title: Prostate_obstruction_Eviprostat_rep2

city: Tsukuba

first: Mitsuhiro

last: Tagaya

state: Ibaraki

address: 3-14-1 Sakura

department: Discovery Research Laboratories

institute: Nippon Shinyaku co.,ltd.

description: Biological replicate 2 of 3. Partial bladder outlet obstruction. Treated twice a day with 18 mg/kg Eviprostat for five days.

hyb_protocol: Blocking Agent and Fragmentation Buffer (Agilent Gene Expression Hybridization kit) were added to the samples, and incubated at 60 C for 30min. GE Hybridization Buffer HI-RPM was added, and samples were applied to microarrays enclosed in Agilent 4x44K gasket slides. Slides were incubated at 65 C for 1 day, and washed sequential with Agilent Gene Expression Wash Pack, following manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2505A scanner. Images were quantified using Agilent Feature Extraction Software (v 9.5.1.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: obstruction, Eviprostat

label_protocol: Total RNA from the pooled prostate tissue from group 1 (1500 ng) and groups 2-4 (300 ng each) was reverse transcribed into cDNA with MMLV-RT and oligo dT-promoter primer, and the resulting cDNA was used for the synthesis of fluorescently labeled cRNA sample probes with the Agilent Quick Amp Labeling Kit, following manufacturer's protocol.

extract_protocol: Total RNA extracted using Sepasol-RNA I (Nacalai Tesque) following manufacturer's protocol.

value: Male

value: 10 week

tag: tissue

value: Prostate

source_name: sham, vehicle


title: Prostate_obstruction_Eviprostat_rep3

status: Public on Jul 21 2009

type: RNA

country: Japan

description: Biological replicate 3 of 3. Partial bladder outlet obstruction. Treated twice a day with 18 mg/kg Eviprostat for five days.

molecule: total RNA

tag: gender

tag: age


title: poly(I:C) - 12 hr - repeat 1 - mAdbID:93922

city: Frederick

first: Debra

last: Tross

state: MD

country: USA

institute: NCI

description: mAdb experiment ID: 93922

hyb_protocol: Hybridization Protocol Other: Hybridization was performed to 36K mouse 60 mer oligonucleotide array slides (NCI Mouse Array Set Mm MEEBO v1.3) at 42ƒÏC for 18 h in a MAUI hybridization system (BioMicro Systems, Salt Lake City, UT) followed by washing, centrifugation and air drying (Klaschik et al., 2007).

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4785;; 3.55907 Temperature: 27.4255

data_processing:
Data Processing Protocol
Calculation Method: An intensity filter of 120 minimum was used for both red and green channels. Lowess normalization was applied. Data missing from 50% of the arrays was filtered out. Ratios were log base 2 transformed.

organism: Mus musculus

source_name: Universal Mouse Reference RNA

label_protocol:
Cy3 Sample Labeling Protocol
Other: Synthesized cDNA samples were purified using a MinElute PCR Purification Kit (Qiagen Sciences, Valencia, CA) and labeled with Cy3 (universal reference cDNA) as described previously (Klaschik et al., 2007).

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: cell type

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: poly(I:C) Treated - 12 hours

label_protocol:
Cy5 Sample Labeling Protocol
Other: Synthesized cDNA samples were purified using a MinElute PCR Purification Kit (Qiagen Sciences, Valencia, CA) and labeled with Cy5 (sample cDNA) as described previously (Klaschik et al., 2007).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was extracted from resting and stimulated RAW 264.7 cells using TRIzol Reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: small molecule
Agent: poly(I:C)
Treatment dose: 32 ug/ml
Treatment time: 12 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 32 ug/ml poly(I:C) for 12 hr.

tag: cell line

value: Macrophages


title: Untreated - 4 hr - repeat 1 - mAdbID:92403

description: mAdb experiment ID: 92403

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48735;; 3.57311 Temperature: 27.3644

source_name: Untreated - 4 hours


title: WT1

status: Public on Jul 22 2009

city: New Haven

first: Rachel

last: Rutishauser

state: CT

address: 1 Gilbert St., TAC Building

department: Immunobiology

institute: Yale University

description: WT replicate 1

hyb_protocol: Hybridizations of biotinylated cRNA to Illumina Sentrix MouseRef-8 BeadChip v1.0 Expression BeadChips (Illumina, San Diego, CA) were perfomed at the Genomic Resource Center at the Rockefeller University as per the manufacturer's protocol.

scan_protocol: BeadChips were scanned according to the Manufacturer's protocol.

data_processing: The data were normalized using quantile-quantile normalization algorithm implemented in Affy microarray analysis package for Bioconductor (Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England) 19, 185-193 (2003).)

label: biotin

source_name: day 8 LCMV tetramer+ CD8+ T cells; FACS sorted

label_protocol: 0.1 mg of total RNA was amplified and biotinylated cRNA was generated by using the IlluminaRNA Amplification Kit (Ambion, Austin, TX). RNA was analyzed for integrity with an Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Mice raised in specific-pathogen free conditions with and experiments were performed with approved Institutional Animal Care and Use Committee protocols.

extract_protocol: RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) followed by Rneasy mini elute Kit (Qiagen, Valencia, CA).

treatment_protocol: Mice were infected with 2x10^5 PFU LCMV-Armstrong. Splenocytes were harvested 8 days later, stained with an antibody to CD8 and Class I MHC tetramers (DbGP33-41 and DbNP396-404), and sorted by FACS.

value: spleen

tag: genotype

value: wildtype

tag: replicate


title: poly(I:C) - 4 hr - repeat 3 - mAdbID:92661

description: mAdb experiment ID: 92661

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48064;; 3.56792 Temperature: 28.0663

source_name: poly(I:C) Treated - 4 hours

treatment_protocol:
Treatment type: small molecule
Agent: poly(I:C)
Treatment dose: 32 ug/ml
Treatment time: 4 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 32 ug/ml poly(I:C) for 4 hr.


title: Okra 7 dpa rep 1 versus Pima 7 dpa rep 1

city: Canberra

first: Yves

last: Al-Ghazi

state: ACT

address: Clunies Ross

department: Plant Industry

country: Australia

institute: CSIRO

description: Fibres dissected from seed in liquid N2

hyb_protocol: Slides were pre hybridized in 50 mL of prehybridation buffer (25 mL formamide, 12.5 mL 20XSSC, 500 μL 10% SDS, 5 mL 10% BSA, 7mL H2O) for 45 min at 42C. Probes were resuspended in a (10:10:10:6:4) mix of formamide, 20X SSC, 2 μg/mL salmon sperm, H2O, 1%SDS and heated 5 minutes at 95C before transfer onto microarray slide. After 24h of hybridization, slides were washed successively for 2 minutes of 0.1% SDS, 2X SSC; 10 minutes of 0.1%SDS, 0.1X SSC; and four washes of 0.1X SSC for 2 minutes each.

scan_protocol: Slides were scanned with an Axon GenePix 4000 and tiff files were analysed with Genepix Pro 6 software.

data_processing: GPR files were loaded into Bioconductor R and processed with the Limma (Wettenhall & Smyth 2004) package. All functions mentioned, including “Normalisation”, “Single channel” and “Pair wise comparisons” are described in the limma user guide for Bioconductor v 1.9.

molecule: polyA RNA

organism: Gossypium hirsutum

source_name: Okra 7 dpa rep 1

label_protocol: 150 μg of total RNA were purified for polyA+ messenger RNA isolation (Qiagen Oligotex mRNA kit) and 0.5-1 μg of polyA+ RNA was used for microarray labelling as described in Schenk (Schenk et al. 2000).

growth_protocol: G. hirsutum var. Siokra V-15, and G. barbadense var. Pima S7 plants were grown in a glasshouse with temperature of 30oC /22oC (16h day/8h night) natural lighting completed with artificial lamps. Flower buds where tagged at the day of anthesis and the corresponding bolls where harvested at various times after that day and snap frozen in liquid nitrogen.

extract_protocol: RNA preparation was carried out according to Wan and Wilkins (1994), and their Buffer E was used for all extractions. Up to two grams of ground liquid N2 frozen fibres were incubated in 50 mL falcon tubes with 20 mL of extraction buffer supplemented with 5 mg of proteinase K and 10 mM DTT for 90 min at 42C and mild agitation. Following incubation, 4 mL of cold 1N KCl was added and incubated 1h on ice. The resulting precipitate was decanted 15 min at 3000 g. The supernatant (around 20 mL) was filtered through miracloth and precipitated overnight with 25 mL of 4 M LiCl at 4C.  RNAs were pelleted at 13000 g for 30 minutes and rinsed twice with cold 2M LiCl. RNA pellets were re-suspended in 9 mL ultrapure water for 5 min on ice. A last step of protein precipitation with 1 mL of  2 M KAc (pH 5.5) for 10 minutes on ice and  centrifugation at 13000 g for 15 minutes allowed the recovery of clean RNA (10 mL) that were precipitated with 11 mL of isopropanol. The clean RNAs were centrifuged 30 min and 13000 g, rinsed with 80% ethanol and pellets dried for 5 min at room temperature. RNA were re-suspended in 500 μL of ultra pure water, ran on electrophoresis gel and measured at 260 and 280 nm in spectrophotometer for quality assessment.

treatment_protocol: Bolls were harvested at 7, 11and 21 day post anthesis.

