title: high humidity phyllosphere treatment - rep2

description:
Gene expression after 2 days at 97% relative air humidity in bean phyllosphere
Sample name: High-Phy2


title: high humidity phyllosphere treatment - rep1

status: Public on Jun 21 2013

type: RNA

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description:
Gene expression after 2 days at 97% relative air humidity in bean phyllosphere
Sample name: High-Phy1

hyb_protocol: The volume of different samples was adjusted for the hybridization in order to have at least 2 pmol of labelled Cy3 per array on the slide. Sixty ng of labeled cDNA were loaded onto each microarray, hybridized for 17 hours at 65°C, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60°C for 30 minutes) was omitted.

scan_protocol: Microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (G2505), immediately after hybridization using the One-Color microarray -based gene expression analysis protocol provided by Agilent (scan area 61x21.6mm XDRHi:100% XDRLo:10%).

data_processing: Data were normalized by quantile and scaled with the baseline to the median of all samples. All genes were filtered by expression and were retained when the signal intensity was above the 20th percentile in at least one of the samples.

molecule: total RNA

organism: Pseudarthrobacter chlorophenolicus A6

source_name: Arthrobacter chlorophenolicus A6, high humidity phyllosphere

label_protocol: An amount of 2-5 µg of RNA was mixed with 1.25 µl random primers (500 µg/ml; Promega) in a total volume of 12 µl and incubated at 70 °C for 10 min followed by 4 °C for 5 min. Each tube received 13 µl of mastermix containing 0.625 µl Cyanine 3-dCTP (1 mM; Perkin-Elmer), 0.625 µl Superase-In (20 U/µl; Ambion), 1 µl Superscript II (200 U/µl; Invitrogen), 5 µl 5x 1st strand buffer, 2.5 µl DTT (100 mM), 0.25 µl dATP-dGTP-dTTP mixture (10 mM each), 0.125 µl dCTP (5 mM) and 2.875 µl nuclease-free water. Labeled cDNA was produced by incubation at 42 °C for 120 min, followed by 70 °C for 10 min and 4 °C for 5 min. RNA was hydrolyzed under alkaline conditions as follows. After the addition of 2.5 µl 1 M NaOH, samples were heated at 65 °C for 20 min, allowed to cool to room temperature for 10 min and neutralized by the addition of 2.5 µl 3 M Na-acetate (pH 5.2) and 2.5 µl 1 M HCl. The labeled cDNA was then purified using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer’s instructions. The product was eluted in 20 µl EB buffer and quantity and incorporation efficiency were determined using the MICROARRAY function on a NanoDrop spectrophotometer (ThermoFisher Scientific, Waltham, MA).

growth_protocol: Arthrobacter chlorophenolicus strain A6 was grown at 28 °C and 250 rpm in Lysogeny broth (LB). At mid-exponential phase, the bacterial culture was centrifuged for 10 min at 3838 ×g. The pellet was resuspended in sterile demineralized water to obtain a bacterial suspension with an optical density at 600 nm (OD600) of 0.15.

extract_protocol: Bacterial pellets were thawed at room temperature and then resuspended in 200 µl TE buffer (30 mM Tris-Cl, 1 mM EDTA, pH 8.0) containing 15 mg of lysozyme and 2 mg of proteinase K per ml. The suspension was incubated at room temperature for 30 min with regular vortexing. Then 700 µl lysis solution of the Biorad Aurum Total RNA Mini Kit (Bio-Rad Laboratories; Veenendaal, The Netherlands) was added and the total volume was transferred to a 2 ml screw cap tube containing 100 mg of 0.1:0.5 mm beads (1:1) (Merlin Bioproducts; Breda, The Netherlands). Tubes were shaken in a Mini-Beadbeater (Biospec Products, Breukelen, The Netherlands) twice for 1 min at 5000 rpm with a 1 min interval on ice. Tubes were centrifuged for 10 sec and the solution without beads was transferred to a fresh tube. After the addition of 500 µl 70% isopropanol, samples were further treated according to the Biorad Aurum Total RNA Mini Kit protocol. Columns were eluted with 80 µl elution buffer. An additional 30 min DNase treatment was performed with Ambion TURBO DNA-free (Applied Biosystems; Nieuwerkerk a/d ijssel, The Netherlands). After the DNase treatment, the RNA was precipitated with 1/10 volume of 7.5 M ammonium acetate (Sigma-Aldrich; Zwijndrecht, The Netherlands), 1/50 volume glycogen (5 mg/ml) (Fermentas; St. Leon-Rot, Germany) and 2.5 volumes of ethanol. RNA pellets were washed with 80% ethanol and resuspended in 12 µl nuclease-free water. RNA quality was verified with Experion RNA StdSens (Bio-Rad Laboratories).

treatment_protocol: Two-week old bean plants (Phaseolus vulgaris, green snap bean, variety Blue Lake Bush 274) with the first two leaves fully expanded were dipped into the bacterial suspension. Five plants were incubated at 97% air humidity for two days in a growth chamber; this was the high humidity phyllosphere treatment. Five other plants were incubated for 1 day at 97% air humidity, followed by a second day at 50% air humidity; this was the low humidity phyllosphere treatment. In addition, 500 µl of bacterial suspension was spread on 1/10 strength Tryptone Soy Agar (TSA; Oxoid, Cambridge, UK) with 15 g agar per liter; this was the agar surface treatment. Another 500 µl was spread on 1/10 strength TSA supplemented with 1 mM 4-chlorophenol; this was the chlorophenol treatment. Both agar treatments were incubated at 97% humidity for two days. The growth chamber maintained a day-night cycle of 16 h and 8 h at 21 °C and 16 °C, respectively. For each treatment, four replications were prepared independently. Bacteria were collected from leaves by sequentially putting five leaves from five different plants in 20 ml RNA protection solution [two parts RNAprotect bacteria reagent (Qiagen; Venlo, The Netherlands) and one part phosphate-buffered saline (PBS)] with 5 sec vortexing, 7 min sonication and 5 sec vortexing for each leaf. The solution was centrifuged for 20 min at 3838 × g and bacterial pellets were frozen at -80 °C until RNA extraction. Bacteria from agar plates were washed from the surface with 1 ml RNAprotect solution according to the manufacturer’s instructions (Qiagen) and frozen at -80 °C until RNA extraction.

