional differences between strains cultured in M2 minimal medium supplemented with either nitrate or ammonium as the sole nitrogen source.

tag: agent

value: ammonium

value: nitrate


title: DIO_CB1R-/-_KO_10mpk_AM251_Liver_46

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_Liver_46

tag: tissue


title: log phase Caulobacter-NONOate treated versus untreated, biol_rep 3

source_name: log phase Caulobacter, untreated

label_protocol: Labeled indocarbocyanine-dCTP (Cy5) cDNA was generated from 20 µg of total RNA by reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using 1 µg of random hexamer primers (Invitrogen, Carlsbad, CA).

growth_protocol: Caulobacter crescentus grown to a density of 0.3 (at OD660).  Cells were harvested and RNA isolated.

value: untreated (control)

source_name: log phase Caulobacter, NONOate treated

label_protocol: Labeled indodicarbocyanine-dCTP (Cy3) cDNA was generated from 20 µg of total RNA by reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) using 1 µg of random hexamer primers (Invitrogen, Carlsbad, CA).

growth_protocol: Caulobacter crescentus grown to a density of 0.3 (at OD660).  Cell were then treated with 100 mM DETA NONOate for 30 minutes.  Cells were harvested and RNA isolated.

value: NONOate

tag: dose

tag: treatment time

value: 30 minutes


title: Lean WT_10mpk_AM251_Liver_8

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_Liver_8


title: DIO_CB1R-/-_KO_10mpk_AM251_eWAT_49

description: DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_eWAT_49


title: Lean WT_10mpk_AM251_Liver_13

description: Lean WT Vehicle (n=5) Virtual Pool  vs. Lean WT_10mpk_AM251_Liver_13


title: log phase Caulobacter-NONOate treated versus untreated, biol_rep 1


title: DIO_CB1R-/-_KO_10mpk_AM251_Liver_47

description: DIO CB1R-/- KO vehicle (n=4) Virtual Pool vs. DIO_CB1R-/-_KO_10mpk_AM251_Liver_47


title: aerated culture-2

source_name: Caulobacter (aerated)

value: control


title: hypoxic culture-1


title: aerated culture-1


title: ammonium_vs_nitrate_1


title: colon WT 7 day DSS rep4

city: blacksburg

first: Saroj

middle: K

last: Mohapatra

state: VA

address: washington Street

department: VBI

institute: Virginia Tech

hyb_protocol: The samples were hybridized and stained per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

scan_protocol: The samples were scanned per standard Affymetrix protocols at VBI core laboratory on Mouse 430 2.0 expression arrays (Affymetrix Inc., Santa Clara, CA).

data_processing: The data were normalized using GC-RMA algorithm in R statistical environment (version 2.10.1). Linear modeling was performed using the bioconductor package 'limma'.

source_name: colonic mucosa, wild-type epithelial cells (VC-), 7 day of DSS treatment, replicate 4

label_protocol: RNA was processed and labeled according to the standard target labeling protocols.

growth_protocol: Intestine tissue and intestinal epithelial cells were obtained from tissue-specific PPARγ fl/fl; Villin Cre+ (VC+) and Villin Cre- control mice (WT). Duodenum, jejunum, ileum, cecum and colon were excised. For cell isolation, the different parts of the intestine were washed with PBS, minced and digested twice in CMF/FBS/EDTA media at 37oC for 15 minutes. The digest was passed through a nylon mesh and supernatants were collected and centrifuged. Cells were washed and resuspended in lysis buffer. DNA was extracted by using the QIAamp DNA Mini Kit, Blood and Body Fluid Spin Protocol (Qiagen). For whole tissue DNA isolation, each part of the intestine was collected and homogenized and then genomic DNA was extracted by QIAamp DNA Mini Kit, Tissue Protocol (Qiagen).  And PCR was performed as previously described [Adachi2006] and PCR amplifications were resolved through ethidium bromide staining on a 2% agarose gel and run at 120 V for 30 minutes.

extract_protocol: After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.