tag: Age

tag: Tissue

value: Fibre

tag: Gossypium hirsutum Okra v15

organism: Gossypium barbadense

source_name: Pima 7 dpa rep 1

tag: Gossypium barbadense Pima S7


title: Prostate_sham_Eviprostat_rep3

description: Biological replicate 3 of 3. Sham operation. Treated twice a day with 18 mg/kg Eviprostat for five days.

source_name: sham, Eviprostat


title: Prostate_obstruction_Eviprostat_rep1

description: Biological replicate 1 of 3. Partial bladder outlet obstruction. Treated twice a day with 18 mg/kg Eviprostat for five days.


title: WT-OVX-E2-3

type: other

city: bukyo-ku

first: kaoru

last: yamagata

state: Tokyo

address: yayoi 1-1-1

institute: university of tokyo

description: E2 treatment of ovariectomized wild type mouse

hyb_protocol: A 3x miRNA Hybridization Buffer (Ambion) was added to the fluorescently labeled miRNAs and the solution was heated at 95ºC for 3 min.  Slides were hybridized form 12 to 16 h at 42 ºC in sealed cassettes using a water bath. Following hybridization, the slides were washed and dried prior to a high-resolution scan.

scan_protocol: Scan on a GenePix 4000B (Axon Instruments, CA, USA).  Raw data were normalized and analyzed using Array-Pro Analyzer Version 4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA).

data_processing: We used Array-Pro Analyzer Ver4.5 (Media Cybernetics, Inc., Silver Spring, MD, USA) to determine the signal intensity of each spot and its local background on microarrays.  We calculated net intensity by subtracting the mean intensity of all pixels within the local background area from the mean intensity of all pixels within the spot areas.

molecule: other

source_name: uterus from ovariectomized and E2 treated wild type mouse

label_protocol: mirVanaTM miRNA Labeling Kit (Ambion) and amine-reactive dyes as recommended by the manufacturer.

extract_protocol: To isolate miRNA fractions from total RNA, 100μｇ total RNA was fractionated and cleaned up with the flashPAGETM fractionator System and reagents (Ambion) per the manufacturer’s recommendation.

treatment_protocol: At 15 week old, female mice were ovariectomized, and after one week, estradiol (E2) was delivered at a concentration of 0.050 mg/kg body weight/day. 24 hours after chemical treatment, uteruses were dissected.

tag: Strain

tag: Gender

value: female

value: the uterus


title: WT2

description: WT replicate 2


title: Okra 7 dpa rep 3 versus Pima 7 dpa rep 3

description: Fibres dissected from seed in liquid N2

source_name: Okra 7 dpa rep 3

source_name: Pima 7 dpa rep 3


title: Okra 7 dpa rep 2 versus Pima 7 dpa rep 2

description: Fibres dissected from seed in liquid N2

source_name: Okra 7 dpa rep 2

source_name: Pima 7 dpa rep 2


title: Prostate_obstruction_vehicle_rep3

description: Biological replicate 3 of 3. Partial bladder outlet obstruction. Treated twice a day with vehicle (0.1% (w/v) Tween 80) for five days.

source_name: obstruction, vehicle


title: Prostate_obstruction_vehicle_rep2

description: Biological replicate 2 of 3. Partial bladder outlet obstruction. Treated twice a day with vehicle (0.1% (w/v) Tween 80) for five days.


title: Prostate_obstruction_vehicle_rep1

description: Biological replicate 1 of 3. Partial bladder outlet obstruction. Treated twice a day with vehicle (0.1% (w/v) Tween 80) for five days.


title: poly(I:C) - 12 hr - repeat 2 - mAdbID:93898

description: mAdb experiment ID: 93898

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4846;; 3.48674 Temperature: 24.8009


title: 2L3(13581600)

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: no additional information

hyb_protocol: 1. Mark the slide with a diamond pen to indicate the array position. 2. Place slide face down on a chamber filled with 3x SSC and rehydrate for 5-10 min. Immediatly dry the array on a 100C heat block for 2-3 sec. 3. Place slide in glass chamber and prehybridize arrays in 6x SSC, 0.5% SDS, 1%BSA at 42C water bath for at least 1h. 4. Wash with H20 and denaturate the slides for 2 min by placing the slide in boiling water. Dry the slide. 5. Prepare the probe for hybridisation as follows:  -Resuspend the probe in 25 ul hybridization buffer containing 50% dionized formamide, 6x SSC, 0.5% SDS and 5x Denhardt`s.  -Tab the bottom of the tube to dissolve the probe. Try to avoid generating bubbles.  -Denaturate probe at 95C for 2min. Allow the probe to cool down at RT. 6. Wait for the probe to cool down and pipet onto an inverted cover slip, with the spots facing the cover slip and allow the probe to smoothly spread allover the array. Avoid making bubbles but don`t worry too much about the very small ones. Lift the slide up, turn it into its normal position and transfer into hybridisation chamber. 7. Pipet 2 drops of 3xSSC into the special trays of the chamber to keep it humidified. Seal the hybridisation chamber and place it in a 42C water bath for 12-16h. 8. Prepare the following washing solutions:  I - 0.1xSSC, 0.1% SDS  II - 0.1xSSC Don`t use distilled or millipore water for washing buffers. Use just de-ionised. 9. Remove slides from the HybChfmber and submerge them in washing solution I until the cover slip falls off. It may be necessary to aggressivly shake the slide a few times to remove the cover slip. Be careful not to scratch the array. 10. Place the slides in slide rack and transfer in a glass chamber containing washing solution I. Wash for 10 min with continuous shaking. Transfer into fresh solution I and wash for another 5 min. Transfer into solution II and wash for 5 min. Wash in fresh solution II for another 5 min. All washes are carried out at RT. Do not wash  with water. 11. Spin to dry the arrays by either placing them in falcontubes or by spinning the slidee rack, if you have the appropriate centrifuge buckets. 12 Scan the arrays.

scan_protocol: The slide was scanned on the ScanArray Lite instrument (Perkin Elmer) at 10um resolution.

data_processing: Data was processed using TIGR Spotfinder 3.1.1 (Circle segmentation method, QC filter on, Bcg correction off). Then it was normalised with TIGR MIDAS v2.19 program (LocFit normalisation, SD regularisation)

organism: Drosophila melanogaster

source_name: reference, mixture of rnas from all stages

label_protocol: Labeling was perfomed using Invitrogen SuperScript Direct cDNA Labeling System protocol

extract_protocol:
For RNA extraction protocol from BGRC webcite was used:
1.  To 50 mg frozen flies (or frozen fly tissue) in a 1.5 ml microcentrifuge tube add 1 ml Trizol reagent and homogenize immediately with a disposable plastic pestle.
(Note: Work quickly.  RNA is protected from RNase in the frozen tissue and in the phenolic solution but is susceptible to degradation during the homogenization process)
2.  Incubate at room temperature for 5 minutes.
3.  Centrifuge at 12,000 rcf for 10 minutes at 4oC to pellet insoluble debris such as exoskeleton.
4.  Transfer the supernatant to a new microcentrifuge tube.  (Note:  Take great care not to take pellet or fat layer, which can lead to phenol contamination of the aqueous layer when the phenol becomes trapped in fat micelles.)
5.  Add 200 ul of Chloroform (no isoamyl alcohol) to each tube.
6.  Shake vigorously by hand (do not vortex which will lead to DNA Contamination).
7.  Incubate tubes at room temperature for 3 minutes.
8.  Centrifuge at 10,000 rcf for 15 minutes at 4oC.
9.  Transfer upper aqueous phase (~0.6 ml) to a fresh RNAse-free microcentrifuge tube.  (Note: Make sure to avoid RNase contamination from this point on.)
10.  Add 0.5 ml isopropanol
11.  Incubate at room temperature for 10 minutes.
12.  Centrifuge at 12,000 rcf for 10 minutes at 4oC.
13.  Remove the supernatant and wash the pellet with 1ml 75% ethanol.
14.  Centrifuge at 7,500 rcf for 5 minutes. at 4oC.
15.  Remove the supernatant.
16.  Centrifuge briefly and carefully remove the last of the supernatant with a micropipette.
17.  Air dry for 10 minutes.  (Note:  Do not dry under vacuum or heat.)
18.  Resuspend the pellet in 100 ul RNase-free water.
19.  Quantify a 1/100 dilution of the RNA on spectrophotometer.

tag: reference

value: mixture of rnas from all stages

tag: development stage

value: 0-1h embryos

value: 5-6h embryos

value: 11-12h embryos

value: 1st instar larvae

value: 2nd instar larvae

value: 3rd instar larvae

value: 0-1h prepupae

value: 13-14 h pupae

value: 3 days adult males

value: 3 days adult females


title: Prostate_sham_Eviprostat_rep1

description: Biological replicate 1 of 3. Sham operation. Treated twice a day with 18 mg/kg Eviprostat for five days.

value: Male

value: 10 week

value: Prostate


title: CpG ODN and poly(I:C) - 4 hr - repeat 2 - mAdbID:92149

description: mAdb experiment ID: 92149

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48735;; 3.52397 Temperature: 25.8995

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: CpG ODN and ploy(I:C) Treated - 4 hours

treatment_protocol:
Treatment type: small molecule
Agent: CpG Oligonucleotide
Treatment dose: 3.2 ug/ml
Treatment time: 4 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 3.2 ug/ml CpG ODN for 4 hr.
Treatment type: small molecule
Agent: poly(I:C)
Treatment dose: 32 ug/ml
Treatment time: 4 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 32 ug/ml poly(I:C) for 4 hr.