tag: growth medium

value: bean phyllosphere

tag: humidity


title: 10xG vs 1xG rep2

status: Public on Jun 22 2013

city: Derby

first: Nathaniel

middle: J

last: Szewczyk

address: Uttoxeter Road

department: MRC/Arthritis Research UK Centre for Musculoskeletal Ageing Research

country: United Kingdom

institute: University of Nottingham, Royal Derby Hospital

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31435.gif
Physical Characteristics: 10g

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 1 to Channel 2

organism: Caenorhabditis elegans

source_name: mixed stage worms spun at 10 X G, 4d on 20G centrifuge

label_protocol: not provided

extract_protocol: not provided

treatment_protocol: Growing worms in centrifuge; The experiments were mixed stage C. elegans cultures grown in CeMM in tissue culture flasks. The control (red) channel for all three data sets is mixed stage C. elegans cultures. For the experimental channel (green) for all three data sets the experimental condition is G force. All worms were grown in CeMM in tissue culture flasks as mixed stage populations for 4 days. In the case of the control these worms were not placed on the long arm centrifuge at NASA Ames Research Center. In the case of the experimental worms these worms were placed at three different positions on the long arm centrifuge such that the cultures experienced 5x unit gravity, 10x unit gravity, or 15x unit gravity. In each experiment set there are 3 replicates for each G level vs. non centrifuged worms.

tag: culture

value: mixed stage worms

tag: treatment

value: spun at 10 X G, 4d on 20G centrifuge

source_name: mixed stage worms 1 X G control

value: 1 X G control


title: Skluy_ammonia_rep3

city: Lund

first: Anna

middle: Andersson

last: Rasmussen

address: Sölvegatan 23

department: Molecular Cellbiology

country: Sweden

institute: Lund University

description:
N3
biological replicate 3 of 4

hyb_protocol: Hybridization was performed overnight at 42 degrees using a MAUI hybridization system (BioMicro Systems), and slides were washed according to the Corning Pronto Plus system instructions.

scan_protocol: Fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).

data_processing: The raw data was normalized by within-print-tip-group lowess location normalization. Genes were ranked according to significance based on a standard t-test.

organism: Lachancea kluyveri

source_name: L. kluyveri cells grown on ammonia

label_protocol: cDNA was sythesised using SuperScript III RT (Invitrogen) the Oligo(dT)12–18 primers, and then labelled using Pronto! Plus labelling kit (Promega) according to the manufacturers protocol. Samples were labeled with Cy3-dCTP (Amersham) and reference was labeled with Cy5-dCTP.

growth_protocol: Growth in N-minimal media with 0,1% N-source added (uracil, dihydrouracil, uridine, ammonia or proline). 25°C, 200 rpm, to OD600 = 0.3-0.5 (early logaritmic phase)

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacures recommendations. RNA integrity was checked on a Bioanalyzer (Agilent).

treatment_protocol: no further treatment

tag: strain

tag: nitrogen source in growth media

value: ammonia

source_name: L. kluyveri cells grown on proline (reference)

value: proline


title: A549, NS1 M106I 3

city: Ottawa

first: Earl

middle: Garnet

last: Brown

state: Ontario

address: 451 Smyth Rd

department: Biochemistry Microbiology and Immunology

country: Canada

institute: University of Ottawa

description: Affy#4353_1.0: biological replicate 3

hyb_protocol: Target cDNA were hybridized to the Human Gene 1.0 ST array according to Affymetrix standard protocol (Genechip WT Terminal Labeling and Hybridization Manual Rev.7, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA normalization and scaling of data was performed with Affymetrix Expression Console v. 1.2

label: Biotin

organism: Homo sapiens

label_protocol: Sense strand target cDNA were prepared using the Ambion WT Expression kit (Life Technologies cat# 4411973/4) from 250 ng of total RNA.  Fragmentation and labeling were performed according to the standard Affymetrix protocol from 5.5 ug of cDNA (Genechip WT Terminal Labeling and Hybridization Manual Rev.7, Affymetrix).

growth_protocol: A549 cells (ATCC) were maintained in minimum essential medium (MEM).  MEM was supplemented with L-glutamine (2 mM), Penicillin (100 U/ml), Streptomycin (100 ug/ml) and fetal bovine serum (FBS) (10%). All cells were incubated at 37°C in the presence of 5% CO2.

extract_protocol: At 8 hpi, the cellular RNA was collected using manufacturer’s protocol (QIAGEN RNeasy mini-kit) quantified using a PowerWave XS2, Microplate Spectrophotometer  (BioTek Instruments, Inc. Winooski, VT, United States).

treatment_protocol: Confluent monolayers of 1.5E6 A549 cells in 35 mm dishes were infected with rHK-wt or rHK NS mutant viruses (MOI = 2) or mock-infected with PBS in triplicate for n=3 biological replicates before overflay with 3 ml  of MEM fro 8 h at 37 C.

tag: cell line

tag: cell type

value: lung epithilium


title: Skluy_uridine_rep4

description:
R4
biological replicate 4 of 4

source_name: L. kluyveri cells grown on uridine

value: uridine


title: ATiPS-263 cells at passage 27

type: genomic

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip array was scanned using the iScan (Illumina)

data_processing: Genomic DNA extracted from breast tumors was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: iPS cells derived from AT1OS cells

label_protocol: Illumina's standard protocol

growth_protocol: All cultures were maintained at 37°C in a humidified atmosphere containing 95% air and 5% CO2. When the cultures reached subconfluence, the cells were harvested with Trypsin-EDTA Solution (cat# 23315, IBL CO., Ltd, Gunma, Japan), and re-plated at a density of 5 x 105 cells in a 100-mm dish. Medium changes were carried out twice a week thereafter.

extract_protocol: Genomic DNA extracted from cells using QIAamp DNA Mini Kit (Qiagen).