treatment_protocol: PPAR g flfl; Villin Cre+ (VC+, n=45) and control PPAR g flfl; Villin Cre- (WT, n=42) mice were used for these experiments. These mice express a transgenic recombinase under the control of the Villin-Cre promoter .  The mice were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 750 F, with a 12:12 h light-dark cycle starting from 6:00 AM.  All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.  Mice were challenged with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 molecular weight (ICN Biomedicals, Aurora, OH) in the drinking water.  After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection).  For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score . Briefly, disease activity index consisted of a scoring for diarrhea and lethargy (0–3), whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area (0–4).  Mice in the DSS study were euthanized on days 0, 2, and 7 of the DSS challenge by carbon dioxide narcosis followed by secondary thoracotomy and blood was withdrawn from the heart.  Spleen and mesenteric lymph nodes (MLN) were scored based on size and macroscopic inflammatory lesions (0-3), excised, and single-cell suspensions were prepared as previously described  for flow cytometry.

tag: genotype

value: Villin-CRE- (Wild-type epithelial cell)

tag: day of dss treatment

value: colonic mucosa


title: nitrate_vs_ammonium_4


title: colon WT 0 day DSS rep1

source_name: colonic mucosa, wild-type epithelial cells (VC-), 0 day of DSS treatment, replicate 1


title: Oregon Rhesus Macaque Embryonic Stem9 (ORMES9),biological rep C

city: Beaverton

first: Hathaitip

last: Sritanaudomchai

state: OR

institute: OHSU

description: Gene expression profile of ORMES9C is homozygous parthenote profile, only one allele inherited from the mother, in biological replicate C.

hyb_protocol: Labeled target is fragmented at 95C in the presence of high magnesium concentration.  The fragmented material is combined with biotinylated hybridization control oligomer and biotinylated control cRNAs for BioB, BioC, BioD and CreX (Affymetrix) in hybridization buffer.  Ten micrograms of target is hybridized for 16 hours at 45C to the GeneChip Rhesus Macaque Genome array (Affymetrix), followed by washing, staining with streptavidin-phycoerythrin (Molecular Probes), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs), and a final staining step on the Fluidics Station 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with the 7G upgrade (Affymetrix) and GCOS version 1.4.0 software (Affymetrix), yielding cell fluorescence intensity (.CEL files).  Image inspection was performed manually immediately following each scan.

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2).After normalization, GeneSifter (VizX Labs) microarray expression analysis software was used to analyze the resultant data.

organism: Macaca mulatta

source_name: ORMES9C were embryonic stem cells which dereived from IVF blastocyst.

label_protocol: Messenger RNA is amplified and labeled from 2 micrograms of total RNA in two steps according to the standard Affymetrix one-cycle cDNA protocol (Expression Analysis Technical Manual Rev.4). In the first step, mRNA is converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (Affymetrix).  In the second step, amplified and labeled cRNA (the target) is produced in an in vitro transcription reaction using T7 RNA polymerase and biotin-UTP (Affymetrix). Following removal of free nucleotides, target yield is measured by UV260 absorbance.

growth_protocol: ORMES9C were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions, and total RNA obtained by Trizol extraction was further purified using RNeasy spin columns (Qiagen) following manufacturer instructions.

treatment_protocol: ORMES9C established from rhesus monkey IVF blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.16.

value: female

tag: embryo

value: Blastocyst

tag: cell type

value: embryonic stem cell


title: nitrate_vs_ammonium_2


title: colon WT 0 day DSS rep3

source_name: colonic mucosa, wild-type epithelial cells (VC-), 0 day of DSS treatment, replicate 3


title: log phase Caulobacter-NONOate treated versus untreated, biol_rep 2

source_name: log phase Caulobacter culture, NONOate treated

growth_protocol: Caulobacter crescentus grown to a density of 0.3 (at OD660). Cell were then treated with 100 mM DETA NONOate for 30 minutes. Cells were harvested and RNA isolated.


title: colon WT 0 day DSS rep2

source_name: colonic mucosa, wild-type epithelial cells (VC-), 0 day of DSS treatment, replicate 2


title: colon WT 7 day DSS rep1

source_name: colonic mucosa, wild-type epithelial cells (VC-), 7 day of DSS treatment, replicate 1


title: colon VC 7 day DSS rep4

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 7 day of DSS treatment, replicate 4

value: Villin-CRE+ (PPAR g null epithelial cell)


title: colon WT 7 day DSS rep3

source_name: colonic mucosa, wild-type epithelial cells (VC-), 7 day of DSS treatment, replicate 3


title: colon WT 7 day DSS rep2

source_name: colonic mucosa, wild-type epithelial cells (VC-), 7 day of DSS treatment, replicate 2


