title: 254706910039_b2 - xrn4-5_1 vs col0_1

hyb_protocol: col0_1 Cy5 / xrn4-5_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: L1 DD, repeat 2

status: Public on Aug 01 2015

type: RNA

city: Nasvhille

first: Siwei

last: He

state: TN

address: 465 21st Ave South

department: Cell and Developmental Biology

country: USA

institute: Vanderbilt University

description: L1 DD repeat 2

hyb_protocol: Affymetrix

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Data were normalized using quantile normalization and Robust Multiarray Analysis (RMA) summarization available in RMAExpress.

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: DD neurons from L1 larvae

label_protocol: 5-10 ng of total RNA was ampified using the NuGEN WT-Ovation Pico Amplification System. Amplified cDNA was fragmented and labeled according to manufacturer's instructions in NuGEN Biotin RNA Amplification and Labeling System.

growth_protocol: Nematodes were grown on bacterial strain NA22.

extract_protocol: Total RNA was extracted from Trizol and DNase-treated using Zymo’s RNA cleanup kit: the “DNA-Free RNA Kit” (R1013) as described by the manufacturers.

treatment_protocol: Embryos were prepared by standard bleach-prep protocol and allowed to hatch overnight in M9 buffer at 20 C to produce a population of growth-arrested L1 stage larvae.

tag: tissue

value: DD motor neurons

tag: age

value: L1 larva

tag: genotype

value: CZ8332 [juIs223 (pttr-39::mcherry, pttx-3::GFP) IV]

tag: label

value: GFP


title: L1 DD, repeat 1

description: L1 DD repeat 1


title: Ckro Cellulose v. Switchgrass

status: Public on Jul 31 2015

city: Raleigh

first: Jeffrey

last: Zurawski

state: NC

address: 840 Main Campus Drive Room 3309

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

hyb_protocol: Sample preparation steps for microarray hybridization: Prepare Prehyb buffer: 225mL water, 75mL 20X SSC, 0.3g SDS, 0.3g BSA. Preheat Prehyb buffer 45 min 42 degree C. Prehybidize slides at 42°C for 45 min. Wash slides by dipping 5 time in sterile dH2O at RT. Dip twice in isopropanol at RT. Dry slide in slide spinner. Add 1 ul COT1-DNA (20mg/ml) to samples. Heat probe mixture to 95°C in heat block for 2 min to denature DNA, do a quick spin. Add 30 ul of 2x hyb. buffer that has been preheated to 42°C to each tube. Hybridization buffer: 27.2uL water, 20uL 20X SSC, 8uL 50X Denhardts solution, 24uL formamide, 0.8uL 10% SDS. Apply hyb. mix to slide and cover with a 20x60 mm polyethylene hydrophobic coverslip. Place slide in water proof container, cover well with foil and place in 42°C bath for 18-20 hours. The following is a standard hybridization method that seems to work well for this procedure: 1 wash cycle at 42°C for 4 min with 2X SSC w/ 0.2% SDS. 1 wash cycle at RT for 4 min with 0.5X SSC w/ 0.2% SDS. 2 wash cycles at RT for 2 min each with 0.5X SSC. 1 wash cycle at RT for 1 min with 0.05X SSC.

scan_protocol: Images were acquired with a GenePix 4000B scanner (Molecular Devices) using 532 nm and 635 nm lasers simultaneously. An automatic photomultiplier (PMT) gain adjustment was used to balance the 532 nm and 635 nm channels prior to scanning the whole slide. A pixel size of 10 microns was selected for the image resolution. Separate images were saved for the 532 and 635 nm scans, and analyzed together using GenePix Pro (v7.0) software.

data_processing: Signals for each channel were obtained using GenePix Pro (v7.0) using circular features and were background subtracted using the median local intensity around the spot. Once all the slides were quantitated, data from the loop was analyzed with JMP Genomics 5.0 (SAS, NC), normalized using ANOVA to estimate the global fixed effects of dye & treatment and the random effects array and block followed by using a mixed effects ANOVA model [Wolfinger et al. J Comput Biol 8 625-637 (2001)

organism: Caldicellulosiruptor kronotskyensis

source_name: Cell Pellet

label_protocol: Producing cDNA: In a sterile PCR tube combine 17 ug RNA with 6 ug random primers. Then add nuclease free water so the volume is 10 uL. Incubate at 70°C for 10 min. Place tube on ice for 1 min. Add 8 uL of RT Master Mix (recipe below) to each tube and swirl to mix. Quick spin before incubation. RT Master Mix: 4uL 5X strand buffer, 1uL 0.1M DTT, 1uL dNTP mix (see below), 2uL superscript III Invitrogen. dNTP mix: 3uL dATP (100mM), 3uL dGTP (100mM), 3uL dCTP(100mM), 1.8uL dTTP (100mM), 2.4uL aa-dUTP(50mM) Ambion, 6.8uL nuclease free water. Incubate at 46°C for at least 3 hours. Hydrolyze RNA by adding 10uL 1N NaOH to each tube. To stop reaction add 10 uL 0.5M EDTA to each tube. Mix and incubate at 65°C for 15 min. Add 10uL 1N HCl to each tube neutralize reaction mix. Transfer samples into labeled tubes of appropriate sizes. Add five volumes PB Buffer (Qiagen) to each tube and mix well. Add 300 ul of RT product to a labeled Qiagen PCR cleanup column. Spin at 1,000 rpm for 15 sec., empty collection tube, and repeat until all of the solution has passed through the column. Complete wash One, add 750 ul of phosphate wash buffer (recipe below) to column and spin at 13,000 rpm for 1 min., empty tube. Complete wash Two, add 750 ul of phosphate wash buffer to column and spin at 13,000 rpm for 1 min., empty tube. Phosphate wash buffer: 0.1mL 1M KPO4( pH 8.5), 3.05mL autoclaved dH2O and 16.85mL 95% EtOH. Spin an additional 1 min. with the same collection tube and discard the flow through. Transfer to new 1.5 mL tube, add 60uL phosphate elution buffer to the membrane and incubate @ R. T. for 1 min. Spin at 13,000 rpm. Phosphate elution buffer: 4mM KPO4. Repeat phosphate elution into same tube using 60uL. Fluorescent Labeling: Dry all RT samples completely in speed vac. Resuspend each dried sample cDNA in 4.5 uL of 0.1M sodium carbonate buffer, pH 9.0. Mix up and down with pipette for good mixing. Dissolve and mix thoroughlythe Cy™ dye to be used with 20uL of DMSO. Tpically Cye dyes contain four applications in each vial. Mix 4.5 uL of dye with prepared cDNA sample. Incubate in the dark for 2 hour @ R.T. Mix RT-PCR products with 35uL 100mM NaOAc PH 5.2 and mix by vortexing. Mix with 250uL Qiagen Buffer PB and filter through spin columns (13,000 rpm). Wash spin column with 750 uL of Buffer PE (Qiagen). Spin an additional 1 min. with the same collection tube and discard the flow through. Elute labeled cDNA 2 times with 30 uL of EB Buffer (Qiagen). Combine different labeled probes Speed vacuum sample until dry (not too dry, i.e. don’t leave in speed vacuum for over 1 hour). Combine different labeled probes and speed vacuum sample until dry. Resuspend samples in 29uL sterilized dH2O.

growth_protocol: Cells were grown in DSMZ 671 (671d) medium in which yeast extract and Na2S·9H2O were not added, the nominal vitamin solution was replaced with 1 ml/L of a modified vitamin solution, and 1 g/L cysteine-HCl·H2O was added. The modified vitamin solution contained: biotin (20 mg/L), folic acid (20 mg/L), pyridoxine-HCl (100 mg/L), pantothenic acid (50 mg/L), thiamine-HCl (100 mg/L), nicotinamide (50 mg/L), cobalamin (50 mg/L), P-aminobenzoic acid (50 mg/L), lipoic acid (50 mg/L), and riboflavin (50 mg/L). Either Avicel (5 g/L) (FMC Bio-Polymer) or unpretreated switchgrass (5 g/L) was used as the sole carbon source. Caldicellulosiruptor was subcultured on either Avicel or unpretreated switchgrass 3 to 4 times prior to inoculating 0.5 liter cultures containing 5 g/L substrate. Cells were grown at 70 °C until mid-logarithmic phase (2-5 x 107 cells/ml).

extract_protocol: Cells were rapidly cooled to 4˚C, then harvested by centrifugation at 6000 × g prior to storage at -80˚C until further processing. Total RNA was isolated using a modified TRIzol (Life Technologies) protocol in combination with an RNAeasy kit (Qiagen). As an additional step, cells were sonicated after re-suspension in TRIzol reagent.