tag: gender

value: male

value: induced pluripotent stem cell


title: 15xG vs 1xG rep2

description:
Simple annotation: C. elegans, Increased gravity
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26104.gif
Physical Characteristics: 15g

source_name: mixed stage worms spun at 15 X G, 4d on 20G centrifuge

value: spun at 15 X G, 4d on 20G centrifuge


title: Skluy_ammonia_rep4

description:
N4
biological replicate 4 of 4


title: ATiPS-024 cells at passage 25


title: Skluy_ammonia_rep2

description:
N2
biological replicate 2 of 4


title: Skluy_ammonia_rep1

description:
N1
biological replicate 1 of 4


title: ATiPS-264 cells at passage 25


title: Skluy_uridine_rep3

description:
R3
biological replicate 3 of 4


title: high humidity phyllosphere treatment - rep3

description:
Gene expression after 2 days at 97% relative air humidity in bean phyllosphere
Sample name: High-Phy3


title: ATiPS-262 cells at passage 17


title: Skluy_uracil_rep3

description:
U3
biological replicate 3 of 4

source_name: L. kluyveri cells grown on uracil

value: uracil


title: Skluy_dihydrouracil_rep2

description:
D2
biological replicate 2 of 4

source_name: L. kluyveri cells grown on dihydrouracil

value: dihydrouracil


title: Skluy_dihydrouracil_rep3

description:
D3
biological replicate 3 of 4


title: Skluy_dihydrouracil_rep4

description:
D4
biological replicate 4 of 4


title: Skluy_dihydrouracil_rep1

description:
D1
biological replicate 1 of 4


title: Skluy_uracil_rep2

description:
U2
biological replicate 2 of 4


title: Skluy_uridine_rep1

description:
R1
biological replicate 1 of 4


title: Skluy_uridine_rep2

description:
R2
biological replicate 2 of 4


title: AT1OS cells

source_name: Fibroblast cells derived from an Ataxia telangiectasia patient (JCRB Cell Bank ID: JCRB0308)

value: fibroblast


title: Peripheral blood RNA from InChianti sample 697

city: Exeter

first: Hanieh

last: Yaghootkar

address: Magdalen Road

department: Genetics

institute: University of Exeter Medical School

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using eQTL Mapping Pipeline software

label: biotin

source_name: Human peripheral blood

label_protocol: RNA was biotinylated and amplified using the Illumina® TotalPrep(tm) -96 RNA Amplification Kit

extract_protocol: RNA was extracted from peripheral blood samples using the PAXgene Blood mRNA kit (Qiagen, Crawley, UK) according to the manufacturer's instructions.

tag: tissue

value: peripheral blood leucocyte


title: Skluy_uracil_rep1

description:
U1
biological replicate 1 of 4


title: Peripheral blood RNA from InChianti sample 705


title: Peripheral blood RNA from InChianti sample 700


title: Peripheral blood RNA from InChianti sample 699


title: agar surface treatment - rep3

description:
Gene expression after 2 days at 97% relative air humidity on agar surface
Sample name: Agar3

source_name: Arthrobacter chlorophenolicus A6, agar surface

value: agar surface


title: Peripheral blood RNA from InChianti sample 701


title: Peripheral blood RNA from InChianti sample 698


title: Peripheral blood RNA from InChianti sample 703


title: Peripheral blood RNA from InChianti sample 696


title: Peripheral blood RNA from InChianti sample 702


title: Peripheral blood RNA from InChianti sample 704


title: Peripheral blood RNA from InChianti sample 694


title: Peripheral blood RNA from InChianti sample 695


title: Peripheral blood RNA from InChianti sample 685


title: Peripheral blood RNA from InChianti sample 689


title: Peripheral blood RNA from InChianti sample 686


title: Peripheral blood RNA from InChianti sample 690


title: Peripheral blood RNA from InChianti sample 692


title: Peripheral blood RNA from InChianti sample 684


title: Peripheral blood RNA from InChianti sample 693


title: Peripheral blood RNA from InChianti sample 683


title: Skluy_uracil_rep4

description:
U4
biological replicate 4 of 4


title: Peripheral blood RNA from InChianti sample 691


title: Peripheral blood RNA from InChianti sample 688


title: Peripheral blood RNA from InChianti sample 687


title: Peripheral blood RNA from InChianti sample 682


title: Peripheral blood RNA from InChianti sample 680


title: Peripheral blood RNA from InChianti sample 681


title: Peripheral blood RNA from InChianti sample 664


title: Peripheral blood RNA from InChianti sample 675


title: SNP6-Pool50individuals_Pool1_rep1

city: Greifswald

first: Georg

last: Homuth

address: F.-L.-Jahn-Str. 15a

department: Interfaculty Institute for Genetics and Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: pooled DNA Hybridized to Genome-Wide Human SNP Array 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
All arrays were scanned and the corresponding CEL files were generated using the Affymetrix® GeneChip® Genotyping Analysis Software Version 4.0. The intensity values for the A and B alleles of each SNP (CHP files) were obtained from the CEL files using the Birdseed2 calling algorithm as implemented in the Affymetrix Power Tools (APT version 1.10.1)
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Chromosomal DNA was purified from whole blood samples using the QIAamp DNA blood mini kit (Qiagen, Hilden, Germany) following the manufacturer's instruction. To remove contaminating RNA, the optional RNase A treatment step (30 min at RT with 20 µl Ribonuclease A (20 mg/ml)) was routinely performed. The DNA quantity was measured with a NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies) and the integrity of the DNA preparations was analyzed by electrophoresis using 0.8% Agarose-1x TBE gels stained with ethidium bromide. Only DNA preparations showing no signs of degradation at all were used for allelotyping.