value: Macrophages


title: Okra 21 dpa rep 3 versus Pima 21 dpa rep 3

description: Fibres dissected from seed in liquid N2

source_name: Okra 21 dpa rep 3

value: Fibre

source_name: Pima 21 dpa rep 3


title: CpG ODN - 4 hr - repeat 3 - mAdbID:92658

description: mAdb experiment ID: 92658

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48766;; 3.49742 Temperature: 25.7775

source_name: Universal Mouse Reference RNA

source_name: CpG ODN Treated - 4 hours

treatment_protocol:
Treatment type: small molecule
Agent: CpG Oligonucleotide
Treatment dose: 3.2 ug/ml
Treatment time: 4 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 3.2 ug/ml CpG ODN for 4 hr.


title: CpG ODN and poly(I:C) - 4 hr - repeat 1 - mAdbID:91769

description: mAdb experiment ID: 91769

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4904;; 3.52153 Temperature: 25.6859


title: poly(I:C) - 4 hr - repeat 1 - mAdbID:91768

description: mAdb experiment ID: 91768

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47026;; 3.54961 Temperature: 28.1274


title: Okra 11 dpa rep 2 versus Pima 11 dpa rep 2

description: Fibres dissected from seed in liquid N2

source_name: Okra 11 dpa rep 2

source_name: Pima 11 dpa rep 2


title: Prostate_sham_vehicle_rep1

description: Biological replicate 1 of 3. Sham operation. Treated twice a day with vehicle (0.1% (w/v) Tween 80) for five days.

source_name: sham, vehicle


title: Prostate_sham_vehicle_rep2

description: Biological replicate 2 of 3. Sham operation. Treated twice a day with vehicle (0.1% (w/v) Tween 80) for five days..


title: 1E11-12(13582028)

description: no additional information

value: mixture of rnas from all stages


title: Okra 21 dpa rep 1 versus Pima 21 dpa rep 1

description: Fibres dissected from seed in liquid N2

source_name: Okra 21 dpa rep 1

source_name: Pima 21 dpa rep 1


title: Prostate_sham_Eviprostat_rep2

description: Biological replicate 2 of 3. Sham operation. Treated twice a day with 18 mg/kg Eviprostat for five days.

source_name: sham, Eviprostat


title: Okra 11 dpa rep 1 versus Pima 11 dpa rep 1

description: Fibres dissected from seed in liquid N2

source_name: Okra 11 dpa rep 1

source_name: Pima 11 dpa rep 1


title: CpG ODN - 4 hr - repeat 2 - mAdbID:92397

description: mAdb experiment ID: 92397

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.47209;; 3.45988 Temperature: 24.8619


title: Pima 7 dpa rep 3 versus Okra 7 dpa rep 3

description: Fibres dissected from seed in liquid N2

source_name: Pima 7 dpa rep 3

source_name: Okra 7 dpa rep 3


title: CpG ODN and poly(I:C) - 4 hr - repeat 3 - mAdbID:92147

description: mAdb experiment ID: 92147

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4904;; 3.56731 Temperature: 27.8222


title: Okra 21 dpa rep 2 versus Pima 21 dpa rep 2

description: Fibres dissected from seed in liquid N2

source_name: Okra 21 dpa rep 2

source_name: Pima 21 dpa rep 2


title: Prostate_sham_vehicle_rep3

description: Biological replicate 3 of 3. Sham operation. Treated twice a day with vehicle (0.1% (w/v) Tween 80) for five days..


title: Okra 11 dpa rep 3 versus Pima 11 dpa rep 3

description: Fibres dissected from seed in liquid N2

source_name: Okra 11 dpa rep 3

source_name: Pima 11 dpa rep 3


title: monoGMP biological replicate 2

city: Berkeley

first: Russell

last: Vance

state: CA

address: 415 Life Science Addition

institute: UC Berkeley

description: monoGMP biological replicate 2

hyb_protocol: Labeled aRNA probe was hybridized in 3X SSC, 25mM HEPES pH 7, 0.25%SDS for 36h at 63°C.  Slides were washed and dried before scanning.

scan_protocol: Scanned on a GenePix 2000 Scanner.

data_processing: Log2 of Cy3/Cy5 representing log2(test/reference).  These values were generated and normalized in GenePix Pro.  Ratio-based normalization was performed by analyzing "good" features and setting the average ratio of medians (Cy5/Cy3) equal to 1. Good features were defined as unsaturated features with a foreground-minus-background value of at least 350, in either channel. Features that were present in at least 1 microarray were selected using Acuity software and were included in the data table.

source_name: B6 bone marrow derived macrophages

label_protocol: RNA was amplified using the Ambion Amino Allyl MessageAmp Kit to incorporate amino-allyl-UTP.  aRNA was labeled with Cy3 or Cy5 for 1h.

growth_protocol: B6 bone marrow derived macrophages were grown in RPMI + 10%FBS, 10%M-CSF, glutamine, and antibiotic.

extract_protocol: Ambion RNaqueous Kit was used to extract total RNA.

treatment_protocol: Macrophages were transfected with the compounds indicated above using Lipofectamine 2000.  RNA was harvested 6h post transfection.

tag: treatment

value: transfected with monoGMP

source_name: total RNA pooled from each experimental sample of B6 mouse macrophages


title: Untreated - 4 hr - repeat 2 - mAdbID:91770

description: mAdb experiment ID: 91770

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48857;; 3.54534 Temperature: 26.632

source_name: Universal Mouse Reference RNA

source_name: Untreated - 4 hours


title: CpG ODN - 4 hr - repeat 1 - mAdbID:91767

description: mAdb experiment ID: 91767

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49528;; 3.56182 Temperature: 27.2118

source_name: CpG ODN Treated - 4 hours


title: CpG ODN - 12 hr - repeat 3 - mAdbID:91714

description: mAdb experiment ID: 91714

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49315;; 3.47392 Temperature: 25.2281

source_name: CpG ODN Treated - 12 hours

treatment_protocol:
Treatment type: small molecule
Agent: CpG Oligonucleotide
Treatment dose: 3.2 ug/ml
Treatment time: 12 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 3.2 ug/ml CpG ODN for 12 hr.


title: Mleprae Biological Rep 3

city: Baton Rouge

first: Diana

middle: L

last: Williams

state: LA

address: Skip Bertman Dr.

department: Laboratory Res Branch

institute: HRSA, BPHC, NHDP

description: Total RNA was labeled with Cy3 and hybridized to M. leprae whole genome DNA microarray

hyb_protocol: Hybridizations were performed at 42C for 12 hrs.

scan_protocol: Each DNA microarray slide was scanned using a BioRad Versarray scanner.  Data was normalized and exported following scanning.

data_processing: Mean channel intensities and background intensity for each feature on the DNA microarray was used to calculate the signal to noise ratio for each feature. The values are the signal to noise ratio for each feature on the DNA microarray representing a open reading frame.

organism: Mycobacterium leprae

source_name: Infection-mouse footpad

label_protocol: Total RNA was converted to cDNA in the presence of Cy3-labeled nucleotides.

growth_protocol: M. leprae 10e7 was inoculated into the hind foot pads of BALB/C nude (nu/nu) mice and propagated for 6 months.

extract_protocol: Tissue was harvested from 4 mice (Truman R et al. Int J Lepr Other Mycob Dis 2001, 69(1):1-12) and RNA was extracted (Williams D et al. BioTechniques 2003, 35:534).

tag: host organism

value: Mus musculus

tag: host strain

value: BALB/C nude (nu/nu)

tag: host tissue

value: hind foot pads

tag: length of infection

value: 6 months


title: Mleprae Biological Rep 2


title: Mleprae Biological Rep 1


title: Pima 21 dpa rep 1 versus Okra 21 dpa rep 1

description: Fibres dissected from seed in liquid N2

source_name: Pima 21 dpa rep 1

source_name: Okra 21 dpa rep 1


title: Mleprae Biological Rep 4


title: Untreated - 12 hr - repeat 3 - mAdbID:91709

description: mAdb experiment ID: 91709

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48766;; 3.42051 Temperature: 23.5496

tag: cell type

source_name: Untreated - 12 hours


title: Untreated - 12 hr - repeat 1 - mAdbID:91355

description: mAdb experiment ID: 91355

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49925;; 3.55937 Temperature: 27.517

tag: cell line


title: Patient 1 Rsv1

city: chennai

first: pavithra

last: shyamsunder

address: iitm

country: India

institute: iit madras

description: no additional information

hyb_protocol: Probe was dissolved in Ocimums salt based Hybridization buffer and  was denatured at 95°C before putting on the chip for hybridization.

scan_protocol: Chips were scanned at 40, 50 and 60 PMT settings of the Affymetrix  428 scanner.

data_processing: The raw data obtained from the image analysis using the imagene software were normalized by log transformation to the base 2 followed by Median Absolute Deviation(MAD) scaling of the samples.