tag: growth condition

value: 70 °C, Defined Media, Substrate sole carbon source

value: Defined Media:Substrate as the sole carbon source


title: control biological replicate 3

city: Portland

first: Tamilla

last: Nechiporuk

state: OR

address: 3181 Sam Jackson Park Road

department: Vollum

institute: OHSU

description:
Rest GTi/GTi, p53 fl/fl.3
control biological replicate 3

hyb_protocol: As per Illumina manufacture protocol

scan_protocol: As per Illumina manufacture protocol

data_processing: quantile normalization method

organism: Mus musculus

source_name: E12.5 mouse brain

label_protocol: As per Illumina manufacture protocol

growth_protocol: embryo to E12.5

extract_protocol: RNA was extracted using Trizol with subsequent Qiagen RNA purification column

treatment_protocol: tissue dissected fresh

tag: strain

value: brain

value: E12.5 embryo

tag: genotype/variation

value: Rest GTi/GTi, p53 fl/fl


title: control biological replicate 2

description:
Rest GTi/GTi, p53 fl/fl.2
control biological replicate 2


title: Hemocytes after 31 days challenge with trophozoites suspension_4

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description:
hemocytes RNA of Ruditapes philippinarum
Healthy and Perkinsus-infected clams (V. philippinarum) were obtained from Carril and Pontevedra shellfish farms, respectively (Galicia, NW Spain).Healthy clams were maintained in an open circuit filtered sea water tanks at 15°C with aeration.All animals were fed daily with a mixture of microalgae containing Phaeodactylum tricornutum, Isochrysis galbana and Rhodomonas lens. Clams were acclimatized to the aquarium conditions for one week before the experiments were conducted.

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using Gene-Spring GX version 11.0.2 software (Agilent Technologies)

label: Cyanine 3

organism: Ruditapes philippinarum

source_name: 31 days after a Perkinsus olseni challenge

label_protocol: Amplified and labeled according to Low Input Quick Amp labeling kit (Agilent Technologies)

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

treatment_protocol: Rphilippinarum injected (intramuscular) with  100 µl of  filtered sea water (FSW) or trophozoites suspension. Hemocytes were collected  5, 10, 14, or 31 days after challenge.

tag: cell type

value: hemocytes

tag: pathogen

value: Perkinsus olseni


title: Hemocytes after 31 days challenge with trophozoites suspension_1


title: Hemocytes after 31 days challenge with filtered sea water (FSW)_1

source_name: 31 days after challenge (control group)


title: knockout biological replicate 2

description:
Nestin Cre+, Rest GTi/GTi, p53 fl/fl.2
knockout biological replicate 2

value: Nestin Cre+, Rest GTi/GTi, p53 fl/fl


title: Hemocytes after 31 days challenge with trophozoites suspension_3


title: Hemocytes after 31 days challenge with filtered sea water (FSW)_2


title: Hemocytes after 14 days challenge with trophozoites suspension_2

source_name: 14 days after a Perkinsus olseni challenge


title: Hemocytes after 31 days challenge with trophozoites suspension_2


title: knockout biological replicate 3

description:
Nestin Cre+, Rest GTi/GTi, p53 fl/fl.3
knockout biological replicate 3


title: Hemocytes after 14 days challenge with trophozoites suspension_3


title: Hemocytes after 10 days challenge with trophozoites suspension_1

source_name: ten days after a Perkinsus olseni challenge


title: Hemocytes after 14 days challenge with filtered sea water (FSW)_1

source_name: 14 days after challenge (control group)


title: Hemocytes after 10 days challenge with trophozoites suspension_3


title: Hemocytes after 10 days challenge with filtered sea water (FSW)_3

source_name: ten days after challenge (control group)


title: Hemocytes after 10 days challenge with filtered sea water (FSW)_4


title: Hemocytes after 14 days challenge with filtered sea water (FSW)_2


title: Hemocytes after 14 days challenge with trophozoites suspension_4


title: Hemocytes after 14 days challenge with trophozoites suspension_1


title: Hemocytes after 10 days challenge with filtered sea water (FSW)_2


title: control biological replicate 1

description:
Rest GTi/GTi, p53 fl/fl.1
control biological replicate 1


title: knockout biological replicate 1

description:
Nestin Cre+, Rest GTi/GTi, p53 fl/fl.1
knockout biological replicate 1


title: Hemocytes after 10 days challenge with filtered sea water (FSW)_1


title: Hemocytes after 14 days challenge with filtered sea water (FSW)_3


title: Hemocytes after 5 days challenge with filtered sea water (FSW)

source_name: five days after challenge (control group)


title: Hemocytes after 5 days challenge with trophozoites suspension_2

source_name: five days after a Perkinsus olseni challenge


title: Hemocytes after 5 days challenge with trophozoites suspension_3


title: Hemocytes after 5 days challenge with trophozoites suspension_1


title: Csac Cellulose v. Switchgrass

organism: Caldicellulosiruptor saccharolyticus


title: Hemocytes after 10 days challenge with trophozoites suspension_2


title: sexually mature eel males [LM_29]

description: Liver RNA of mature males of Anguilla anguilla

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization  of gPRocessed signalusing R2.6.1 statistical software

organism: Anguilla anguilla

source_name: Pool of RNA extracted separately from liver of 3 mature males

label_protocol: Amplified and labeled according to Agilent Low input One-Color Microarray-Based Gene Expression Analysis protocol

tag: condition

value: Eel males injected intramuscularly every week over a 140 day period with 2000 IU hCG/kg dissolved in 0.9% saline to induce sexual maturation.


title: sexually mature eel males [LM_31]


title: AA tumor 14 [Agilent]

status: Public on Jul 27 2015

city: Washington

first: Bi-Dar

last: Wang

state: DC

address: 2300 I street, NW

department: Pharmacology and Physiology

institute: The George Washington University Medical Center

hyb_protocol: Cy3-labelled miRNA samples were hybridized in a reaction volume of 45 µl containing 1x Hi-PRM hybridization buffer and 1x GE blocking agent following the manufacturers instructions. The mixed samples were hybridized to Agilent Human miRNA Microarrays (G4112A) for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (scan area: 61 x 21.6 mm, scan resolution: 5 µm, Dye channel: Green, Green PMT: XDR Hi 100%, Lo 5%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters for miRNA array to obtain background subtracted and spatially detrended Processed Signal intensities.  The feature extraction files were imported to Agilent's Genespring program for data analysis. The quantile normalization and log2 transformation was applied to get the normalized data accross the 56 arrays.

organism: Homo sapiens

source_name: prostate biopsy from prostate cancer patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 250 ng RNA using Agilent's miRNA Complete Labeling according to the manufacturer's instructions. T4 RNA ligase and Cy-3-pCp were used for labeling the miRNA samples. The labeled RNA samples were purified by Micro Bio-Spin 6 column.

extract_protocol: RNA was prepared using the miRNeasy kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The protocol includes dhomogenization of prostate biopsy samples, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: prostate cancer samples from AA

tag: tissue source

value: needle biosy core


title: sexually immature eel males [LI_64]

description: Liver RNA of immature males of Anguilla anguilla

source_name: Pool of RNA extracted separately from liver of 3 immature males

value: Eel males injected intramuscularly every week over a 140 day period with with 0.9% NaCl


title: sexually immature eel males [LI_62]


title: AA tumor 15 [Agilent]


title: AA normal 13 [Agilent]

value: patient matched normal tissue from AA


title: AA normal 15 [Agilent]


title: EA normal 13 [Agilent]

value: patient matched normal tissue from EA


title: sexually mature eel males [LM_32]


title: EA tumor 13 [Agilent]

value: prostate cancer samples from EA


title: EA normal 12 [Agilent]


title: EA normal 11 [Agilent]


title: AA normal 12 [Agilent]


title: sexually immature eel males [LI_61]


title: Control FAD 0-6h 1h 2

city: Cincinnati

first: Rong-Lin

address: 26 W MLK Dr

institute: US EPA

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 µm resolution

data_processing: Microarray image processing was performed using the latest Agilent's Feature Extraction software available at the time following the manufacturer’s protocol and recommendations.  Data processing was conducted using R package Limma.

organism: Pimephales promelas

source_name: ovary tissue,fish in water control

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: Sexually mature adult fathead minnows (5-6 month old) were obtained from an on-site aquatic culture facility at the US EPA Mid-Continent Ecology Division, Duluth, MN, USA. Fish were held under a 16:8 light:dark photoperiod fed frozen adult brine shrimp (San Francisco Bay Brand, Newark, CA, USA). Fish survival, water temperature (mean ± SD; 25.0±0.3), and dissolved oxygen (mean ± SD; 7.0±0.2) were monitored daily over the duration of the exposure and did not vary significantly between treatment groups.