tag: pool

value: whole blood

tag: replicate


title: Peripheral blood RNA from InChianti sample 678


title: Peripheral blood RNA from InChianti sample 676


title: SNP6-Pool50individuals_Pool2_rep1


title: Peripheral blood RNA from InChianti sample 672


title: Peripheral blood RNA from InChianti sample 673


title: Peripheral blood RNA from InChianti sample 667


title: Peripheral blood RNA from InChianti sample 674


title: Peripheral blood RNA from InChianti sample 677


title: Peripheral blood RNA from InChianti sample 670


title: Peripheral blood RNA from InChianti sample 665


title: Peripheral blood RNA from InChianti sample 663


title: Peripheral blood RNA from InChianti sample 669


title: Peripheral blood RNA from InChianti sample 666


title: Peripheral blood RNA from InChianti sample 662


title: Peripheral blood RNA from InChianti sample 655


title: SNP6-Pool50individuals_Pool2_rep2


title: Peripheral blood RNA from InChianti sample 679


title: SNP6-Pool50individuals_Pool1_rep2


title: Peripheral blood RNA from InChianti sample 671


title: Peripheral blood RNA from InChianti sample 656


title: Peripheral blood RNA from InChianti sample 657


title: Peripheral blood RNA from InChianti sample 660


title: Peripheral blood RNA from InChianti sample 661


title: Peripheral blood RNA from InChianti sample 659


title: Peripheral blood RNA from InChianti sample 668


title: Peripheral blood RNA from InChianti sample 654


title: Peripheral blood RNA from InChianti sample 658


title: Peripheral blood RNA from InChianti sample 653


title: Peripheral blood RNA from InChianti sample 649


title: Peripheral blood RNA from InChianti sample 646


title: Peripheral blood RNA from InChianti sample 651


title: Peripheral blood RNA from InChianti sample 650


title: Peripheral blood RNA from InChianti sample 652


title: Peripheral blood RNA from InChianti sample 648


title: Peripheral blood RNA from InChianti sample 647


title: Peripheral blood RNA from InChianti sample 639


title: Peripheral blood RNA from InChianti sample 641


title: Peripheral blood RNA from InChianti sample 644


title: Peripheral blood RNA from InChianti sample 645


title: Peripheral blood RNA from InChianti sample 638


title: Peripheral blood RNA from InChianti sample 642


title: Peripheral blood RNA from InChianti sample 633


title: Peripheral blood RNA from InChianti sample 636


title: Peripheral blood RNA from InChianti sample 635


title: Peripheral blood RNA from InChianti sample 631


title: Peripheral blood RNA from InChianti sample 643


title: Peripheral blood RNA from InChianti sample 626


title: Peripheral blood RNA from InChianti sample 630


title: Peripheral blood RNA from InChianti sample 627


title: Peripheral blood RNA from InChianti sample 634


title: Peripheral blood RNA from InChianti sample 640


title: Peripheral blood RNA from InChianti sample 625


title: Peripheral blood RNA from InChianti sample 637


title: Peripheral blood RNA from InChianti sample 624


title: Peripheral blood RNA from InChianti sample 629


title: Peripheral blood RNA from InChianti sample 621


title: Peripheral blood RNA from InChianti sample 618


title: Peripheral blood RNA from InChianti sample 632


title: Peripheral blood RNA from InChianti sample 616


title: Peripheral blood RNA from InChianti sample 623


title: Peripheral blood RNA from InChianti sample 628


title: Peripheral blood RNA from InChianti sample 619


title: Peripheral blood RNA from InChianti sample 620


title: Peripheral blood RNA from InChianti sample 622


title: Peripheral blood RNA from InChianti sample 617


title: Peripheral blood RNA from InChianti sample 614


title: Peripheral blood RNA from InChianti sample 615


title: Peripheral blood RNA from InChianti sample 613


title: Peripheral blood RNA from InChianti sample 612


title: Peripheral blood RNA from InChianti sample 607


title: Peripheral blood RNA from InChianti sample 603


title: Peripheral blood RNA from InChianti sample 604


title: Peripheral blood RNA from InChianti sample 611


title: Peripheral blood RNA from InChianti sample 605


title: Peripheral blood RNA from InChianti sample 600


title: Peripheral blood RNA from InChianti sample 597


title: Peripheral blood RNA from InChianti sample 609


title: Peripheral blood RNA from InChianti sample 595


title: Peripheral blood RNA from InChianti sample 598


title: Peripheral blood RNA from InChianti sample 592


title: Peripheral blood RNA from InChianti sample 594


title: Peripheral blood RNA from InChianti sample 602


title: Peripheral blood RNA from InChianti sample 606


title: Peripheral blood RNA from InChianti sample 608


title: Peripheral blood RNA from InChianti sample 601


title: Peripheral blood RNA from InChianti sample 590


title: Peripheral blood RNA from InChianti sample 591


title: Peripheral blood RNA from InChianti sample 610


title: Peripheral blood RNA from InChianti sample 589


title: Peripheral blood RNA from InChianti sample 588


title: Peripheral blood RNA from InChianti sample 599


title: Peripheral blood RNA from InChianti sample 587


title: Peripheral blood RNA from InChianti sample 586


title: Peripheral blood RNA from InChianti sample 583


title: Peripheral blood RNA from InChianti sample 582


title: Peripheral blood RNA from InChianti sample 584


title: Peripheral blood RNA from InChianti sample 575


title: Peripheral blood RNA from InChianti sample 580


title: Peripheral blood RNA from InChianti sample 573


title: Peripheral blood RNA from InChianti sample 572


title: Peripheral blood RNA from InChianti sample 581


title: Peripheral blood RNA from InChianti sample 596


title: Peripheral blood RNA from InChianti sample 574


title: Peripheral blood RNA from InChianti sample 570


title: Peripheral blood RNA from InChianti sample 593


title: Peripheral blood RNA from InChianti sample 579


title: Peripheral blood RNA from InChianti sample 569


title: Peripheral blood RNA from InChianti sample 566


title: Peripheral blood RNA from InChianti sample 567


title: Peripheral blood RNA from InChianti sample 571


title: Peripheral blood RNA from InChianti sample 578


title: Peripheral blood RNA from InChianti sample 563


title: Peripheral blood RNA from InChianti sample 577


title: Peripheral blood RNA from InChianti sample 568


title: Peripheral blood RNA from InChianti sample 564


title: Peripheral blood RNA from InChianti sample 559


title: Peripheral blood RNA from InChianti sample 576


title: Peripheral blood RNA from InChianti sample 585


title: Peripheral blood RNA from InChianti sample 556


title: Peripheral blood RNA from InChianti sample 560


title: Peripheral blood RNA from InChianti sample 561


title: Peripheral blood RNA from InChianti sample 562


title: Peripheral blood RNA from InChianti sample 565


title: Peripheral blood RNA from InChianti sample 554


title: Peripheral blood RNA from InChianti sample 545


title: Peripheral blood RNA from InChianti sample 547


title: Peripheral blood RNA from InChianti sample 555


title: Peripheral blood RNA from InChianti sample 552


title: Peripheral blood RNA from InChianti sample 558


title: Peripheral blood RNA from InChianti sample 553