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

label_protocol: Five microgram of the total RNA was converted to cDNA using anchored oligo(dT) primer and box/randomized mix primer as per the  Express Art® mRNA amplification kit protocol. cDNA was purified to remove residue of the primers and the dNTPs and was kept for in vitro T7 amplification using aaUTP at 37C for 16 hrs. Amplified cRNA from the T7 amplification protocol was purified and quantified using nanodrop. 20 micrograms of the cRNA was labelled with NHS-ester Cy3 in coupling buffer for 1hr at room temperature. Labelled RNA was purified to remove  unincorporated Cy3 molecules and was quantified using nanodrop to check for the quality of the labelled probe. Probe was then fragmented in fragmentation buffer for 15 mins and was lyophilized after purification.

extract_protocol: Total RNA was isolated from Peripheral Blood Mononuclear Cells (PBMCs) of normal individuals (control) and patients. RNA was isolated using Tri reagent and quantified by measuring absorbance at 260nm.

tag: disease state

value: Fanconi anemia

tag: tissue

value: Peripheral blood

tag: age

tag: sex

value: M


title: Pima 21 dpa rep 2 versus Okra 21 dpa rep 2

description: Fibres dissected from seed in liquid N2

scan_protocol: Slides were scanned with an Axon GenePix 4000 and tiff files were analysed with Genepix Pro 6 software.

tag: Age

tag: Tissue

tag: Gossypium hirsutum Okra v15


title: CpG ODN and poly(I:C) - 12 hr - repeat 3 - mAdbID:91712

description: mAdb experiment ID: 91712

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4843;; 3.47209 Temperature: 24.1295

source_name: CpG ODN and ploy(I:C) Treated - 12 hours

treatment_protocol:
Treatment type: small molecule
Agent: CpG Oligonucleotide
Treatment dose: 3.2 ug/ml
Treatment time: 12 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 3.2 ug/ml CpG ODN for 12 hr.
Treatment type: small molecule
Agent: poly(I:C)
Treatment dose: 32 ug/ml
Treatment time: 12 hours
In-vitro treatment: RAW 264.7 cells were cultured for 5 days in DMEM supplemented with 10% FCS, 50 U/ml penicillin, 50 ug/ml streptomycin, and 1mM sodium pyruvate at 37C in a 5% CO2 in air incubator. Cells were washed, transferred into new flasks, and rested for 16 hr before being stimulated with 32 ug/ml poly(I:C) for 12 hr.


title: Patient 2  Rsvf2

description: no additional information

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: F


title: Pima 11 dpa rep 1 versus Okra 11 dpa rep 1

description: Fibres dissected from seed in liquid N2

source_name: Pima 11 dpa rep 1

tag: Gossypium barbadense Pima S7

source_name: Okra 11 dpa rep 1


title: Pima 11 dpa rep 3 versus Okra 11 dpa rep 3

description: Fibres dissected from seed in liquid N2


title: Pima 7 dpa rep 1 versus Okra 7 dpa rep 1

description: Fibres dissected from seed in liquid N2

source_name: Pima 7 dpa rep 1

source_name: Okra 7 dpa rep 1


title: CpG ODN - 12 hr - repeat 1 - mAdbID:91354

description: mAdb experiment ID: 91354

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48949;; 3.57097 Temperature: 27.4865


title: Pima 21 dpa rep 3 versus Okra 21 dpa rep 3

description: Fibres dissected from seed in liquid N2

source_name: Pima 21 dpa rep 3

source_name: Okra 21 dpa rep 3


title: CpG ODN and poly(I:C) - 12 hr - repeat 1 - mAdbID:91589

description: mAdb experiment ID: 91589

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48033;; 3.46294 Temperature: 23.5191


title: Untreated - 12 hr - repeat 2 - mAdbID:91592

description: mAdb experiment ID: 91592

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4904;; 3.52733 Temperature: 24.16


title: Normal

description: no additional information

value: control


title: Pima 11 dpa rep 2 versus Okra 11 dpa rep 2

description: Fibres dissected from seed in liquid N2

source_name: Pima 11 dpa rep 2

source_name: Okra 11 dpa rep 2


title: Pima 7 dpa rep 2 versus Okra 7 dpa rep 2

description: Fibres dissected from seed in liquid N2

source_name: Pima 7 dpa rep 2

source_name: Okra 7 dpa rep 2


title: poly(I:C) - 4 hr - repeat 2 - mAdbID:92400

description: mAdb experiment ID: 92400

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48338;; 3.54228 Temperature: 26.632

source_name: Universal Mouse Reference RNA

source_name: poly(I:C) Treated - 4 hours


title: TNF stimulated synovial fibroblasts (0h), RA patient EB221

status: Public on Jul 20 2009

city: Hannover

first: René

last: Huber

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute for Clinical Chemistry

country: Germany

institute: Hannover Medical School

description: see publication for details

hyb_protocol: according to supplier´s instructions, Affymetrix

scan_protocol: by laser scanning (Hewlett Packard gene scanner)

data_processing: background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix)

source_name: synovial membrane patient EB221 (rheumatoid arthritis)

growth_protocol: Synovial fibroblasts were cultured over 4 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES, and 10% FCS (all from PAA Laboratories, Coelbe, Germany).

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier's recommendation.

treatment_protocol: At the end of the fourth passage, the SFB were stimulated by 10 ng/ml TGFβ or TNFα (PeproTech, Hamburg, Germany) in serum-free DMEM for 0, 1, 2, 4, and 12 h. At the end of each time point, medium was removed and the cells were digested with trypsin/versene (0.25%). Following centrifugation and washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C.

value: f

tag: rheumatoid arthritis


title: TGF stimulated synovial fibroblasts (12h), RA patient EB221

description: see publication for details

label_protocol: according to supplier´s instructions, Affymetrix


title: TGF stimulated synovial fibroblasts (0h), RA patient EB221

description: see publication for details


title: TNF stimulated synovial fibroblasts (1h), RA patient EB221

description: see publication for details


title: TNF stimulated synovial fibroblasts (2h), RA patient EB221

description: see publication for details


title: TGF stimulated synovial fibroblasts (4h), RA patient EB221

description: see publication for details


title: TNF stimulated synovial fibroblasts (12h), RA patient EB221

description: see publication for details


title: TNF stimulated synovial fibroblasts (4h), RA patient EB221

description: see publication for details


title: TGF stimulated synovial fibroblasts (2h), RA patient EB221

description: see publication for details


title: CpG ODN and poly(I:C) - 12 hr - repeat 2 - mAdbID:91591

description: mAdb experiment ID: 91591

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49986;; 3.52306 Temperature: 25.2892


title: TNF stimulated synovial fibroblasts (0h), RA patient EB220

description: see publication for details

source_name: synovial membrane patient EB220 (rheumatoid arthritis)


title: TGF stimulated synovial fibroblasts (1h), RA patient EB221

description: see publication for details


title: TNF stimulated synovial fibroblasts (1h), RA patient EB220

description: see publication for details


title: TGF stimulated synovial fibroblasts (1h), RA patient EB220

description: see publication for details


title: TGF stimulated synovial fibroblasts (0h), RA patient EB220

description: see publication for details


title: TNF stimulated synovial fibroblasts (2h), RA patient EB220

description: see publication for details


title: TGF stimulated synovial fibroblasts (2h), RA patient EB220

description: see publication for details


title: TNF stimulated synovial fibroblasts (4h), RA patient EB220

description: see publication for details


title: TNF stimulated synovial fibroblasts (0h), OA patient EB205

description: see publication for details

source_name: synovial membrane patient EB205 (osteoarthritis)

tag: osteoarthritis


title: TGF stimulated synovial fibroblasts (4h), RA patient EB220

description: see publication for details


title: TNF stimulated synovial fibroblasts (12h), RA patient EB220

description: see publication for details


title: TNF stimulated synovial fibroblasts (4h), OA patient EB205

description: see publication for details


title: TNF stimulated synovial fibroblasts (12h), OA patient EB205

description: see publication for details


title: TGF stimulated synovial fibroblasts (0h), OA patient EB205

description: see publication for details


title: TNF stimulated synovial fibroblasts (1h), OA patient EB205

description: see publication for details


title: TNF stimulated synovial fibroblasts (4h), OA patient EB202

description: see publication for details

source_name: synovial membrane patient EB202 (osteoarthritis)

treatment_protocol: At the end of the fourth passage, the SFB were stimulated by 10 ng/ml TGFβ or TNFα (PeproTech, Hamburg, Germany) in serum-free DMEM for 0, 1, 2, 4, and 12 h. At the end of each time point, medium was removed and the cells were digested with trypsin/versene (0.25%). Following centrifugation and washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at 70°C.


title: TNF stimulated synovial fibroblasts (0h), OA patient EB202

description: see publication for details


title: TGF stimulated synovial fibroblasts (12h), RA patient EB220

description: see publication for details


title: TGF stimulated synovial fibroblasts (12h), OA patient EB205

description: see publication for details


title: TGF stimulated synovial fibroblasts (1h), OA patient EB205

description: see publication for details


title: TGF stimulated synovial fibroblasts (2h), OA patient EB202

description: see publication for details


title: TNF stimulated synovial fibroblasts (2h), OA patient EB205

description: see publication for details


title: TGF stimulated synovial fibroblasts (0h), OA patient EB202

description: see publication for details


title: TNF stimulated synovial fibroblasts (12h), OA patient EB202

description: see publication for details


title: TNF stimulated synovial fibroblasts (2h), OA patient EB202

description: see publication for details


title: TNF stimulated synovial fibroblasts (1h), OA patient EB202

description: see publication for details


title: TGF stimulated synovial fibroblasts (2h), OA patient EB205

description: see publication for details


title: TGF stimulated synovial fibroblasts (12h), OA patient EB202

description: see publication for details


title: TNF stimulated synovial fibroblasts (12h), OA patient EB190

description: see publication for details

source_name: synovial membrane patient EB190 (osteoarthritis)


title: TGF stimulated synovial fibroblasts (4h), OA patient EB202

description: see publication for details


title: TNF stimulated synovial fibroblasts (4h), OA patient EB190

description: see publication for details


title: TGF stimulated synovial fibroblasts (1h), OA patient EB202

description: see publication for details


title: BCR-ABL1 leukemia AID-negative_20080801_167

type: genomic

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description:
Mononuclear cells from peripheral blood or bone marrow.
Genomic DNA was extracted from samples, in which blast counts were higher than 80%

hyb_protocol: The SNP mapping assay was performed according to the protocol of the manufacturer (Affymetrix, Santa Clara, CA).