extract_protocol: Total RNA was isolated from ovary tissue of both fathead minnow using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was evaluated using an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and RNA was quantified spectrophotometrically (Nanodrop). Total RNA samples were stored at -80oC until used for microarray analyses.

treatment_protocol:
To initiate a typical experiment, four males and four females were placed together in a glass test tank holding 10 L of Lake Superior water (4 µM filtered, UV sterilized) or test chemical dissolved in Lake Superior water, which was continuously renewed at a rate of about 45 mL/min. There were two such tanks for each treatment condition. The animals were held at 25 +/- 0.5 °C under a 16:8 L:D photoperiod, and were fed brine shrimp to satiation twice per day.
chemical abbreviations: BPA, bisphenol-A; EE2, 17a-ethynyl estradiol; FAD, fadrozole; FLU, flutamide; GEM, Gemfibrozil; KTC, ketoconazole; PRO,prochloraz; RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine; TB, 17 -trenbolone; TNT, 2,4,6-trinitrotoluene; TRI,trilostane; VIN, vinclozolin; WLSSD, effluent from Western Lake Superior Sanitary District

value: ovary

tag: age (month)

tag: treatment

value: in water control

tag: treatment duration

value: 1 h

tag: experiment

tag: sampling date

tag: scan date

tag: rna date

tag: rna person

value: rnaX

tag: chip id


title: AA normal 9 [Agilent]

tag: tissue


title: EA normal 9 [Agilent]


title: AA normal 11 [Agilent]


title: Cbes Cellulose v. Switchgrass

organism: Caldicellulosiruptor bescii

tag: growth condition

value: 70 °C, Defined Media, Substrate sole carbon source

value: Defined Media:Substrate as the sole carbon source


title: sexually mature eel males [LM_30]


title: EA tumor 11 [Agilent]


title: AA tumor 12 [Agilent]


title: AA normal 14 [Agilent]


title: EA tumor 9 [Agilent]


title: AA tumor 13 [Agilent]


title: AA tumor 9 [Agilent]


title: EA normal 10 [Agilent]


title: EA normal 7 [Agilent]


title: AA normal 8 [Agilent]


title: EA normal 5 [Agilent]


title: EA normal 6 [Agilent]


title: EA tumor 12 [Agilent]


title: AA normal 5 [Agilent]


title: AA normal 7 [Agilent]


title: AA normal 6 [Agilent]


title: EA normal 4 [Agilent]


title: EA tumor 10 [Agilent]


title: AA normal 3 [Agilent]


title: EA normal 3 [Agilent]


title: AA normal 4 [Agilent]


title: AA normal 2 [Agilent]


title: EA normal 2 [Agilent]


title: EA normal 1 [Agilent]


title: sexually immature eel males [LI_63]


title: EA cancer 8 [Agilent]


title: EA cancer 7 [Agilent]


title: AA tumor 11 [Agilent]


title: AA normal 1 [Agilent]


title: EA cancer 6 [Agilent]


title: EA cancer 5 [Agilent]


title: AA cancer 8 [Agilent]


title: AA cancer 7 [Agilent]


title: EA normal 8 [Agilent]


title: EA tumor 139 [Affymetrix]

description: needle biopsy specimen from prostate

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChIP Scanner 3000

data_processing:
Data were processed using Partek Genomics Suite software. Quantile normalization and GC-RMA background correction were applied to probe intensities, gene level expression were summarized from the corrected/normalized intensities. Only core probe sets were used for data analysis.
HuEx-1_0-st-v2.r2.pgf

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Samples were collected from patients, so there was no growth protocol.

extract_protocol: All RNA samples were purified by using Qiagen RNeasy micro kit (Qiagen). Samples were then treated with the RiobMinus, rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: No treatment was performed on the collected tissue samples.


title: AA cancer 5 [Agilent]


title: EA cancer 4 [Agilent]


title: AA cancer 6 [Agilent]


title: AA cancer 4 [Agilent]


title: AA cancer 3 [Agilent]


title: EA tumor 124 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 115 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA cancer 1 [Agilent]


title: EA tumor 121 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA cancer 2 [Agilent]


title: AA tumor 106 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA cancer 2 [Agilent]


title: EA tumor 105 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA cancer 1 [Agilent]


title: AA tumor 75 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 57 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 84 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 87 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 58 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 51 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 43 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 49 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 155 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 44 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 48 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 35 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 34 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 60 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 30 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 29 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 28 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA cancer 3 [Agilent]


title: AA tumor 21 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 19 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 32 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 10 [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 15 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 4  [Affymetrix]

description: needle biopsy specimen from prostate


title: EA tumor 16 [Affymetrix]

description: needle biopsy specimen from prostate


title: AA tumor 13 [Affymetrix]

description: needle biopsy specimen from prostate


title: aortic_vessel-KI-VEGF-rep2

status: Public on Jun 24 2015

city: London

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

country: United Kingdom

institute: King's College London

hyb_protocol: Labelled, fragmented cDNA was applied to Affymetrix Mouse Gene 2.0 ST arrays using standard protocols as recommended by manufacturers. Arrays were washed in FS450 fluidics station using standard wash and stain protocols and the hyb wash stain kit from Affymetrix

scan_protocol: Arrays were scanned using Affymetrix automated GCS3000 7G scanner with autoloader.

data_processing:
CEL files were imported into Expression Console software (Affymetrix) and processed using the RMA-Sketch algorithm to generate CHP files for further analysis.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.1.20

label: Biotin

label_protocol: RNA (50ng per sample) was processed and labelled using the Ovation WTA PicoSL V2 kit (NuGEN). 5ug SPIA cDNA was prepared for fragmentation and labelling using the Encore Biotin module from NuGEN.

growth_protocol: Each isolated ring was rinsed in fresh sterile PBS before being placed into individual wells on a 96-well plate pre-coated with BME (60 ul/well, Trevigen). After 1 hour incubation at 37oC in a cell culture incubator (95% O2/5% CO2) 100ul of culture media containing EBM-2, 1% FBS and 1% P/S was placed in each well.

extract_protocol: Total RNA was extracted using an RNeasy Plus Universal Kit (Qiagen).

treatment_protocol: After 24 hours incubation at 37oC in a cell culture incubator (95% O2/5% CO2) vessels were supplemented with fresh media with or without the addition of 50ng/ml VEGF. After a further 24 hours vessels were snap-frozen in liquid nitrogen and RNA extracted.

value: C17S PKARI knock-in

value: freshly isolated aortic vessel

tag: treated with

value: 50ng/ml VEGF


title: No.12_CD_Ileum_Upper

status: Public on Jun 11 2015

city: Bunkyo-ku

first: Kiichiro

last: Tsuchiya

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

description: CD patient-2

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: biopsy specimen

label_protocol: Total RNA was extracted using standard protocols (Affymetrix). Targets were prepared and hybridized to GeneChip Human Gene 1.0 ST arrays (Affymetrix), according to standard protocols. GeneChip data sets were analyzed using GeneSpring GX 7.3.1 (Agilent). Array data were normalized using robust multi-array analysis considering guanine and cytosine content algorithms. Target specific transcripts for probe sets A and B were categorized using NCBI Reference Sequence (RefSeq) and NCBI GenBank databases. Non-IBD patients were performed endoscopy because of the obscure gastrointestinal bleeding. To analyze the structure of normal small intestine, we selected biopsy specimens from non-IBD patients who showed no abnormality in small intestine.