title: colon WT 2 day DSS rep1

source_name: colonic mucosa, wild-type epithelial cells (VC-), 2 day of DSS treatment, replicate 1


title: colon WT 2 day DSS rep3

source_name: colonic mucosa, wild-type epithelial cells (VC-), 2 day of DSS treatment, replicate 3


title: colon VC 7 day DSS rep3

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 7 day of DSS treatment, replicate 3


title: colon WT 2 day DSS rep2

source_name: colonic mucosa, wild-type epithelial cells (VC-), 2 day of DSS treatment, replicate 2


title: colon VC 7 day DSS rep2

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 7 day of DSS treatment, replicate 2


title: Oregon Rhesus Macaque Embryonic Stem9 (ORMES9),biological rep B

description: Gene expression profile of ORMES9B is homozygous parthenote profile, only one allele inherited from the mother, in biological replicate B.

source_name: ORMES9B were embryonic stem cells which dereived from IVF blastocyst.

growth_protocol: ORMES9B were grown at 37oC, 3% CO2, 5%O2 and 92% N2 upon mitotically inactivated mouse embryonic fibroblast (MEF) feeder cells in Dulbecco modified Eagle medium (DMEM/F12) that was supplemented with 15% fetal bovine serum (FBS), 0.1 mM B-mercaptoethanol, 1% nonessential amino acids, 2 mM L-glutamine, with the pH adjusted to 7.2 with NaOH. Medium was changed daily and ESC colonies were split every 5-7 days by manual disaggregation and replating collected cells onto dishes with fresh feeder layers.

treatment_protocol: ORMES9B established from rhesus monkey IVF blastocyst generated by the application of the assisted reproductive technologies at the Oregon National Primate Research Center. RNA were isolated from only nice undifferentiated colonies passage no.14.


title: colon VC 2 day DSS rep3

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 2 day of DSS treatment, replicate 3


title: colon VC 2 day DSS rep5

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 2 day of DSS treatment, replicate 5


title: C2C12 NegControl IgG, rep 2

city: Newark

first: Ju Youn

last: Lee

address: 185 South Orange Ave. MSB-E501

institute: UMDNJ-New Jersey Medical School

description: This sample was negative IP

hyb_protocol: 100ng of total RNA for immunoprecipitation arrays were used to generate labeled cDNA fragments for hybridization to Mouse Affymetrix Gene 1.0 ST Arrays following the manufacturer’s protocol (GeneChipTM WT cDNA Synthesis Kit #900652 and #900720).

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000G

data_processing: Transcripts whose probe sets with detection above background (DABG) P-value < 0.05 in at least 2 out of 3 replicates at the 0 min time point were considered expressed and used for subsequent analyses. All probe set values were normalized to the 5th percentile value of all probe sets on the same array.

source_name: C2C12 Negative IP(IgG)

label_protocol: Biotinylated DNA probes were prepared according to Whole Transcript Sense Target Labeling Manual (Affymetrix)

growth_protocol: C2C12 cells were obtained from ATCC (CRL-1772). These cell lines were cultured in DMEM with 10% FBS, 10 U/ml penicillin, 10 µg/ml streptomycin, and 1g/ml puromycin.  The cells were maintained below 70% confluency to prevent differentiation.

extract_protocol: Cells were collected in Trizol™ (Invitrogen) at the indicated time points following the incubation and total RNA was prepared according to the manufacturers instructions.  RNA concentration, purity, and quality were determined via Bioanalyzer (Agilent).

treatment_protocol: Immunoprecipitates were isolated by incubating 100µl of cleared lysate with 7µl of normal IgG (Santa Cruz sc-3877) or αCUGBP1 antibody (monoclonal 3B1) for 1 hour on ice. Following brief centrifugation at 4°C, the reaction was transferred to 100µl of a 10% slurry of Protein-G sepharose beads (Sigma) in NT-2 buffer (50mM Tris pH7.4, 150mM NaCl, 1mM MgCl2, 0.05% Nonidet P-40) and rocked for 1 hour at 4˚C. Beads were washed twice with 250µl of NT-2 buffer, transferred to a micro-spin column (Pierce) and washed four more times with 200L of NT-2 buffer.

tag: antibody

value: normal IgG

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog #

value: proliferating C2C12 (LKO-1) cells (<70% confluency)


title: colon VC 2 day DSS rep2

source_name: colonic mucosa, PPARg null epithelial cells (VC+), 2 day of DSS treatment, replicate 2