data_processing:
Affymetrix GeneChip Genotyping Analysis Software (GTYPE) v 4.0
Affymetrix CEL files were analyzed for genomic copy number variations using Partek® Genomic SuiteTM software (Partek GS).

label: standard

molecule: genomic DNA

source_name: Mononuclear cells from peripheral blood or bone marrow (AID-negative)

extract_protocol: DNA Blood Mini Kit (Qiagen, Valencia, CA)


title: TNF stimulated synovial fibroblasts (2h), OA patient EB190

description: see publication for details


title: BCR-ABL1 leukemia AID-negative_20080507_149

scan_protocol: The SNP mapping assay was performed according to the protocol of the manufacturer (Affymetrix, Santa Clara, CA).

tag: Mononuclear cells from peripheral blood or bone marrow.

tag: Genomic DNA was extracted from samples, in which blast counts were higher than 80%


title: TNF stimulated synovial fibroblasts (1h), OA patient EB190

description: see publication for details


title: BCR-ABL1 leukemia AID-positive_20080907_153

description: Genomic DNA was extracted from samples, in which blast counts were higher than 80%

source_name: Mononuclear cells from peripheral blood or bone marrow (AID-positive)

label_protocol: The SNP mapping assay was performed according to the protocol of the manufacturer (Affymetrix, Santa Clara, CA).


title: hepatic_exposed_P21

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

description: Further details are available in Gunnarsson et al 2009.

hyb_protocol: Chemical fragmentation of the cRNA was performed at 94°C for 35 min, using 40 mM Tris-acetat, 100 mM K-acetate and 30 mM Mg-acetat at a concentration of 1.6 µg cRNA/µl giving an average fragment length of 100 bp. Fragmented cRNA (6 µg/array) was dissolved in hybridization buffer (final concentration: 5X SSPE, 20% formamide, 0.5 m BSA/ml, 0.1X TE, 0.1 mg mouse CotI, 0.01% Tween 20). Samples were denatured at 95°C for 3 min and hybridized to the arrays at 45°C for 15 h. Arrays were washed using 6xSSPE at 25°C and 0.5xSSPE at 45°C. Fluorescent staining of the hybridized cRNA was performed by incubating the arrays with SAPE (streptavidin, R-phycoerythrin conjugate, Invitrogen, Carlsbad, USA) diluted in 6xSSPE (5 µg SAPE/ml). Signal amplification was performed using biotinylated α-streptavidin antibodies (Vector Laboratories, Burlingame, USA) followed by and additional incubation with SAPE, according to the Consecutive Signal Enhancement protocol.

scan_protocol: Signals were detected using the CCD-based camera located in the Geniom instrument and quantified using the Geniom Wizard.

data_processing: The data was imported into the statistical language R 2.7.2 (R Development Core Team, 2006, [http ://www. R-project.org]) and analyzed with Bioconductor (Gentleman et al., 2004). To remove signal bias and intensity-dependent trends, all arrays were normalized using the quantile-quantile algorithm (Bolstad et al., 2003). The resulting values was then log-transformed.

label: Biotin

organism: Oncorhynchus mykiss

source_name: hepatic, exposed, experiment 2, aquarium 2, pool 21 (F2_A2E_P21)

label_protocol: Biotinylated cRNA was prepared using the Message Amp II-Biotin Enhanced single round Amplification kit (Ambion) starting with 1 µg of total RNA and performing the in vitro transcription for 14 h.

extract_protocol: Total RNA was extracted with the Qiagen RNeasy Mini Kit and RNase-Free DNase Set or RNeasy Plus Mini Kit, following the manufacturer’s instructions (Qiagen, Hilden, Germany).

treatment_protocol: Fish were exposed for five days to water or 0.2% effluent (described in Gunnarsson 2009).

tag: gender

value: Female

value: juvenile rainbow trout. Farmed.


title: TGF stimulated synovial fibroblasts (12h), OA patient EB190

description: see publication for details


title: TGF stimulated synovial fibroblasts (4h), OA patient EB190

description: see publication for details


title: hepatic_control_P15

source_name: hepatic, control, experiment 2, aquarium 4, pool 15 (F2_A4K_P15)


title: hepatic_control_P13

source_name: hepatic, control, experiment 2, aquarium 3, pool 13 (F2_A3K_P13)


title: BCR-ABL1 leukemia AID-positive_20080507_151

data_processing: Affymetrix GeneChip Genotyping Analysis Software (GTYPE) v 4.0 Affymetrix CEL files were analyzed for genomic copy number variations using Partek® Genomic SuiteTM software (Partek GS).


title: hepatic_exposed_P18

source_name: hepatic, exposed, experiment 2, aquarium 5, pool 18 (F2_A5E_P18)


title: hepatic_control_P19

source_name: hepatic, control, experiment 2, aquarium 6, pool 19 (F2_A6K_P19)


title: BCR-ABL1 leukemia AID-positive_20080801_165


title: BCR-ABL1 leukemia AID-negative_20080111_82


title: BCR-ABL1 leukemia AID-positive_20080111_80


title: TGF stimulated synovial fibroblasts (2h), OA patient EB190

description: see publication for details


title: BCR-ABL1 leukemia AID-positive_20080801_164


title: BCR-ABL1 leukemia AID-negative_20070803_68


title: TGF stimulated synovial fibroblasts (1h), OA patient EB190

description: see publication for details


title: hepatic_exposed_P17

source_name: hepatic, exposed, experiment 2, aquarium 5, pool 17 (F2_A5E_P17)


title: BCR-ABL1 leukemia AID-positive_20071030_70


title: hepatic_control_P16

source_name: hepatic, control, experiment 2, aquarium 4, pool 16 (F2_A4K_P16)


title: TGF stimulated synovial fibroblasts (4h), OA patient EB205

description: see publication for details


title: hepatic_control_P10

source_name: hepatic, control, experiment 2, aquarium 1, pool 10 (F2_A1K_P10)


title: hepatic_exposed_P11

source_name: hepatic, exposed, experiment 2, aquarium 2, pool 11 (F2_A2E_P11)


title: TNF stimulated synovial fibroblasts (0h), OA patient EB190

description: see publication for details

treatment_protocol: At the end of the fourth passage, the SFB were stimulated by 10 ng/ml TGFβ or TNFα (PeproTech, Hamburg, Germany) in serum-free DMEM for 0, 1, 2, 4, and 12 h. At the end of each time point, medium was removed and the cells were digested with trypsin/versene (0.25%). Following centrifugation and washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at  70°C.


title: TGF stimulated synovial fibroblasts (0h), OA patient EB190

description: see publication for details


title: hepatic_exposed_P12

source_name: hepatic, exposed, experiment 2, aquarium 2, pool 12 (F2_A2E_P12)


title: BCR-ABL1 leukemia AID-negative_20070803_67


title: hepatic_exposed_P8

source_name: hepatic, exposed, experiment 1, aquarium 4, pool 8 (F1_A4E_P8)


title: hepatic_control_P9

source_name: hepatic, control, experiment 2, aquarium 1, pool 9 (F2_A1K_P9)


title: BCR-ABL1 leukemia AID-positive_20080507_147


title: TNF stimulated synovial fibroblasts (4h), RA patient EB87

description: see publication for details

source_name: synovial membrane patient EB87 (rheumatoid arthritis)


title: TGF stimulated synovial fibroblasts (12h), RA patient EB87

description: see publication for details


title: TNF stimulated synovial fibroblasts (12h), RA patient EB87

description: see publication for details


title: TGF stimulated synovial fibroblasts (4h), RA patient EB87

description: see publication for details


title: BCR-ABL1 leukemia AID-positive_20070629_38


title: BCR-ABL1 leukemia AID-negative_20070712_55


title: hepatic_control_P6

source_name: hepatic, control, experiment 1, aquarium 3, pool 6 (F1_A3K_P6)


title: BCR-ABL1 leukemia AID-positive_20070629_37


title: TNF stimulated synovial fibroblasts (2h), RA patient EB87

description: see publication for details


title: hepatic_exposed_P7

source_name: hepatic, exposed, experiment 1, aquarium 4, pool 7 (F1_A4E_P7)


title: BCR-ABL1 leukemia AID-positive_20070629_39


title: hepatic_control_P5

source_name: hepatic, control, experiment 1, aquarium 3, pool 5 (F1_A3K_P5)


title: BCR-ABL1 leukemia AID-positive_20070609_31

source_name: Mononuclear cells from peripheral blood or bone marrow (AID-positive)


title: hepatic_exposed_P4

source_name: hepatic, exposed, experiment 1, aquarium 2, pool 4 (F1_A2E_P4)


title: TGF stimulated synovial fibroblasts (1h), RA patient EB87

description: see publication for details


title: hepatic_control_P2

source_name: hepatic, control, experiment 1, aquarium 1, pool 2 (F1_A1K_P2)


title: TNF stimulated synovial fibroblasts (1h), RA patient EB87

description: see publication for details

treatment_protocol: At the end of the fourth passage, the SFB were stimulated by 10 ng/ml TGFβ or TNFα (PeproTech, Hamburg, Germany) in serum-free DMEM for 0, 1, 2, 4, and 12 h. At the end of each time point, medium was removed and the cells were digested with trypsin/versene (0.25%). Following centrifugation and washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at  -70°C.