extract_protocol: Trizol

tag: disease state

value: Crohn Disease

value: CD Ileum Upper


title: EA tumor 9 [Affymetrix]

description: needle biopsy specimen from prostate


title: aortic_vessel-WT-veh-rep1

tag: genotype/variation

value: wild-type

value: vehicle


title: EA tumor 18 [Affymetrix]

description: needle biopsy specimen from prostate


title: aortic_vessel-KI-veh-rep1


title: aortic_vessel-WT-VEGF-rep1


title: aortic_vessel-WT-VEGF-rep3


title: aortic_vessel-WT-veh-rep3


title: aortic_vessel-WT-veh-rep2


title: aortic_vessel-WT-VEGF-rep2


title: No.12_CD_colon

description: CD patient-2

value: CD colon


title: No.12_CD_Ileum_ Lower

description: CD patient-2

value: CD Ileum  Lower


title: No.12_CD_Jejunum_Middle

description: CD patient-2

value: CD Jejunum Middle


title: aortic_vessel-KI-VEGF-rep1


title: aortic_vessel-KI-veh-rep3


title: No.12_CD_Jejunum_Upper_ulcer

description: CD patient-2

value: CD Jejunum Upper ulcer


title: aortic_vessel-KI-VEGF-rep3


title: aortic_vessel-KI-veh-rep2


title: No.12_CD_Jejunum_Upper_np

description: CD patient-2

value: CD Jejunum Upper np


title: No.9_nonIBD_Ileum_Upper

description: nonIBD control-4

value: nonIBD

value: nonIBD Ileum Upper


title: No.12_CD_Jejunum_ Lower

description: CD patient-2

value: CD Jejunum  Lower


title: No.9_nonIBD_Jejunum_Lower

description: nonIBD control-4

value: nonIBD Jejunum Lower


title: No.9_nonIBD_Jejunum_Middle

description: nonIBD control-4

value: nonIBD Jejunum Middle


title: No.9_nonIBD_Jejunum_Upper

description: nonIBD control-4

value: nonIBD Jejunum Upper


title: No.11_CD_Jejunum_Lower

description: CD patient-4

value: CD Jejunum Lower


title: No.9_nonIBD_colon

description: nonIBD control-4

value: nonIBD colon


title: No.9_CD_Jejunum_Lower

description: CD patient-3

value: Crohn Disease


title: No.6_nonIBD_Jejunum_Upper

description: nonIBD control-2


title: IBD_ascending colon

description: CD patient-1

value: IBD ascending colon


title: No.9_CD_Jejunum_Upper

description: CD patient-3

value: CD Jejunum Upper


title: No7_nonIBD_Jejunum_Lower

description: nonIBD control-3


title: AA tumor 17 [Affymetrix]

description: needle biopsy specimen from prostate

value: prostate cancer samples from AA


title: No.9_nonIBD_Ileum_Middle

description: nonIBD control-4

value: nonIBD Ileum Middle


title: No.6_nonIBD_Jejunum_Lower

description: nonIBD control-2


title: IBD_ileum_middle

description: CD patient-1

value: IBD ileum middle


title: No.11_CD_Jejunum_Upper

description: CD patient-4


title: IBD_jejunum_upper

description: CD patient-1

value: IBD jejunum upper


title: IBD_jejunum_lower

description: CD patient-1

value: IBD jejunum lower


title: nonIBD_jejunum_lower

description: nonIBD control-1

value: nonIBD jejunum lower


title: nonIBD_ascending colon

description: nonIBD control-1

value: nonIBD

value: nonIBD ascending colon


title: nonIBD_jejunum_upper

description: nonIBD control-1

value: nonIBD jejunum upper


title: No7_nonIBD_Jejunum_Upper

description: nonIBD control-3


title: nonIBD_ileum_lower

description: nonIBD control-1

value: nonIBD ileum lower


title: IBD_ileum_upper

description: CD patient-1

value: IBD ileum upper


title: AA tumor 6 [Affymetrix]

description: needle biopsy specimen from prostate


title: bisulfite converted genomic DNA from reduction mammoplasty sample 18

status: Public on Apr 15 2015

type: genomic

city: Chapel Hill

first: Melissa

last: Troester

address: 2104H McGavran-Greenberg 135 Dauer Drive Campus Box 7435 27599-7435

department: Center for Environmental Health Sciences Integrated Sciences Facility Corencer Center

institute: University of North Carolina at Chapel Hill

description:
Sample name: 98
breast sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: breast sample 98