title: Peripheral blood RNA from InChianti sample 551


title: Peripheral blood RNA from InChianti sample 544


title: Peripheral blood RNA from InChianti sample 557


title: Peripheral blood RNA from InChianti sample 549


title: Peripheral blood RNA from InChianti sample 546


title: Peripheral blood RNA from InChianti sample 548


title: Peripheral blood RNA from InChianti sample 542


title: Peripheral blood RNA from InChianti sample 543


title: Peripheral blood RNA from InChianti sample 550


title: Peripheral blood RNA from InChianti sample 538


title: Peripheral blood RNA from InChianti sample 539


title: Peripheral blood RNA from InChianti sample 537


title: Peripheral blood RNA from InChianti sample 540


title: Peripheral blood RNA from InChianti sample 541


title: Peripheral blood RNA from InChianti sample 535


title: Peripheral blood RNA from InChianti sample 536


title: Peripheral blood RNA from InChianti sample 533


title: Peripheral blood RNA from InChianti sample 534


title: Peripheral blood RNA from InChianti sample 531


title: Peripheral blood RNA from InChianti sample 530


title: Peripheral blood RNA from InChianti sample 528


title: Peripheral blood RNA from InChianti sample 529


title: Peripheral blood RNA from InChianti sample 527


title: Peripheral blood RNA from InChianti sample 525


title: Peripheral blood RNA from InChianti sample 524


title: Peripheral blood RNA from InChianti sample 532


title: Peripheral blood RNA from InChianti sample 526


title: Peripheral blood RNA from InChianti sample 506


title: Peripheral blood RNA from InChianti sample 511


title: Peripheral blood RNA from InChianti sample 512


title: Peripheral blood RNA from InChianti sample 523


title: Peripheral blood RNA from InChianti sample 517


title: Peripheral blood RNA from InChianti sample 504


title: Peripheral blood RNA from InChianti sample 505


title: Peripheral blood RNA from InChianti sample 515


title: Peripheral blood RNA from InChianti sample 514


title: Peripheral blood RNA from InChianti sample 522


title: Peripheral blood RNA from InChianti sample 499


title: Peripheral blood RNA from InChianti sample 507


title: Peripheral blood RNA from InChianti sample 518


title: Peripheral blood RNA from InChianti sample 516


title: Peripheral blood RNA from InChianti sample 519


title: Peripheral blood RNA from InChianti sample 520


title: Peripheral blood RNA from InChianti sample 513


title: Peripheral blood RNA from InChianti sample 508


title: Peripheral blood RNA from InChianti sample 503


title: Peripheral blood RNA from InChianti sample 509


title: Peripheral blood RNA from InChianti sample 510


title: Peripheral blood RNA from InChianti sample 500


title: Peripheral blood RNA from InChianti sample 502


title: Peripheral blood RNA from InChianti sample 501


title: Peripheral blood RNA from InChianti sample 521


title: Peripheral blood RNA from InChianti sample 495


title: Peripheral blood RNA from InChianti sample 497


title: Peripheral blood RNA from InChianti sample 490


title: Peripheral blood RNA from InChianti sample 491


title: Peripheral blood RNA from InChianti sample 498


title: Peripheral blood RNA from InChianti sample 488


title: Peripheral blood RNA from InChianti sample 492


title: Peripheral blood RNA from InChianti sample 493


title: Peripheral blood RNA from InChianti sample 484


title: Peripheral blood RNA from InChianti sample 485


title: Peripheral blood RNA from InChianti sample 483


title: Peripheral blood RNA from InChianti sample 479


title: Peripheral blood RNA from InChianti sample 481


title: Peripheral blood RNA from InChianti sample 489


title: Peripheral blood RNA from InChianti sample 472


title: Peripheral blood RNA from InChianti sample 487


title: Peripheral blood RNA from InChianti sample 496


title: Peripheral blood RNA from InChianti sample 474


title: Peripheral blood RNA from InChianti sample 473


title: Peripheral blood RNA from InChianti sample 482


title: Peripheral blood RNA from InChianti sample 469


title: Peripheral blood RNA from InChianti sample 475


title: Peripheral blood RNA from InChianti sample 478


title: Peripheral blood RNA from InChianti sample 477


title: Peripheral blood RNA from InChianti sample 471


title: Peripheral blood RNA from InChianti sample 486


title: Peripheral blood RNA from InChianti sample 480


title: Peripheral blood RNA from InChianti sample 470


title: Peripheral blood RNA from InChianti sample 461


title: Peripheral blood RNA from InChianti sample 476


title: Peripheral blood RNA from InChianti sample 460


title: Peripheral blood RNA from InChianti sample 462


title: Peripheral blood RNA from InChianti sample 459


title: Peripheral blood RNA from InChianti sample 466


title: Peripheral blood RNA from InChianti sample 457


title: Peripheral blood RNA from InChianti sample 464


title: Peripheral blood RNA from InChianti sample 468


title: Peripheral blood RNA from InChianti sample 450


title: Peripheral blood RNA from InChianti sample 453


title: Peripheral blood RNA from InChianti sample 463


title: Peripheral blood RNA from InChianti sample 454


title: Peripheral blood RNA from InChianti sample 448


title: Peripheral blood RNA from InChianti sample 455


title: Peripheral blood RNA from InChianti sample 451


title: Peripheral blood RNA from InChianti sample 456


title: Peripheral blood RNA from InChianti sample 458


title: Peripheral blood RNA from InChianti sample 452


title: Peripheral blood RNA from InChianti sample 449


title: Peripheral blood RNA from InChianti sample 441


title: Peripheral blood RNA from InChianti sample 447


title: Peripheral blood RNA from InChianti sample 494


title: Peripheral blood RNA from InChianti sample 443


title: Peripheral blood RNA from InChianti sample 444


title: Peripheral blood RNA from InChianti sample 442


title: Peripheral blood RNA from InChianti sample 446


title: Peripheral blood RNA from InChianti sample 445


title: Peripheral blood RNA from InChianti sample 440


title: Peripheral blood RNA from InChianti sample 467


title: Peripheral blood RNA from InChianti sample 439


title: Peripheral blood RNA from InChianti sample 438


title: Peripheral blood RNA from InChianti sample 435


title: Peripheral blood RNA from InChianti sample 434


title: Peripheral blood RNA from InChianti sample 436


title: Peripheral blood RNA from InChianti sample 432


title: Peripheral blood RNA from InChianti sample 437


title: Peripheral blood RNA from InChianti sample 428


title: Peripheral blood RNA from InChianti sample 429


title: Peripheral blood RNA from InChianti sample 430


title: Peripheral blood RNA from InChianti sample 426


title: Peripheral blood RNA from InChianti sample 427


title: Peripheral blood RNA from InChianti sample 433


title: Peripheral blood RNA from InChianti sample 431


title: Peripheral blood RNA from InChianti sample 421


title: C2C12 differentiating in poor medium

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
C2C12-DF
C2C12 cell line from the RIKEN cell bank.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with the mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals.