title: BCR-ABL1 leukemia AID-positive_20070605_17


title: BCR-ABL1 leukemia AID-positive_20070712_53


title: BCR-ABL1 leukemia AID-positive_20070512_14


title: BCR-ABL1 leukemia AID-positive_20070609_30


title: TGF stimulated synovial fibroblasts (2h), RA patient EB87

description: see publication for details


title: TGF stimulated synovial fibroblasts (0h), RA patient EB87

description: see publication for details


title: TNF stimulated synovial fibroblasts (0h), RA patient EB87

description: see publication for details


title: BCR-ABL1 leukemia AID-negative_20070512_12

source_name: Mononuclear cells from peripheral blood or bone marrow (AID-negative)


title: Early serous ovarian cancer 33

status: Public on Jul 19 2009

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

institute: Niigata University

description: Serous ovarian cancer-33

hyb_protocol: Cy3-labeled cRNAs (1.5 µg) were hybridized for 17 hours at 65 degrees Celsius to an Agilent Human 1A (v2) Oligo Microarray.

scan_protocol: The hybridized microarray was washed and then scanned in Cy3 channel with the Agilent DNA Microarray Scanner (model G2565AA).

data_processing: Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver8.5 (Agilent Technologies) in the default settings.

source_name: ovarian cancer

label_protocol: Five hundred nanograms of total RNA were converted into labeled cRNA with nucleotides coupled to a cyanine 3-CTP (Cy3) (PerkinElmer, Boston, MA, USA) using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from tissue sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and examined with 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) using an RNA 6000 Nano LabChip (Agilent Technologies)

tag: Gender

value: female

value: serous ovarian cancer

tag: Stage

value: early stage


title: Early serous ovarian cancer 65

description: Serous ovarian cancer-65


title: hepatic_control_P1

source_name: hepatic, control, experiment 1, aquarium 1, pool 1 (F1_A1K_P1)


title: Advanced serous ovarian cancer 58

description: Serous ovarian cancer-58

value: advanced stage


title: Early serous ovarian cancer 35

description: Serous ovarian cancer-35


title: Early serous ovarian cancer 8

description: Serous ovarian cancer-8


title: Early serous ovarian cancer 28

description: Serous ovarian cancer-28


title: Advanced serous ovarian cancer 62

description: Serous ovarian cancer-62


title: Advanced serous ovarian cancer 56

description: Serous ovarian cancer-56


title: Early serous ovarian cancer 9

description: Serous ovarian cancer-9


title: Advanced serous ovarian cancer 55

description: Serous ovarian cancer-55


title: Advanced serous ovarian cancer 53

description: Serous ovarian cancer-53


title: BCR-ABL1 leukemia AID-positive_20070512_13


title: Advanced serous ovarian cancer 45

description: Serous ovarian cancer-45


title: Advanced serous ovarian cancer 50

description: Serous ovarian cancer-50


title: Advanced serous ovarian cancer 52

description: Serous ovarian cancer-52


title: Advanced serous ovarian cancer 64

description: Serous ovarian cancer-64


title: Advanced serous ovarian cancer 60

description: Serous ovarian cancer-60


title: Advanced serous ovarian cancer 42

description: Serous ovarian cancer-42


title: hepatic_exposed_P3

source_name: hepatic, exposed, experiment 1, aquarium 2, pool 3 (F1_A2E_P3)


title: Advanced serous ovarian cancer 10

description: Serous ovarian cancer-10


title: Advanced serous ovarian cancer 15

description: Serous ovarian cancer-15


title: Advanced serous ovarian cancer 39

description: Serous ovarian cancer-39


title: Advanced serous ovarian cancer 43

description: Serous ovarian cancer-43


title: Early serous ovarian cancer 32

description: Serous ovarian cancer-32


title: Advanced serous ovarian cancer 27

description: Serous ovarian cancer-27


title: Advanced serous ovarian cancer 51

description: Serous ovarian cancer-51


title: Early serous ovarian cancer 5

description: Serous ovarian cancer-5

source_name: ovarian cacner


title: Advanced serous ovarian cancer 23

description: Serous ovarian cancer-23


title: Advanced serous ovarian cancer 46

description: Serous ovarian cancer-46


title: Advanced serous ovarian cancer 37

description: Serous ovarian cancer-37


title: Advanced serous ovarian cancer 61

description: Serous ovarian cancer-61


title: Advanced serous ovarian cancer 25

description: Serous ovarian cancer-25


title: Advanced serous ovarian cancer 49

description: Serous ovarian cancer-49


title: Advanced serous ovarian cancer 18

description: Serous ovarian cancer-18


title: Advanced serous ovarian cancer 54

description: Serous ovarian cancer-54


title: Advanced serous ovarian cancer 36

description: Serous ovarian cancer-36


title: Advanced serous ovarian cancer 38

description: Serous ovarian cancer-38


title: Advanced serous ovarian cancer 24

description: Serous ovarian cancer-24


title: Advanced serous ovarian cancer 17

description: Serous ovarian cancer-17


title: Advanced serous ovarian cancer 20

description: Serous ovarian cancer-20


title: Advanced serous ovarian cancer 2

description: Serous ovarian cancer-2

value: ovarian cancer


title: Advanced serous ovarian cancer 6

description: Serous ovarian cancer-6


title: Advanced serous ovarian cancer 57

description: Serous ovarian cancer-54


title: Peritoneum normal 30

source_name: normal peritoneum

value: normal peritoneum


title: Advanced serous ovarian cancer 11

description: Serous ovarian cancer-11


title: Peritoneum normal 21


title: Peritoneum normal 7


title: Peritoneum normal 18


title: Peritoneum normal 23


title: Peritoneum normal 15


title: Peritoneum normal 16


title: Peritoneum normal 12


title: Advanced serous ovarian cancer 7

description: Serous ovarian cancer-7


title: Peritoneum normal 4


title: Peritoneum normal 3


title: 3T3 cells SV40LT

status: Public on Jul 18 2009

city: Hamburg

first: Genrich

last: Tolstonog

department: Department of Tumor Virology

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description:
BALB/c mouse embryo fibroblasts
Gene expression in MEFs expressing wt-p53 and stably transfected with the SV40 large T antigen-expressing vector

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_10_Apr08 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 3T3 cells, SV40 LT-expressing vector

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

extract_protocol: Total RNA was isolated from cells using TRIzol® (Invitrogen) and digested with RNase-free DNase I (Qiagen) according to the manufacturer’s instructions. The quality and integrity of the total RNA was evaluated with the Agilent 2100 Bioanalyzer and the concentration was measured using a NanoDrop spectrophotometer.

treatment_protocol: Cells were cultured in complete medium (Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum) maintained at 37°C  in a humidified atmosphere of 5% CO2.

value: 3T3 LT

tag: genotype

value: wild type


title: Patient ID 11538

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

country: United Kingdom

institute: Newcastle University

description: Patient ID 11538 DNA

hyb_protocol: as per manufacturers protocol for GPL4093 105K arrays

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and liner and LOWESS normalisation.

source_name: DNA from bone marrow

extract_protocol: Patient DNA received from regional cytogenetic laboratories. Cell-lines DNA extracted using Qiagen Blood and Tissue Kit.

value: male

tag: patient id

source_name: gender matched reference DNA

tag: reference

value: gender matched reference DNA


title: Patient ID 9534

description: Patient ID 9534 DNA

scan_protocol: as per manufacturers protocol for GPL4093 105K arrays


title: A101_100_8341_MUFA_END

status: Public on Jul 17 2009

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: no additional information

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

source_name: peripheral blood mononuclear cells, individual 8341, group HOSF, measurement after 6 months of intervention

label_protocol: The Ambion MessageAmp aRNA Amplification Kit was used to prepare labelled cRNA from 500ng of total RNA. The protocol was conducted using the reagents provided by Ambion (P/N 1751), as per the manufacturer's instructions.

growth_protocol: Healthy men and women of 65 years and over were screened and recruited according to the following exclusion criteria: current or recent (<4 weeks) use of fish oil supplements or intake of fish more than four times per week or more than 800 mg of EPA-DHA from fish per day as estimated by a fish consumption questionnaire, serious liver disease, consumption of more than 4 glasses of alcohol per day, unable to participate as judged by the responsible medical physician, allergy to fish(oil), swallowing problems, or participation in another clinical trial less than 2 months before the start of the trial or at the same time. Additionally, compliance to capsule use during a 2-week placebo run-in period had to be at least 80% on basis of self-report. 302 subjects were included in the study and detailed baseline characteristics of these participants have been described elsewhere (van de Rest, Neurology, 2008) From these participants, 111 subjects were randomly included in the present study. All subjects gave written informed consent to participate in the study and the study protocol was approved by the Medical Ethical Committee of Wageningen University, the Netherlands.