label_protocol: Standard Illumina Protocol

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

value: breast

tag: gender

value: female

tag: race

value: white

tag: bmi

tag: alcohol use

value: yes

tag: menopausal status

value: post

tag: age at surgery

tag: diagnosis at surgery

value: IDC w/DCIS

tag: tissue type

value: mastectomy


title: bisulfite converted genomic DNA from tumor adjacent sample 68

description:
Sample name: 95
breast sample

source_name: breast sample 95

value: pre


title: bisulfite converted genomic DNA from reduction mammoplasty sample 15

description:
Sample name: 90
breast sample

source_name: breast sample 90

value: IDC w/mucinous, DCIS


title: bisulfite converted genomic DNA from reduction mammoplasty sample 17

description:
Sample name: 93
breast sample

source_name: breast sample 93

value: black

value: no


title: bisulfite converted genomic DNA from tumor adjacent sample 67

description:
Sample name: 94
breast sample

source_name: breast sample 94


title: bisulfite converted genomic DNA from tumor adjacent sample 65

description:
Sample name: 89
breast sample

source_name: breast sample 89

value: other

value: reduction


title: bisulfite converted genomic DNA from tumor adjacent sample 62

description:
Sample name: 86
breast sample

source_name: breast sample 86


title: bisulfite converted genomic DNA from tumor adjacent sample 66

description:
Sample name: 92
breast sample

source_name: breast sample 92

value: nR

value: unkn

value: IDC


title: bisulfite converted genomic DNA from tumor adjacent sample 57

description:
Sample name: 81
breast sample

source_name: breast sample 81

value: mixed-IDC Dominant, D


title: bisulfite converted genomic DNA from reduction mammoplasty sample 16

description:
Sample name: 91
breast sample

source_name: breast sample 91

value: breast


title: bisulfite converted genomic DNA from tumor adjacent sample 61

description:
Sample name: 85
breast sample

source_name: breast sample 85

value: female


title: bisulfite converted genomic DNA from tumor adjacent sample 70

description:
Sample name: 97
breast sample

source_name: breast sample 97

value: peri


title: bisulfite converted genomic DNA from tumor adjacent sample 56

description:
Sample name: 80
breast sample

source_name: breast sample 80

value: white

value: yes


title: bisulfite converted genomic DNA from tumor adjacent sample 60

description:
Sample name: 84
breast sample

source_name: breast sample 84

value: post

value: IDC NOS


title: bisulfite converted genomic DNA from tumor adjacent sample 49

description:
Sample name: 73
breast sample

source_name: breast sample 73

value: pre

value: IDC, ILC, LCIS, DCIS

value: mastectomy


title: bisulfite converted genomic DNA from tumor adjacent sample 51

description:
Sample name: 75
breast sample

source_name: breast sample 75

value: no

value: IDC w/DCIS


title: bisulfite converted genomic DNA from tumor adjacent sample 52

description:
Sample name: 76
breast sample

source_name: breast sample 76

value: other


title: bisulfite converted genomic DNA from tumor adjacent sample 54

description:
Sample name: 78
breast sample

source_name: breast sample 78


title: bisulfite converted genomic DNA from tumor adjacent sample 63

description:
Sample name: 87
breast sample

source_name: breast sample 87


title: bisulfite converted genomic DNA from tumor adjacent sample 55

description:
Sample name: 79
breast sample

source_name: breast sample 79

value: black

value: IDC w/medullary


title: bisulfite converted genomic DNA from tumor adjacent sample 50

description:
Sample name: 74
breast sample

source_name: breast sample 74

value: IDC


title: bisulfite converted genomic DNA from tumor adjacent sample 53

description:
Sample name: 77
breast sample

source_name: breast sample 77

value: IDC - papillary


title: bisulfite converted genomic DNA from tumor adjacent sample 64

description:
Sample name: 88
breast sample

source_name: breast sample 88

value: breast

value: reduction


title: bisulfite converted genomic DNA from tumor adjacent sample 58

description:
Sample name: 82
breast sample

source_name: breast sample 82

value: female


title: bisulfite converted genomic DNA from tumor adjacent sample 47

description:
Sample name: 69
breast sample

source_name: breast sample 69

value: white

value: peri


title: bisulfite converted genomic DNA from reduction mammoplasty sample 14

description:
Sample name: 70
breast sample

source_name: breast sample 70

value: yes

value: IDC w/lobular, DCIS


title: bisulfite converted genomic DNA from tumor adjacent sample 46

description:
Sample name: 68
breast sample

source_name: breast sample 68

value: nR

value: unkn


title: bisulfite converted genomic DNA from tumor adjacent sample 45

description:
Sample name: 67
breast sample

source_name: breast sample 67

value: post

value: mastectomy


title: bisulfite converted genomic DNA from tumor adjacent sample 48

description:
Sample name: 72
breast sample

source_name: breast sample 72

value: IDC w/DCIS


title: bisulfite converted genomic DNA from tumor adjacent sample 43

description:
Sample name: 65
breast sample

source_name: breast sample 65

value: no


title: bisulfite converted genomic DNA from reduction mammoplasty sample 13

description:
Sample name: 61
breast sample

source_name: breast sample 61

value: black


title: bisulfite converted genomic DNA from tumor adjacent sample 37

description:
Sample name: 58
breast sample

source_name: breast sample 58

value: pre


title: bisulfite converted genomic DNA from tumor adjacent sample 39

description:
Sample name: 60
breast sample

source_name: breast sample 60


title: bisulfite converted genomic DNA from tumor adjacent sample 34

description:
Sample name: 55
breast sample

source_name: breast sample 55

value: Mixed-IDC Dominant


title: bisulfite converted genomic DNA from tumor adjacent sample 36

description:
Sample name: 57
breast sample

source_name: breast sample 57


title: bisulfite converted genomic DNA from tumor adjacent sample 69

description:
Sample name: 96
breast sample

source_name: breast sample 96


title: bisulfite converted genomic DNA from reduction mammoplasty sample 12

description:
Sample name: 52
breast sample

source_name: breast sample 52


title: bisulfite converted genomic DNA from tumor adjacent sample 35

description:
Sample name: 56
breast sample

source_name: breast sample 56

value: IDC


title: bisulfite converted genomic DNA from tumor adjacent sample 59

description:
Sample name: 83
breast sample

source_name: breast sample 83

value: breast

value: IDC NOS, DCIS


title: bisulfite converted genomic DNA from reduction mammoplasty sample 9

description:
Sample name: 44
breast sample

source_name: breast sample 44

value: female

value: reduction


title: bisulfite converted genomic DNA from tumor adjacent sample 32

description:
Sample name: 53
breast sample

source_name: breast sample 53

value: white


title: bisulfite converted genomic DNA from tumor adjacent sample 42

description:
Sample name: 64
breast sample

source_name: breast sample 64

value: yes


title: bisulfite converted genomic DNA from reduction mammoplasty sample 11

description:
Sample name: 47
breast sample

source_name: breast sample 47

value: other


title: bisulfite converted genomic DNA from tumor adjacent sample 30

description:
Sample name: 50
breast sample

source_name: breast sample 50


title: bisulfite converted genomic DNA from tumor adjacent sample 40

description:
Sample name: 62
breast sample

source_name: breast sample 62

value: nR


title: bisulfite converted genomic DNA from tumor adjacent sample 41

description:
Sample name: 63
breast sample

source_name: breast sample 63


title: bisulfite converted genomic DNA from tumor adjacent sample 28

description:
Sample name: 45
breast sample

source_name: breast sample 45


title: bisulfite converted genomic DNA from reduction mammoplasty sample 5

description:
Sample name: 40
breast sample

source_name: breast sample 40


title: bisulfite converted genomic DNA from tumor adjacent sample 33

description:
Sample name: 54
breast sample

source_name: breast sample 54

value: IDC NOS, DCIS, LCIS


title: bisulfite converted genomic DNA from tumor adjacent sample 29

description:
Sample name: 48
breast sample

source_name: breast sample 48

value: post


title: bisulfite converted genomic DNA from reduction mammoplasty sample 7

description:
Sample name: 42
breast sample

source_name: breast sample 42


title: bisulfite converted genomic DNA from reduction mammoplasty sample 10

description:
Sample name: 46
breast sample

source_name: breast sample 46


title: bisulfite converted genomic DNA from reduction mammoplasty sample 4

description:
Sample name: 39
breast sample

source_name: breast sample 39


title: bisulfite converted genomic DNA from tumor adjacent sample 31

description:
Sample name: 51
breast sample

source_name: breast sample 51


title: bisulfite converted genomic DNA from prophylactic sample 7

description:
Sample name: 35
breast sample

source_name: breast sample 35

value: peri

value: prophylactic


title: bisulfite converted genomic DNA from prophylactic sample 4

description:
Sample name: 32
breast sample

source_name: breast sample 32

value: unkn


title: bisulfite converted genomic DNA from prophylactic sample 8

description:
Sample name: 36
breast sample

source_name: breast sample 36


title: bisulfite converted genomic DNA from reduction mammoplasty sample 6

description:
Sample name: 41
breast sample

source_name: breast sample 41

value: black

value: no


title: bisulfite converted genomic DNA from tumor adjacent sample 21

description:
Sample name: 21
breast sample

source_name: breast sample 21

value: mastectomy


title: bisulfite converted genomic DNA from reduction mammoplasty sample 3

description:
Sample name: 38
breast sample

source_name: breast sample 38


title: bisulfite converted genomic DNA from prophylactic sample 1

description:
Sample name: 29
breast sample

source_name: breast sample 29


title: bisulfite converted genomic DNA from tumor adjacent sample 25

description:
Sample name: 25
breast sample

source_name: breast sample 25

value: IDC W/lobular, DCIS


title: bisulfite converted genomic DNA from reduction mammoplasty sample 2

description:
Sample name: 37
breast sample

source_name: breast sample 37

value: breast

value: pre


title: bisulfite converted genomic DNA from prophylactic sample 3

description:
Sample name: 31
breast sample

source_name: breast sample 31

value: female


title: bisulfite converted genomic DNA from tumor adjacent sample 24

description:
Sample name: 24
breast sample

source_name: breast sample 24

value: IDC NOS, DCIS


title: bisulfite converted genomic DNA from prophylactic sample 5

description:
Sample name: 33
breast sample

source_name: breast sample 33


title: bisulfite converted genomic DNA from tumor adjacent sample 23

description:
Sample name: 23
breast sample

source_name: breast sample 23

value: white

value: IDC w/DCIS


title: bisulfite converted genomic DNA from prophylactic sample 6

description:
Sample name: 34
breast sample

source_name: breast sample 34

value: yes


title: bisulfite converted genomic DNA from tumor adjacent sample 26

description:
Sample name: 26
breast sample

source_name: breast sample 26

value: other


title: bisulfite converted genomic DNA from prophylactic sample 2

description:
Sample name: 30
breast sample

source_name: breast sample 30


title: bisulfite converted genomic DNA from tumor adjacent sample 20

description:
Sample name: 20
breast sample

source_name: breast sample 20


title: bisulfite converted genomic DNA from tumor adjacent sample 19

description:
Sample name: 19
breast sample

source_name: breast sample 19


title: bisulfite converted genomic DNA from tumor adjacent sample 27

description:
Sample name: 27
breast sample

source_name: breast sample 27


title: bisulfite converted genomic DNA from reduction mammoplasty sample 1

description:
Sample name: 28
breast sample

source_name: breast sample 28

value: reduction


title: bisulfite converted genomic DNA from tumor adjacent sample 18

description:
Sample name: 18
breast sample

source_name: breast sample 18

value: post

value: IDC w/lobular, DCIS


title: bisulfite converted genomic DNA from tumor adjacent sample 22

description:
Sample name: 22
breast sample

source_name: breast sample 22


title: bisulfite converted genomic DNA from tumor adjacent sample 17

description:
Sample name: 17
breast sample

source_name: breast sample 17

value: IDC NOS


title: jos1984

status: Public on Feb 05 2015

city: Boston

first: Sudha

last: Biddinger

state: Massachusetts

address: CLSB 16027 300 Longwood Ave

department: Endocrinology

institute: Boston Children's Hospital

hyb_protocol: Per manufacturer's protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Data were analyzed with the Bioconductor packages affy to normalize and background correct using RMA

source_name: LIRKO liver sample 2

label_protocol: Per manufacturer's protocol

growth_protocol: Control and LIRKO mice aged 2-3 months were fed ad libitium with a normal chow diet

extract_protocol: Extracted total RNA using Qiagen RNEasy Column kits

treatment_protocol: Livers harvested from non-fasted animals

value: liver

tag: genotype

value: IR flox/flox albumin:CRE +


title: bisulfite converted genomic DNA from tumor adjacent sample 14

description:
Sample name: 14
breast sample

source_name: breast sample 14


title: bisulfite converted genomic DNA from tumor adjacent sample 16

description:
Sample name: 16
breast sample

source_name: breast sample 16


title: jos1986

source_name: Control liver sample 1

value: IR flox/flox albumin:CRE -


title: jos1985

source_name: LIRKO liver sample 3


title: bisulfite converted genomic DNA from tumor adjacent sample 15

description:
Sample name: 15
breast sample

source_name: breast sample 15

value: IDC w/lobular, LCIS

value: mastectomy


title: WSU_no_stroma_24h

status: Public on Aug 04 2014

city: Bethesda

first: Patricia

last: Perez-Galan

state: MD

address: 10 center drive

department: Hematology Branch

institute: NHLBI-NIH

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: FL cell line (WSU-FSCCL)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

extract_protocol: Total RNA was extracted using the Trizol  reagent and cleaned up with RNAeasy kit (invitrogen)

treatment_protocol:
[Isolation protocol] After the coculture, FL primary cells were isolated  by CD20 magnetic purification (Miltenyi)  and WSU-FSCCL  were used directly
FL cells were cultured in standard conditions  without stroma or on top of pre-established HK layers (ratio HK:FL=1:10)

tag: cell line

value: FL cell line (WSU-FSCCL)