organism: Mus musculus

source_name: C2C12 cells, differentiating

label_protocol: Amino Allyl aRNA was synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye coupling and fragmentation were performed according to the protocol supplied by TORAY Industries, Inc.

growth_protocol: Cells were grown in either proliferation medim containing 10% fetal bovine serum in Dulbecco's Modified Eagle Medium (DMEM) or differentiation medium containing 2% horse serum in DMEM. Cells were cultured for two days in a culture dish with 100-mm diameter.

extract_protocol: RNA samples were extracted from cells using the miRNeasy Mini Kit (Qiagen).

value: myoblasts

tag: condition

value: differentiating


title: Peripheral blood RNA from InChianti sample 422


title: Peripheral blood RNA from InChianti sample 423


title: Peripheral blood RNA from InChianti sample 418


title: Wnt4-overexpressing C2C12 subline proliferating in rich medium

description:
C2C12-W4-08
Wnt4-overexpressing subline was obtained in our laboratory after transfecting Wnt4-expressing plasmids in C2C12 cells, and cell cloning with blasticidin selection of the transfectants.

source_name: C2C12-derived Wnt4-overexpressing cells, proliferating

value: Wnt4-overexpressing C2C12 subline

value: Wnt4-overexpressing myoblasts

value: proliferating


title: Peripheral blood RNA from InChianti sample 424


title: Peripheral blood RNA from InChianti sample 420


title: Peripheral blood RNA from InChianti sample 414


title: C2C12 proliferating in rich medium

description:
C2C12-PR
C2C12 cell line from the RIKEN cell bank.