extract_protocol: Fasting venous blood samples were collected at baseline and after 26 weeks of intervention. For PBMC isolation four ml of blood was collected,in BD Vacutainer Cell Preparation Tubes with sodium citrate (BD, Breda, The Netherlands). PBMCs were isolated immediately after blood collection according to the manufacturer's instructions. Isolated PBMCs were lysed in Qiagen RLT buffer and homogenized using seringes with 0.4 mm needles, whereafter purified total RNA was isolated using Qiagen RNEasy columns according to the manufacturer's instructions.

treatment_protocol: Subjects were randomly allocated to receive a daily dose of fish oil containing a dose of 1800 mg EPA/DHA, or a high oleic acid sunflower oil (HOSF) for a period of 26 weeks (Lipid Nutrition/ Loders Croklaan, Wormerveer, the Netherlands), in addition to their regular diet. The oils were administered in six soft gelatin capsules daily, each containing 900 mg oil and 2.7 mg tocopherol as antioxidant (Banner Pharmacaps Europe B.V., Tilburg, the Netherlands). The fatty acid composition of the capsules was measured in 20 capsules taken at regular times during the study.

tag: age over 65


title: A101_099_8335_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8335, group HOSF, measurement after 6 months of intervention


title: 10-1 cells SV40LT

description:
BALB/c mouse embryo fibroblasts
Gene expression in MEFs lacking p53 and stably transfected with the SV40 large T antigen-expressing vector

source_name: 10-1 cells, SV40 LT-expressing vector

tag: cell line

value: p53 null


title: 10-1 cells empty vector

description:
BALB/c mouse embryo fibroblasts
Gene expression in MEFs lacking p53 and stably transfected with the empty vector

source_name: 10-1 cells, empty vector


title: A101_101_8348_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8348, group HOSF, measurement after 6 months of intervention


title: 3T3 cells empty vector

description:
BALB/c mouse embryo fibroblasts
Gene expression in MEFs expressing wt-p53 and stably transfected with the empty vector

source_name: 3T3 cells, empty vector


title: A101_098_8327_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8327, group HOSF, measurement after 6 months of intervention


title: A101_102A_8362_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8362, group HOSF, measurement after 6 months of intervention


title: Patient ID L1200/02

description: Patient ID L1200/02 DNA

hyb_protocol: as per Agilent protocol

scan_protocol: as per Agilent protocol

label_protocol: as per Agilent protocol


title: Patient ID 7104

description: Patient ID 7104 DNA

label_protocol: as per manufacturers protocol for GPL4093 105K arrays


title: Patient ID 6119

description: Patient ID 6119 DNA


title: Patient ID 4318

description: Patient ID 4318 DNA


title: Patient ID 7219

description: Patient ID 7219 DNA


title: A101_096_8287_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8287, group HOSF, measurement after 6 months of intervention


title: Patient ID L326/05

description: Patient ID L326/05 DNA


title: A101_095A_8240_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8240, group HOSF, measurement after 6 months of intervention


title: Patient ID 11687  from relapse sample

description: Patient ID 11687  DNA from relapse sample

value: 11687  from relapse sample


title: Patient ID L889/01

description: Patient ID L889/01 DNA


title: Patient ID 8765

description: Patient ID 8765 DNA


title: A101_094_8217_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8217, group HOSF, measurement after 6 months of intervention


title: A101_093_8194_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8194, group HOSF, measurement after 6 months of intervention


title: A101_097A_8288_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8288, group HOSF, measurement after 6 months of intervention


title: Patient ID L759/02

description: Patient ID L759/02 DNA


title: Patient ID MHH-CALL-4

description: Patient ID MHH-CALL-4 DNA


title: A101_091_8352_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8352, group HOSF, measurement after 6 months of intervention


title: Patient ID 7243

description: Patient ID 7243 DNA


title: A101_090A_8349_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8349, group HOSF, measurement after 6 months of intervention


title: A101_086_8306_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8306, group HOSF, measurement after 6 months of intervention


title: A101_092_8163_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8163, group HOSF, measurement after 6 months of intervention


title: A101_082A_8089_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8089, group HOSF, measurement after 6 months of intervention


title: A101_081_8082_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8082, group HOSF, measurement after 6 months of intervention


title: A101_083_8211_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8211, group HOSF, measurement after 6 months of intervention


title: A101_080_8058_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8058, group HOSF, measurement after 6 months of intervention


title: A101_088_8323_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8323, group HOSF, measurement after 6 months of intervention


title: A101_079_8044_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8044, group HOSF, measurement after 6 months of intervention


title: Patient ID 11687  from diagnostic sample

description: Patient ID 11687  DNA from diagnostic sample

source_name: DNA from bone marrow

value: 11687  from diagnostic sample

source_name: gender matched reference DNA


title: Patient ID MUTZ5

description: Patient ID MUTZ5 DNA


title: A101_084_8252_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8252, group HOSF, measurement after 6 months of intervention


title: A101_085_8281_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8281, group HOSF, measurement after 6 months of intervention


title: A101_078_8197_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8197, group HOSF, measurement after 6 months of intervention


title: A101_077_8183_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8183, group HOSF, measurement after 6 months of intervention


title: A101_076_8331_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8331, group EPADHA, measurement after 6 months of intervention


title: A101_075_8320_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8320, group EPADHA, measurement after 6 months of intervention


title: A101_071_8289_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8289, group EPADHA, measurement after 6 months of intervention


title: A101_073_8303_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8303, group EPADHA, measurement after 6 months of intervention


title: A101_074_8305_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8305, group EPADHA, measurement after 6 months of intervention


title: A101_070_8233_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8233, group EPADHA, measurement after 6 months of intervention


title: A101_072_8294_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8294, group EPADHA, measurement after 6 months of intervention


title: A101_069_8200_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8200, group EPADHA, measurement after 6 months of intervention


title: A101_068_8186_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8186, group EPADHA, measurement after 6 months of intervention


title: A101_062_8345_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8345, group EPADHA, measurement after 6 months of intervention


title: A101_061A_8337_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8337, group EPADHA, measurement after 6 months of intervention


title: A101_065_8364_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8364, group EPADHA, measurement after 6 months of intervention


title: A101_060_8300_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8300, group EPADHA, measurement after 6 months of intervention


title: A101_066_8037_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8037, group EPADHA, measurement after 6 months of intervention


title: A101_059_8299_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8299, group EPADHA, measurement after 6 months of intervention


title: A101_064_8363_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8363, group EPADHA, measurement after 6 months of intervention


title: A101_067_8145_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8145, group EPADHA, measurement after 6 months of intervention


title: A101_058_8282_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8282, group EPADHA, measurement after 6 months of intervention


title: A101_063_8346_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8346, group EPADHA, measurement after 6 months of intervention


title: A101_056_8253_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8253, group EPADHA, measurement after 6 months of intervention


title: A101_051_8362_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8362, group HOSF, baseline measurement


title: A101_043_8217_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8217, group HOSF, baseline measurement


title: A101_054_8030_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8030, group EPADHA, measurement after 6 months of intervention


title: A101_050_8348_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8348, group HOSF, baseline measurement


title: A101_055_8169_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8169, group EPADHA, measurement after 6 months of intervention


title: A101_045_8287_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8287, group HOSF, baseline measurement


title: A101_048_8335_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8335, group HOSF, baseline measurement


title: A101_049_8341_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8341, group HOSF, baseline measurement


title: A101_046_8288_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8288, group HOSF, baseline measurement


title: A101_047_8327_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8327, group HOSF, baseline measurement


title: A101_041_8163_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8163, group HOSF, baseline measurement


title: A101_040_8352_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8352, group HOSF, baseline measurement


title: A101_042_8194_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8194, group HOSF, baseline measurement


title: A101_057_8263_EPADHA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8263, group EPADHA, measurement after 6 months of intervention


title: A101_039A_8349_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8349, group HOSF, baseline measurement


title: A101_089_8338_MUFA_END

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8338, group HOSF, measurement after 6 months of intervention


title: A101_044_8240_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8240, group HOSF, baseline measurement


title: A101_037_8323_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8323, group HOSF, baseline measurement


title: A101_038_8338_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8338, group HOSF, baseline measurement


title: A101_033_8252_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8252, group HOSF, baseline measurement


title: A101_034A_8281_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8281, group HOSF, baseline measurement


title: A101_025_8331_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8331, group EPADHA, baseline measurement


title: A101_023_8305_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8305, group EPADHA, baseline measurement


title: A101_029_8058_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8058, group HOSF, baseline measurement


title: A101_031_8089_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8089, group HOSF, baseline measurement


title: A101_028A_8044_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8044, group HOSF, baseline measurement


title: A101_032_8211_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8211, group HOSF, baseline measurement


title: A101_017_8186_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8186 group, EPADHA, baseline measurement


title: A101_026_8183_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8183, group HOSF, baseline measurement


title: A101_030_8082_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8082, group HOSF, baseline measurement


title: A101_014_8364_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8364, group EPADHA, baseline measurement


title: A101_015_8037_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8037, group EPADHA, baseline measurement


title: A101_024_8320_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8320, group EPADHA, baseline measurement


title: A101_019A_8233_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8233, group EPADHA, baseline measurement


title: A101_010_8337_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8337, group EPADHA, baseline measurement


title: A101_027_8197_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8197, group HOSF, baseline measurement


title: A101_013_8363_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8363, group EPADHA, baseline measurement


title: A101_022_8303_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8303, group EPADHA, baseline measuremen


title: A101_021_8294_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8294, group EPADHA, baseline measurement


title: A101_011A_8345_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8345, group EPADHA, baseline measurement


title: A101_012A_8346_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8346, group EPADHA, baseline measurement


title: A101_018_8200_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8200, group EPADHA, baseline measurement


title: A101_016_8145_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8145, group EPADHA, baseline measurement


title: A101_035_8306_MUFA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8306, group HOSF, baseline measurement


title: A101_003_8030_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8030, group EPADHA, baseline measurement


title: A101_009_8300_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8300, group EPADHA, baseline measurement


title: A101_004_8169_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8169, group EPADHA, baseline measurement


title: PA14 constitutively expressing PqsE from a plasmid rep2

city: Boston

first: Laurence

middle: G

last: Rahme

state: MA

address: 50 Blosson St, Thier 340

department: Surgery

institute: Massachusetts General Hospital

description: PA14 was transformed with the plasmid pDN19pqsE that contain a constitutive expressed PqsE under ptac promoter.