tag: culture conditions

value: without stroma

tag: time


title: jos1988

source_name: Control liver sample 3

tag: tissue


title: jos1983

source_name: LIRKO liver sample 1


title: bisulfite converted genomic DNA from reduction mammoplasty sample 8

description:
Sample name: 43
breast sample

source_name: breast sample 43

value: breast

value: female

value: pre


title: WSU_cc_HK_48h

value: on top of pre-established FDC cell line HK layers


title: bisulfite converted genomic DNA from tumor adjacent sample 44

description:
Sample name: 66
breast sample

source_name: breast sample 66

value: white

value: yes

value: IDC w/DCIS


title: bisulfite converted genomic DNA from tumor adjacent sample 3

description:
Sample name: 3
breast sample

source_name: breast sample 3

value: post

value: IDC


title: bisulfite converted genomic DNA from tumor adjacent sample 13

description:
Sample name: 13
breast sample

source_name: breast sample 13


title: bisulfite converted genomic DNA from tumor adjacent sample 4

description:
Sample name: 4
breast sample

source_name: breast sample 4

value: black

value: no


title: bisulfite converted genomic DNA from tumor adjacent sample 10

description:
Sample name: 10
breast sample

source_name: breast sample 10


title: bisulfite converted genomic DNA from tumor adjacent sample 6

description:
Sample name: 6
breast sample

source_name: breast sample 6


title: FL3_cc_HK_48h

source_name: CD20 purified FL primary cells

value: CD20 purified FL primary cells


title: bisulfite converted genomic DNA from tumor adjacent sample 11

description:
Sample name: 11
breast sample

source_name: breast sample 11

value: other


title: bisulfite converted genomic DNA from tumor adjacent sample 9

description:
Sample name: 9
breast sample

source_name: breast sample 9


title: WSU_no_stroma_48h


title: bisulfite converted genomic DNA from tumor adjacent sample 8

description:
Sample name: 8
breast sample

source_name: breast sample 8


title: bisulfite converted genomic DNA from tumor adjacent sample 2

description:
Sample name: 2
breast sample

source_name: breast sample 2

value: IDC w/lobular, DCIS


title: WSU_cc_HK_24h


title: FL3_no_stroma_24h


title: bisulfite converted genomic DNA from tumor adjacent sample 38

description:
Sample name: 59
breast sample

source_name: breast sample 59

value: IDC, apocrine carcino

value: mastectomy


title: FL2_cc_HK_48h


title: jos1987

source_name: Control liver sample 2

value: liver

value: IR flox/flox albumin:CRE -


title: FL2_cc_HK_24h


title: FL3_cc_HK_24h


title: bisulfite converted genomic DNA from tumor adjacent sample 12

description:
Sample name: 12
breast sample

source_name: breast sample 12

value: breast

value: female


title: FL3_no_stroma_48h

value: without stroma


title: bisulfite converted genomic DNA from tumor adjacent sample 1

description:
Sample name: 1
breast sample

source_name: breast sample 1

value: white

value: pre


title: bisulfite converted genomic DNA from tumor adjacent sample 7

description:
Sample name: 7
breast sample

source_name: breast sample 7

value: yes

value: IDC w/DCIS


title: FL2_no_stroma_24h


title: FL2_no_stroma_48h


title: bisulfite converted genomic DNA from tumor adjacent sample 5

description:
Sample name: 5
breast sample

source_name: breast sample 5

value: post


title: genomic DNA from PBMC 104 Control

status: Public on Feb 27 2014

city: Iowa City

first: Robert

middle: A

last: Philibert

state: Iowa

address: MEB, 500 Newton Road, Room 2-126D

department: Psychiatry

institute: University of Iowa

description: non-smoker PBMC sample

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: Genome Studios V2011.1

source_name: PBMC 104

extract_protocol: genomic DNA was extracted and purified from PBMC samples using QIAamp DNA Blood Mini Kit according to standard instructions