source_name: C2C12 cells, proliferating


title: Peripheral blood RNA from InChianti sample 416


title: Peripheral blood RNA from InChianti sample 425


title: Peripheral blood RNA from InChianti sample 417


title: Peripheral blood RNA from InChianti sample 412


title: Peripheral blood RNA from InChianti sample 413


title: Peripheral blood RNA from InChianti sample 405


title: Peripheral blood RNA from InChianti sample 415


title: Peripheral blood RNA from InChianti sample 410


title: Peripheral blood RNA from InChianti sample 408


title: Peripheral blood RNA from InChianti sample 419


title: Peripheral blood RNA from InChianti sample 409


title: Peripheral blood RNA from InChianti sample 411


title: Peripheral blood RNA from InChianti sample 406


title: Peripheral blood RNA from InChianti sample 403


title: Peripheral blood RNA from InChianti sample 465


title: Peripheral blood RNA from InChianti sample 404


title: Peripheral blood RNA from InChianti sample 401


title: Peripheral blood RNA from InChianti sample 407


title: Peripheral blood RNA from InChianti sample 400


title: Peripheral blood RNA from InChianti sample 394


title: Peripheral blood RNA from InChianti sample 402


title: Peripheral blood RNA from InChianti sample 393


title: Peripheral blood RNA from InChianti sample 390


title: Peripheral blood RNA from InChianti sample 399


title: Peripheral blood RNA from InChianti sample 391


title: Peripheral blood RNA from InChianti sample 398


title: Peripheral blood RNA from InChianti sample 396


title: Peripheral blood RNA from InChianti sample 397


title: Peripheral blood RNA from InChianti sample 389


title: Peripheral blood RNA from InChianti sample 395


title: Peripheral blood RNA from InChianti sample 377


title: Peripheral blood RNA from InChianti sample 374


title: Peripheral blood RNA from InChianti sample 383


title: Peripheral blood RNA from InChianti sample 392


title: Peripheral blood RNA from InChianti sample 375


title: Peripheral blood RNA from InChianti sample 388


title: Peripheral blood RNA from InChianti sample 386


title: Peripheral blood RNA from InChianti sample 380


title: Peripheral blood RNA from InChianti sample 385


title: Peripheral blood RNA from InChianti sample 379


title: Peripheral blood RNA from InChianti sample 376


title: Peripheral blood RNA from InChianti sample 382


title: Peripheral blood RNA from InChianti sample 378


title: Peripheral blood RNA from InChianti sample 372


title: Peripheral blood RNA from InChianti sample 384


title: Peripheral blood RNA from InChianti sample 381


title: Peripheral blood RNA from InChianti sample 387


title: Peripheral blood RNA from InChianti sample 373


title: Peripheral blood RNA from InChianti sample 357


title: Peripheral blood RNA from InChianti sample 368


title: Peripheral blood RNA from InChianti sample 370


title: Peripheral blood RNA from InChianti sample 367


title: Peripheral blood RNA from InChianti sample 369


title: Peripheral blood RNA from InChianti sample 361


title: Peripheral blood RNA from InChianti sample 356


title: Peripheral blood RNA from InChianti sample 363


title: Peripheral blood RNA from InChianti sample 362


title: Peripheral blood RNA from InChianti sample 353


title: Peripheral blood RNA from InChianti sample 355


title: Peripheral blood RNA from InChianti sample 351


title: Peripheral blood RNA from InChianti sample 350


title: Peripheral blood RNA from InChianti sample 359


title: Peripheral blood RNA from InChianti sample 358


title: Peripheral blood RNA from InChianti sample 365


title: Peripheral blood RNA from InChianti sample 360


title: Peripheral blood RNA from InChianti sample 349


title: Peripheral blood RNA from InChianti sample 354


title: Peripheral blood RNA from InChianti sample 352


title: Peripheral blood RNA from InChianti sample 366


title: Peripheral blood RNA from InChianti sample 346


title: Peripheral blood RNA from InChianti sample 344


title: Peripheral blood RNA from InChianti sample 364


title: Peripheral blood RNA from InChianti sample 348


title: Peripheral blood RNA from InChianti sample 345


title: Peripheral blood RNA from InChianti sample 347


title: Peripheral blood RNA from InChianti sample 342


title: Peripheral blood RNA from InChianti sample 343


title: Peripheral blood RNA from InChianti sample 341


title: Peripheral blood RNA from InChianti sample 338


title: Peripheral blood RNA from InChianti sample 327


title: Peripheral blood RNA from InChianti sample 336


title: Peripheral blood RNA from InChianti sample 335


title: Peripheral blood RNA from InChianti sample 340


title: Peripheral blood RNA from InChianti sample 332


title: Peripheral blood RNA from InChianti sample 339


title: Peripheral blood RNA from InChianti sample 337


title: Peripheral blood RNA from InChianti sample 324


title: Peripheral blood RNA from InChianti sample 322


title: Peripheral blood RNA from InChianti sample 333


title: Peripheral blood RNA from InChianti sample 329


title: Peripheral blood RNA from InChianti sample 325


title: Peripheral blood RNA from InChianti sample 320


title: Peripheral blood RNA from InChianti sample 334


title: Peripheral blood RNA from InChianti sample 331


title: Peripheral blood RNA from InChianti sample 330


title: Peripheral blood RNA from InChianti sample 328


title: Peripheral blood RNA from InChianti sample 318


title: Peripheral blood RNA from InChianti sample 319


title: Peripheral blood RNA from InChianti sample 321


title: Peripheral blood RNA from InChianti sample 371


title: Peripheral blood RNA from InChianti sample 326


title: Peripheral blood RNA from InChianti sample 323


title: Peripheral blood RNA from InChianti sample 311


title: Peripheral blood RNA from InChianti sample 308


title: Peripheral blood RNA from InChianti sample 305


title: Peripheral blood RNA from InChianti sample 315


title: Peripheral blood RNA from InChianti sample 307


title: Peripheral blood RNA from InChianti sample 317


title: Peripheral blood RNA from InChianti sample 297


title: Peripheral blood RNA from InChianti sample 312


title: Peripheral blood RNA from InChianti sample 298


title: Peripheral blood RNA from InChianti sample 291


title: Peripheral blood RNA from InChianti sample 289


title: Peripheral blood RNA from InChianti sample 299


title: Peripheral blood RNA from InChianti sample 292


title: Peripheral blood RNA from InChianti sample 310


title: Peripheral blood RNA from InChianti sample 304


title: Peripheral blood RNA from InChianti sample 301


title: Peripheral blood RNA from InChianti sample 303


title: Peripheral blood RNA from InChianti sample 288


title: Peripheral blood RNA from InChianti sample 300


title: Peripheral blood RNA from InChianti sample 309


title: Peripheral blood RNA from InChianti sample 294


title: Peripheral blood RNA from InChianti sample 314


title: Peripheral blood RNA from InChianti sample 290


title: Peripheral blood RNA from InChianti sample 295


title: Peripheral blood RNA from InChianti sample 316


title: Peripheral blood RNA from InChianti sample 296


title: Peripheral blood RNA from InChianti sample 302


title: Peripheral blood RNA from InChianti sample 313


title: Peripheral blood RNA from InChianti sample 293


title: Peripheral blood RNA from InChianti sample 286


title: Peripheral blood RNA from InChianti sample 287


title: Peripheral blood RNA from InChianti sample 280


title: Peripheral blood RNA from InChianti sample 284


title: Peripheral blood RNA from InChianti sample 285


title: Peripheral blood RNA from InChianti sample 282


title: Peripheral blood RNA from InChianti sample 274


title: Peripheral blood RNA from InChianti sample 283


title: Peripheral blood RNA from InChianti sample 270


title: Peripheral blood RNA from InChianti sample 279


title: Peripheral blood RNA from InChianti sample 271


title: Peripheral blood RNA from InChianti sample 276


title: Peripheral blood RNA from InChianti sample 273


title: Peripheral blood RNA from InChianti sample 277


title: Peripheral blood RNA from InChianti sample 275


title: Peripheral blood RNA from InChianti sample 269


title: Peripheral blood RNA from InChianti sample 278


title: Peripheral blood RNA from InChianti sample 262


title: Peripheral blood RNA from InChianti sample 281


title: Peripheral blood RNA from InChianti sample 264