hyb_protocol: According to Affymetrix GeneChip® Fluidics Station 450 protocol.

scan_protocol: According to Affymetrix scanner 3000 protocol

data_processing: Affymetrix Microarray Suite version 5.0

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PA14 constitutively expressed PqsE

label_protocol: According to Enzo Life sciences BioArray terminal labeling kit with biotin ddUTP.

growth_protocol: Cells were inoculated from -80C stock, grown in LB with tetracycline (120ug/ml) at 37C over night, diluted 1:100 and grown to OD600nm of 3.0

extract_protocol: According to Qiagen RNAeasy mini kit

tag: bacteria

value: Pseudomonas aeruginosa

tag: strain

tag: plasmid

value: pDN19pqsE, tetracycline resistant


title: PA14 constitutively expressing PqsE from a plasmid rep3


title: A101_005_8253_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8253, group EPADHA, baseline measurement


title: PQS treated mvfR mutant constitutively expressing PqsE from a plasmid rep1

description: The effect of PQS at concentration of 20ug/ml was tested on a PA14 mvfR mutant that was transformed with the plasmid pDN19pqsE containing a constitutive expressed PqsE under ptac promoter.

source_name: Pseudomonas aeruginosa PA14 mvfR mutant constitutively expressed PqsE

growth_protocol: Cells were inoculated from -80C stock, grown in LB with tetracycline (120ug/ml) and PQS (20ug/ml) at 37C over night, diluted 1:100 and grown to OD600nm of 3.0

treatment_protocol: PQS was added to the LB at 20ug/ml.

tag: mutant

value: mvfR

tag: compound

value: PQS (20ug/ml)


title: mvfR OD2.5 rep1

description: mvfR mutant in PA14

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

source_name: mvfR mutant of P. aeruginosa PA14

growth_protocol: Cells were inoculated from -80C stock, grown in LB at 37C over night, diluted 1:100 and grown to OD600nm of 2.5

value: mvfR mutant

tag: protocol


title: PA14 OD2.5 rep1

description: PA14 is a virulent strain of Pseudomonas aeruginosa. Therefore it is under intensive research. This wild-type strain serves as a control for treatments and mutants.

source_name: Pseudomonas aeruginosa PA14

value: grown to OD 2.5


title: mvfR mutant constitutively expressing PqsE from a plasmid rep1

description: PA14 mvfR mutant was transformed with the plasmid pDN19pqsE that contain a constitutive expressed PqsE under ptac promoter.


title: mvfR mutant constitutively expressing PqsE from a plasmid rep3


title: PA14 constitutively expressing PqsE from a plasmid rep1


title: PA14 OD3 rep3

growth_protocol: Cells were inoculated from -80C stock, grown in LB at 37C over night, diluted 1:100 and grown to OD600nm of 3.0


title: mvfR OD2.5 rep2

description: mvfR mutant in PA14


title: A101_008_8299_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8299, group EPADHA, baseline measurement


title: PA14 OD2.5 rep2


title: PA14 OD3 rep2


title: PQS treated mvfR mutant constitutively expressing PqsE from a plasmid rep2


title: A101_006_8263_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8263, group EPADHA, baseline measurement


title: PA14 OD3 rep1


title: PQS treated mvfR mutant constitutively expressing PqsE from a plasmid rep3


title: A101_020_8289_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8289, group EPADHA, baseline measurement


title: A101_007_8282_EPADHA_BASE

description: no additional information

source_name: peripheral blood mononuclear cells, individual 8282, group EPADHA, baseline measurement


title: mvfR mutant constitutively expressing PqsE from a plasmid rep2


title: 6CABA rep1

description: 2-amino-6-chlorobenzoic acid (6CABA) is a halogenated anthranilic acid analog that specifically inhibits intercellular signals and virulence mediated by the MvfR pathway (PLoS Pathog. 2007 September; 3(9): e126).

treatment_protocol: 6CABA was added at concentration of 6mM dissolved in LB medium.

tag: strain:

value: treated with 6mM of 6CABA


title: 4CABA rep1

description: 2-amino-4-chlorobenzoic acid (4CABA) is a halogenated anthranilic acid analog that specifically inhibits intercellular signals and virulence mediated by the MvfR pathway (PLoS Pathog. 2007 September; 3(9): e126).

treatment_protocol: 4CABA was added at concentration of 1.5mM dissolved in LB medium.

value: treated with 1.5mM of 4CABA


title: pqsE rep2

description: pqsE is a key gene in virulence of P. aeruginosa.

source_name: pqsE mutant OD 3

value: pqsE

value: LB at 37C until OD 3


title: 4CABA rep2


title: PNF1-treated cells, 4 h post-supplementation.

city: Charlottesville

first: Erwin

middle: P

last: Gianchandani

state: VA

department: Office of the Vice President for Research

institute: University of Virginia

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 4 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

hyb_protocol: Biotin-labeled cRNA was generated from the total RNA samples and fragmented in preparation for array hybridization, according to standard Affymetrix GeneChip protocols. Fragmented cRNA (10 µg) was hybridized to Affymetrix Human Genome U133 Plus 2.0 probe arrays for 16 h.

scan_protocol: The arrays were washed and stained in an Affymetrix Automated Fluidics Station 400 and scanned with the Affymetrix GeneArray Scanner. Scanned images were examined for visible defects and checked for proper grid alignment, and acceptable image files were analyzed to generate raw data in the form of ‘CEL’ files. Quality control, including replicate analysis, measurement of noise and background levels, and assessment of the 3'/5' ratio of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-actin) was performed with Microarray Analysis Suite 5.0 (MAS 5.0, Affymetrix).

data_processing: Using MAS 5.0, each gene transcript was detected as ‘present’, ‘absent’ or ‘marginal’, and the change between the experimental (PNF1-stimulated) and baseline (control) conditions at each timepoint was assigned to one of several standard categories, i.e., increase, marginal increase, no change, marginal decrease and decrease, depending on the P-value (calculated using the Wilcoxon signed rank test). The ranges for each call were 0.0000–0.0025, 0.0025–0.0030, 0.0030–0.9970, 0.9970–0.9975 and 0.9975 to 1.0000, respectively. These data were then inputted into dChip version 1.3 (Li and Wong, 2001), where they were normalized using the invariant set approach.

source_name: Human microvascular endothelial cells (HMVEC), 4 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).

label_protocol: RNA samples were prepared for hybridization using the GeneChip One-Cycle Target Labeling and Control Reagents kit (Affymetrix, Santa Clara, CA, USA).  Total RNA integrity was assessed by analysis with an Agilent Bioanalyzer using RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA).

value: HMVEC


title: 6CABA rep2


title: Control cells, 16 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 16 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 16 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.


title: pqsE rep1

scan_protocol: According to Affymetrix scanner 3000 protocol.


title: PNF1-treated cells, 8 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 8 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 8 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).


title: PNF1-treated cells, 24 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 24 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 24 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).


title: WT dorsal skin at P39, biological replicate 2

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: Hair cycle phase: early catagen

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Drosophila Genome Array using manufacturer's standard protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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.

source_name: Mouse dorsal skin at postnatal day 39, early catagen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 11 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

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

tag: Strain

tag: Age

value: postnatal day 39

value: Female


title: Control cells, 8 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 0.6% dimethyl sulfoxide (DMSO) vehicle control was added to the sample. Total RNA from the cultures was isolated 8 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 8 h post-supplementation with 0.6% dimethyl sulfoxide (DMSO) vehicle control.


title: PNF1-treated cells, 48 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 48 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 48 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).


title: PNF1-treated cells, 2 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 2 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 2 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).


title: PNF1-treated cells, 16 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 16 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 16 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).


title: PNF1-treated cells, 1 h post-supplementation.

description: HMVEC (Cambrex, Walkersville, MD, USA) were cultured in endothelial growth medium 2-microvascular (bulletkit, BioWhittaker, Walkersville, MD, USA) supplemented as directed with 5% fetal bovine serum. The cells (passage 9) were plated at 2.5 x 104 cells/cm^2 at 37 degrees Celsius in a humidified chamber with 5% carbon dioxide. They were grown to confluence. After confluence, medium was refreshed, and 30 µM PNF1 was added to the sample. Total RNA from the cultures was isolated 1 h post-supplementation using an RNeasy kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer's protocol.

source_name: Human microvascular endothelial cells (HMVEC), 1 h post-supplementation with 30 µM phthalimide neovascular factor 1 (PNF1).