value: Female

tag: sample type

value: PBMC

value: Control


title: genomic DNA from PBMC 103 Control

description: non-smoker PBMC sample

source_name: PBMC 103


title: genomic DNA from PBMC 108 Control

description: non-smoker PBMC sample

source_name: PBMC 108


title: genomic DNA from PBMC 110 Control

description: non-smoker PBMC sample

source_name: PBMC 110


title: genomic DNA from PBMC 98 Control

description: non-smoker PBMC sample

source_name: PBMC 98


title: genomic DNA from PBMC 100 Control

description: non-smoker PBMC sample

source_name: PBMC 100


title: genomic DNA from PBMC 111 Control

description: non-smoker PBMC sample

source_name: PBMC 111


title: genomic DNA from PBMC 95 Control

description: non-smoker PBMC sample

source_name: PBMC 95


title: genomic DNA from PBMC 105 Control

description: non-smoker PBMC sample

source_name: PBMC 105


title: genomic DNA from PBMC 99 Control

description: non-smoker PBMC sample

source_name: PBMC 99


title: genomic DNA from PBMC 109 Control

description: non-smoker PBMC sample

source_name: PBMC 109


title: genomic DNA from PBMC 89 Control

description: non-smoker PBMC sample

source_name: PBMC 89


title: genomic DNA from PBMC 96 Control

description: non-smoker PBMC sample

source_name: PBMC 96


title: genomic DNA from PBMC 102 Control

description: non-smoker PBMC sample

source_name: PBMC 102


title: genomic DNA from PBMC 97 Control

description: non-smoker PBMC sample

source_name: PBMC 97


title: genomic DNA from PBMC 88 Control

description: non-smoker PBMC sample

source_name: PBMC 88


title: genomic DNA from PBMC 91 Control

description: non-smoker PBMC sample

source_name: PBMC 91


title: genomic DNA from PBMC 107 Control

description: non-smoker PBMC sample

source_name: PBMC 107


title: genomic DNA from PBMC 106 Control

description: non-smoker PBMC sample

source_name: PBMC 106


title: genomic DNA from PBMC 84 Control

description: non-smoker PBMC sample

source_name: PBMC 84


title: genomic DNA from PBMC 101 Control

description: non-smoker PBMC sample

source_name: PBMC 101


title: genomic DNA from PBMC 86 Control

description: non-smoker PBMC sample

source_name: PBMC 86


title: genomic DNA from PBMC 90 Control

description: non-smoker PBMC sample

source_name: PBMC 90


title: genomic DNA from PBMC 94 Control

description: non-smoker PBMC sample

source_name: PBMC 94


title: genomic DNA from PBMC 85 Control

description: non-smoker PBMC sample

source_name: PBMC 85


title: genomic DNA from PBMC 83 Control

description: non-smoker PBMC sample

source_name: PBMC 83


title: genomic DNA from PBMC 92 Control

description: non-smoker PBMC sample

source_name: PBMC 92


title: genomic DNA from PBMC 87 Control

description: non-smoker PBMC sample

source_name: PBMC 87


title: genomic DNA from PBMC 93 Control

description: non-smoker PBMC sample

source_name: PBMC 93


title: genomic DNA from PBMC 82 Control

description: non-smoker PBMC sample

source_name: PBMC 82


title: genomic DNA from PBMC 79 Control

description: non-smoker PBMC sample

source_name: PBMC 79


title: genomic DNA from PBMC 81 Control

description: non-smoker PBMC sample

source_name: PBMC 81


title: genomic DNA from PBMC 77 Smoker

description: smoker PBMC sample

source_name: PBMC 77

value: Smoker


title: genomic DNA from PBMC 74 Smoker

description: smoker PBMC sample

source_name: PBMC 74


title: genomic DNA from PBMC 80 Control

description: non-smoker PBMC sample

source_name: PBMC 80


title: genomic DNA from PBMC 76 Smoker

description: smoker PBMC sample

source_name: PBMC 76


title: genomic DNA from PBMC 75 Smoker

description: smoker PBMC sample

source_name: PBMC 75


title: genomic DNA from PBMC 66 Smoker

description: smoker PBMC sample

source_name: PBMC 66


title: genomic DNA from PBMC 71 Smoker

description: smoker PBMC sample

source_name: PBMC 71


title: genomic DNA from PBMC 67 Smoker

description: smoker PBMC sample

source_name: PBMC 67


title: genomic DNA from PBMC 78 Control

description: non-smoker PBMC sample

source_name: PBMC 78


title: genomic DNA from PBMC 70 Smoker

description: smoker PBMC sample

source_name: PBMC 70


title: genomic DNA from PBMC 72 Smoker

description: smoker PBMC sample

source_name: PBMC 72


title: genomic DNA from PBMC 59 Smoker

description: smoker PBMC sample

source_name: PBMC 59


title: genomic DNA from PBMC 68 Smoker

description: smoker PBMC sample

source_name: PBMC 68


title: genomic DNA from PBMC 61 Smoker

description: smoker PBMC sample

source_name: PBMC 61


title: genomic DNA from PBMC 55 Smoker

description: smoker PBMC sample

source_name: PBMC 55


title: genomic DNA from PBMC 58 Smoker

description: smoker PBMC sample

source_name: PBMC 58


title: genomic DNA from PBMC 60 Smoker

description: smoker PBMC sample

source_name: PBMC 60


title: genomic DNA from PBMC 73 Smoker

description: smoker PBMC sample

source_name: PBMC 73


title: genomic DNA from PBMC 53 Smoker

description: smoker PBMC sample

source_name: PBMC 53


title: genomic DNA from PBMC 51 Smoker

description: smoker PBMC sample

source_name: PBMC 51


title: genomic DNA from PBMC 49 Control

description: non-smoker PBMC sample

source_name: PBMC 49


title: genomic DNA from PBMC 40 Control

description: non-smoker PBMC sample

source_name: PBMC 40


title: genomic DNA from PBMC 57 Smoker

description: smoker PBMC sample

source_name: PBMC 57


title: genomic DNA from PBMC 50 Control

description: non-smoker PBMC sample

source_name: PBMC 50


title: genomic DNA from PBMC 62 Smoker

description: smoker PBMC sample

source_name: PBMC 62


title: genomic DNA from PBMC 65 Smoker

description: smoker PBMC sample

source_name: PBMC 65


title: genomic DNA from PBMC 63 Smoker

description: smoker PBMC sample

source_name: PBMC 63


title: genomic DNA from PBMC 43 Control

description: non-smoker PBMC sample

source_name: PBMC 43


title: genomic DNA from PBMC 41 Control

description: non-smoker PBMC sample

source_name: PBMC 41


title: genomic DNA from PBMC 44 Control

description: non-smoker PBMC sample

source_name: PBMC 44


title: genomic DNA from PBMC 48 Control

description: non-smoker PBMC sample

source_name: PBMC 48


title: genomic DNA from PBMC 56 Smoker

description: smoker PBMC sample

source_name: PBMC 56


title: genomic DNA from PBMC 52 Smoker

description: smoker PBMC sample

source_name: PBMC 52


title: genomic DNA from PBMC 46 Control

description: non-smoker PBMC sample

source_name: PBMC 46


title: genomic DNA from PBMC 39 Control

description: non-smoker PBMC sample

source_name: PBMC 39


title: genomic DNA from PBMC 38 Control

description: non-smoker PBMC sample

source_name: PBMC 38


title: genomic DNA from PBMC 64 Smoker

description: smoker PBMC sample

source_name: PBMC 64


title: genomic DNA from PBMC 35 Control

description: non-smoker PBMC sample

source_name: PBMC 35


title: genomic DNA from PBMC 36 Control

description: non-smoker PBMC sample

source_name: PBMC 36


title: genomic DNA from PBMC 37 Control

description: non-smoker PBMC sample

source_name: PBMC 37


title: genomic DNA from PBMC 47 Control

description: non-smoker PBMC sample

source_name: PBMC 47


title: genomic DNA from PBMC 54 Smoker

description: smoker PBMC sample

source_name: PBMC 54


title: genomic DNA from PBMC 31 Control

description: non-smoker PBMC sample

source_name: PBMC 31


title: genomic DNA from PBMC 42 Control

description: non-smoker PBMC sample

source_name: PBMC 42


title: genomic DNA from PBMC 30 Control

description: non-smoker PBMC sample

source_name: PBMC 30


title: genomic DNA from PBMC 32 Control

description: non-smoker PBMC sample

source_name: PBMC 32


title: genomic DNA from PBMC 33 Control

description: non-smoker PBMC sample

source_name: PBMC 33


title: genomic DNA from PBMC 25 Control

description: non-smoker PBMC sample

source_name: PBMC 25


title: genomic DNA from PBMC 21 Smoker

description: smoker PBMC sample

source_name: PBMC 21


title: genomic DNA from PBMC 23 Smoker

description: smoker PBMC sample

source_name: PBMC 23


title: genomic DNA from PBMC 28 Control

description: non-smoker PBMC sample

source_name: PBMC 28


title: genomic DNA from PBMC 26 Control

description: non-smoker PBMC sample

source_name: PBMC 26


title: genomic DNA from PBMC 27 Control

description: non-smoker PBMC sample

source_name: PBMC 27


title: genomic DNA from PBMC 16 Smoker

description: smoker PBMC sample

source_name: PBMC 16


title: genomic DNA from PBMC 13 Smoker

description: smoker PBMC sample

source_name: PBMC 13


title: genomic DNA from PBMC 29 Control

description: non-smoker PBMC sample

source_name: PBMC 29


title: genomic DNA from PBMC 18 Smoker

description: smoker PBMC sample

source_name: PBMC 18


title: genomic DNA from PBMC 12 Smoker

description: smoker PBMC sample

source_name: PBMC 12


title: genomic DNA from PBMC 34 Control

description: non-smoker PBMC sample

source_name: PBMC 34


title: genomic DNA from PBMC 14 Smoker

description: smoker PBMC sample

source_name: PBMC 14


title: genomic DNA from PBMC 17 Smoker

description: smoker PBMC sample

source_name: PBMC 17


title: genomic DNA from PBMC 69 Smoker

description: smoker PBMC sample

source_name: PBMC 69


title: genomic DNA from PBMC 20 Smoker

description: smoker PBMC sample

source_name: PBMC 20


title: genomic DNA from PBMC 45 Control

description: non-smoker PBMC sample

source_name: PBMC 45


title: genomic DNA from PBMC 22 Smoker

description: smoker PBMC sample

source_name: PBMC 22


title: genomic DNA from PBMC 15 Smoker

description: smoker PBMC sample

source_name: PBMC 15


title: genomic DNA from PBMC 19 Smoker

description: smoker PBMC sample

source_name: PBMC 19


title: genomic DNA from PBMC 11 Smoker

description: smoker PBMC sample

source_name: PBMC 11


title: NovelCoV_NHP2013_02_CoV_8_RLL_d3

status: Public on Sep 06 2013

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: standard Agilent protocol

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. For the creation of the normalized data matrix, the limma package was used. Background correction was performed (method=normexp, offset=1). Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed.

organism: Macaca mulatta

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: 6 adult Rhesus macaques (Maccaca mulatta) aged 4-6 years were infected under anesthesia with 7x10e6 TCID50 MERS-CoV by intratracheal, oral, intranasal, and intraocular instillation.  8 hours post-infection, three animals were treated with intravenous RBV and subcutaneous type I interferon.  At 8 hour intervals, maintenance doses of ribavirin were given intramuscularly.  Treated versus untreated animals (n=3 animals per treatment group) were humanely sacrificed for necropsy and collection of lung and lung lesion samples.

extract_protocol: All RLT/ethanol lysates were processed simultaneously: precipitates were dissolved by addition of extra RLT buffer and subsequent adjustment with 70% ethanol, RNA was isolated using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Per the manufacturer's protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC further processing. Lung tissue was removed from RNAlater, homogenized in 10-20 volumes (w/v) RLT buffer, mixed with an equivalent volume of ethanol, and stored at -80°C until RNA isolation.

value: right lower lung lobe

tag: infectioncode

value: MERS-CoV

tag: samplematerial

value: right lung lower lobe

tag: timepoint


title: NovelCoV_NHP2013_02_CoV_10_RLL_d3


title: E0-E1_rep2_b

status: Public on Jul 01 2013

city: Daejeon

first: Haeyoung

last: Jeong

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

description: Block b, biological replicate 2 of 3 (mutant, before vs. after butanol treatment).

hyb_protocol: Labeling and hybridization were performed by the service provider (E-Biogen, Seoul, South Korea).

scan_protocol: The hybridized slides were scanned with GenePix 4000B and scanned images were analyzed by GenePix Pro 6.0.1.25.

data_processing: Background correction and normalization (print-tip loess and quantile) were performed using the limma R package.

organism: Escherichia coli

source_name: mutant E. coli, before butanol treatment

growth_protocol: Cells were grown aerobically in 50 ml LB medium until OD600 reached ~1 (late log phase).

extract_protocol: Qiagen Rneasy column

treatment_protocol: 1-butanol was added at a final concentration of 0.9% (vol/vol) and cells were further incubated for 30 min.

tag: protocol

value: late log phase, LB

tag: strain

source_name: mutant E. coli, after butanol treatment

value: late log phase, LB, 30 min after butanol treatment


title: NovelCoV_NHP2013_02_CoV_12_RLL_d3


title: genomic DNA from PBMC 9 Smoker

description: smoker PBMC sample

source_name: PBMC 9

tag: gender

tag: disease state


title: E0-E1_rep3_b

description: Block b, biological replicate 3 of 3 (mutant, before vs. after butanol treatment).

label_protocol: Labeling and hybridization were performed by the service provider (E-Biogen, Seoul, South Korea).


title: genomic DNA from PBMC 10 Smoker

description: smoker PBMC sample

source_name: PBMC 10


title: genomic DNA from PBMC 7 Smoker

description: smoker PBMC sample

source_name: PBMC 7


title: genomic DNA from PBMC 8 Smoker

description: smoker PBMC sample

source_name: PBMC 8


title: NovelCoV_NHP2013_02_CoV_7_RLL_d3


title: NovelCoV_NHP2013_02_CoV_9_RLL_d3


title: E0-E1_rep3_a

description: Block a, biological replicate 3 of 3 (mutant, before vs. after butanol treatment).


title: genomic DNA from PBMC 24 Control

description: non-smoker PBMC sample

source_name: PBMC 24


title: genomic DNA from PBMC 5 Smoker

description: smoker PBMC sample

source_name: PBMC 5


title: E0-E1_rep2_a

description: Block a, biological replicate 2 of 3 (mutant, before vs. after butanol treatment).


title: genomic DNA from PBMC 6 Smoker

description: smoker PBMC sample

source_name: PBMC 6


title: A0-E0_rep3_a

description: Block a, biological replicate 3 of 3 (wt vs. mutant, before butanol treatment).

source_name: wt E. coli, before butanol treatment

value: KCTC 2571


title: NovelCoV_NHP2013_02_CoV_11_RLL_d3


title: A0-E0_rep3_b

description: Block b, biological replicate 3 of 3 (wt vs. mutant, before butanol treatment).


title: A0-E0_rep2_b

description: Block b, biological replicate 2 of 3 (wt vs. mutant, before butanol treatment).


title: E0-E1_rep1_b

description: Block b, biological replicate 1 of 3 (mutant, before vs. after butanol treatment).


title: E0-E1_rep1_a

description: Block a, biological replicate 1 of 3 (mutant, before vs. after butanol treatment).


title: A0-A1_rep2_a

description: Block a, biological replicate 2 of 3 (wt, before vs. after butanol treatment).

source_name: wt E. coli, after butanol treatment


title: A0-E0_rep1_a

description: Block a, biological replicate 1 of 3 (wt vs. mutant, before butanol treatment).


title: A0-E0_rep1_b

description: Block b, biological replicate 1 of 3 (wt vs. mutant, before butanol treatment).


title: genomic DNA from PBMC 3 Smoker

description: smoker PBMC sample

source_name: PBMC 3


title: A0-E0_rep2_a

description: Block a, biological replicate 2 of 3 (wt vs. mutant, before butanol treatment).


title: genomic DNA from PBMC 2 Smoker

description: smoker PBMC sample

source_name: PBMC 2


title: A0-A1_rep3_b

description: Block b, biological replicate 3 of 3 (wt, before vs. after butanol treatment).


title: A0-A1_rep1_b

description: Block b, biological replicate 1 of 3 (wt, before vs. after butanol treatment).


title: A0-A1_rep1_a

description: Block a, biological replicate 1 of 3 (wt, before vs. after butanol treatment).


title: A0-A1_rep2_b

description: Block b, biological replicate 2 of 3 (wt, before vs. after butanol treatment).


title: A0-A1_rep3_a

description: Block a, biological replicate 3 of 3 (wt, before vs. after butanol treatment).


title: 3CP7

status: Public on Oct 29 2009

city: Cleveland

first: Luis

last: Solchaga

state: OH

address: 2103 Cornell Road

institute: Case Western Reserve University

description: Gene expression data from culture-expanded mesenchymal stem cells

hyb_protocol: cRNA was then fragmented, and 15 µg added to 300 µl hybridization cocktail. The hybridization cocktail is a multi-component, buffered environment (100 mM MES, 1 M NaCl, 20 mM EDTA, 0.01% Tween 20; 0.1 mg/ml Herring Sperm DNA, 0.5 mg/ml acetylated BSA, and Affymetrix IVT controls, as per manufacturer). Four IVT products of bacterial genes were added at final concentrations ranging from 1.5-100 pM. Spiked transcripts served as hybridization controls and were always monitored as part of our quality control regimen. Fragmented biotin-labeled cRNA was added, and the final volume is adjusted to 300 µl with molecular grade water. Samples were hybridized onto Affymetrix (Santa Clara, CA) H-U133A 2.0 human microarrays

scan_protocol: The manufacturer’s standard post-hybridization wash, double-stain, and scanning protocols use an Affymetrix GeneChip Fluidics Station 400 and a Hewlett Packard Gene Array scanner

data_processing: Raw data from microarray scans were initially normalized and analyzed with Affymetrix Microarray Suite (MAS) v.5.0

source_name: hMSCS

label_protocol: Five to eight µg of total RNA were converted into double stranded cDNA using Superscript II reverse transcriptase (Gibco BRL, Rockville, MD) and an oligo-dT primer with a T7 RNA polymerase promoter linked to its 5’ end. cDNA was cleaned and used in an in vitro transcription (IVT) reaction to generate adequate amplified, biotin-labeled cRNA (50-80 µg).

growth_protocol: Bone marrow aspirates were washed with control medium consisting in low glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum from a selected lot (DMEM-LG + 10% FBS) and subjected to a pre-formed Percoll density gradient to isolate mononucleated cells. The mononucleated cells were washed with control medium and seeded at a density of 1.8 x 105 cells/cm2 in control medium to establish primary cultures of human bone marrow-derived MSCs. All cell-culture was done at 37°C in a humidified atmosphere of 95% air and 5% CO2. In order to keep their growth at an exponential rate and prevent spontaneous differentiation or loss of differentiation potential, hMSCs must be subcultured before the cells become confluent. Typically, they were passaged when the cultures were 80 - 90% confluent. Primary cultures were usually subcultured around day 14 (± 3 days). Subsequently, the cells were subcultured approximately every 7 (± 2) days. Plates assigned to the different study groups were subcultured at the same time which resulted in different levels of confluence in the treatment groups as result of the previously reported differences in cell proliferation and cell size.

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

treatment_protocol: From the first medium change (day 4), some of the plates were assigned to receive control medium, while the rest of the plates received medium supplemented with 10 ng/ml of rhFGF-2. This dose was chosen based on previous studies. Cultures were fed twice per week

tag: passage

tag: medium

value: control


title: 3FP7

value: FGF supplemented


title: genomic DNA from PBMC 4 Smoker

description: smoker PBMC sample

source_name: PBMC 4


title: 2FP7


title: 3FP4


title: genomic DNA from PBMC 1 Smoker

description: smoker PBMC sample

source_name: PBMC 1


title: 2CP4


title: 2FP4


title: 1FP4


title: 1FP7


title: 1CP4


title: 3CP1


title: 3FP1


title: 1CP7


title: 2CP7


title: 3CP4


title: NB15899

status: Public on Oct 11 2004

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: tumor sample from neuroblastoma (stage III) patient


title: NB15296

description: tumor sample from neuroblastoma (stage I) patient


title: NB15205


title: EFT1374

description: tumor sample from EWS-FLI1 type I positive Ewing family tumor patient


title: NB14530


title: 1FP1


title: EFTHALSH

source_name: EFTHALSH


title: EFTHALBS

source_name: EFTHALBS


title: EFTHALWM

source_name: EFTHALWM


title: 2CP1


title: NB13586

description: tumor sample from neuroblastoma (stage IV) patient


title: 1CP1


title: EFTHALNP

source_name: EFTHALNP


title: 2FP1


title: SH-SY5Y

description: Neuroblastoma tumor cell line SH-SY5Y

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using a HP G2500A Scanner

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.


title: CHP-126

description: Neuroblastoma tumor cell line CHP-126


title: SK-N-MC

description: Ewing family tumor cell line SK-N-MC

source_name: SK-N-MC


title: Renal cell carcinoma: rccc-2, normal 1 (part 2 of 2)

status: Public on Jul 19 2001

city: Heidelberg

first: Wolfgang

last: Huber

address: Im Neuenheimer Feld 280

department: Molecular Genome Analysis

institute: German Cancer Research Center

description:
sex=m
age=48
RNA=poly-A+
For spot quality assessment / error bars, use duplicate spots (each clone is spotted twice) and foreground/background ratio
Keywords = renal clear cell carcinoma
Keywords = kidney
Lot batch = batch=ReImage2 filter=180225 reuse=3 date=16-Jan-1999

source_name: normal kidney tissue (as reference)


title: SIMA

description: Neuroblastoma tumor cell line SIMA

source_name: SIMA