title: Peripheral blood RNA from InChianti sample 265


title: Peripheral blood RNA from InChianti sample 268


title: Peripheral blood RNA from InChianti sample 266


title: Peripheral blood RNA from InChianti sample 259


title: Peripheral blood RNA from InChianti sample 260


title: Peripheral blood RNA from InChianti sample 267


title: Peripheral blood RNA from InChianti sample 261


title: Peripheral blood RNA from InChianti sample 263


title: Peripheral blood RNA from InChianti sample 258


title: Peripheral blood RNA from InChianti sample 272


title: Peripheral blood RNA from InChianti sample 257


title: Peripheral blood RNA from InChianti sample 306


title: Peripheral blood RNA from InChianti sample 254


title: Peripheral blood RNA from InChianti sample 255


title: Peripheral blood RNA from InChianti sample 248


title: Peripheral blood RNA from InChianti sample 252


title: Peripheral blood RNA from InChianti sample 256


title: Peripheral blood RNA from InChianti sample 249


title: Peripheral blood RNA from InChianti sample 246


title: Peripheral blood RNA from InChianti sample 253


title: Peripheral blood RNA from InChianti sample 251


title: Peripheral blood RNA from InChianti sample 240


title: Peripheral blood RNA from InChianti sample 250


title: Peripheral blood RNA from InChianti sample 242


title: Peripheral blood RNA from InChianti sample 232


title: Peripheral blood RNA from InChianti sample 238


title: Peripheral blood RNA from InChianti sample 244


title: Peripheral blood RNA from InChianti sample 245


title: Peripheral blood RNA from InChianti sample 247


title: Peripheral blood RNA from InChianti sample 230


title: Peripheral blood RNA from InChianti sample 237


title: Peripheral blood RNA from InChianti sample 241


title: Peripheral blood RNA from InChianti sample 234


title: Peripheral blood RNA from InChianti sample 243


title: Peripheral blood RNA from InChianti sample 239


title: Peripheral blood RNA from InChianti sample 236


title: Peripheral blood RNA from InChianti sample 235


title: Peripheral blood RNA from InChianti sample 233


title: Peripheral blood RNA from InChianti sample 229


title: Peripheral blood RNA from InChianti sample 231


title: Peripheral blood RNA from InChianti sample 228


title: Peripheral blood RNA from InChianti sample 219


title: Peripheral blood RNA from InChianti sample 224


title: Peripheral blood RNA from InChianti sample 222


title: Peripheral blood RNA from InChianti sample 227


title: Peripheral blood RNA from InChianti sample 218


title: Peripheral blood RNA from InChianti sample 221


title: Peripheral blood RNA from InChianti sample 216


title: Peripheral blood RNA from InChianti sample 226


title: Peripheral blood RNA from InChianti sample 206


title: Peripheral blood RNA from InChianti sample 217


title: Peripheral blood RNA from InChianti sample 209


title: Peripheral blood RNA from InChianti sample 211


title: Peripheral blood RNA from InChianti sample 215


title: Peripheral blood RNA from InChianti sample 213


title: Peripheral blood RNA from InChianti sample 207


title: Peripheral blood RNA from InChianti sample 223


title: Peripheral blood RNA from InChianti sample 212


title: Peripheral blood RNA from InChianti sample 201


title: Peripheral blood RNA from InChianti sample 210


title: Peripheral blood RNA from InChianti sample 208


title: Peripheral blood RNA from InChianti sample 225


title: Peripheral blood RNA from InChianti sample 214


title: Peripheral blood RNA from InChianti sample 220


title: Peripheral blood RNA from InChianti sample 205


title: Peripheral blood RNA from InChianti sample 202


title: Peripheral blood RNA from InChianti sample 204


title: Peripheral blood RNA from InChianti sample 198


title: Peripheral blood RNA from InChianti sample 200


title: Peripheral blood RNA from InChianti sample 199


title: Peripheral blood RNA from InChianti sample 203


title: Peripheral blood RNA from InChianti sample 195


title: Peripheral blood RNA from InChianti sample 187


title: Peripheral blood RNA from InChianti sample 184


title: Peripheral blood RNA from InChianti sample 197


title: Peripheral blood RNA from InChianti sample 186


title: Peripheral blood RNA from InChianti sample 191


title: Peripheral blood RNA from InChianti sample 182


title: Peripheral blood RNA from InChianti sample 181


title: Peripheral blood RNA from InChianti sample 188


title: Peripheral blood RNA from InChianti sample 177


title: Peripheral blood RNA from InChianti sample 180


title: Peripheral blood RNA from InChianti sample 196


title: Peripheral blood RNA from InChianti sample 190


title: Peripheral blood RNA from InChianti sample 171


title: Peripheral blood RNA from InChianti sample 192


title: Peripheral blood RNA from InChianti sample 183


title: Peripheral blood RNA from InChianti sample 179


title: Peripheral blood RNA from InChianti sample 176


title: Peripheral blood RNA from InChianti sample 174


title: Peripheral blood RNA from InChianti sample 185


title: Peripheral blood RNA from InChianti sample 170


title: Peripheral blood RNA from InChianti sample 172


title: Peripheral blood RNA from InChianti sample 178


title: Peripheral blood RNA from InChianti sample 175


title: Peripheral blood RNA from InChianti sample 194


title: Peripheral blood RNA from InChianti sample 189


title: Peripheral blood RNA from InChianti sample 193


title: Peripheral blood RNA from InChianti sample 168


title: Peripheral blood RNA from InChianti sample 166


title: Peripheral blood RNA from InChianti sample 163


title: Peripheral blood RNA from InChianti sample 162


title: Peripheral blood RNA from InChianti sample 169


title: Peripheral blood RNA from InChianti sample 159


title: Peripheral blood RNA from InChianti sample 146


title: Peripheral blood RNA from InChianti sample 167


title: Peripheral blood RNA from InChianti sample 154


title: Peripheral blood RNA from InChianti sample 165


title: Peripheral blood RNA from InChianti sample 152


title: Peripheral blood RNA from InChianti sample 149


title: Peripheral blood RNA from InChianti sample 173


title: Peripheral blood RNA from InChianti sample 164


title: Peripheral blood RNA from InChianti sample 160


title: Peripheral blood RNA from InChianti sample 156


title: Peripheral blood RNA from InChianti sample 157


title: Peripheral blood RNA from InChianti sample 151


title: Peripheral blood RNA from InChianti sample 158


title: Peripheral blood RNA from InChianti sample 161


title: Peripheral blood RNA from InChianti sample 145


title: Peripheral blood RNA from InChianti sample 153


title: Peripheral blood RNA from InChianti sample 148


title: Peripheral blood RNA from InChianti sample 150


title: Peripheral blood RNA from InChianti sample 155


title: Peripheral blood RNA from InChianti sample 143


title: Peripheral blood RNA from InChianti sample 144


title: Peripheral blood RNA from InChianti sample 142


title: Peripheral blood RNA from InChianti sample 147


title: Peripheral blood RNA from InChianti sample 141


title: Peripheral blood RNA from InChianti sample 139


title: Peripheral blood RNA from InChianti sample 140


title: Peripheral blood RNA from InChianti sample 130


title: Peripheral blood RNA from InChianti sample 127


title: Peripheral blood RNA from InChianti sample 131


title: Peripheral blood RNA from InChianti sample 137


title: Peripheral blood RNA from InChianti sample 129


title: Peripheral blood RNA from InChianti sample 136


title: Peripheral blood RNA from InChianti sample 126


title: Peripheral blood RNA from InChianti sample 128


title: Peripheral blood RNA from InChianti sample 124


title: Peripheral blood RNA from InChianti sample 133


title: Peripheral blood RNA from InChianti sample 121


title: Peripheral blood RNA from InChianti sample 117


title: Peripheral blood RNA from InChianti sample 119


title: Peripheral blood RNA from InChianti sample 125


title: Peripheral blood RNA from InChianti sample 112


title: Peripheral blood RNA from InChianti sample 115


title: Peripheral blood RNA from InChianti sample 114


title: Peripheral blood RNA from InChianti sample 116


title: Peripheral blood RNA from InChianti sample 111


title: Peripheral blood RNA from InChianti sample 123


title: Peripheral blood RNA from InChianti sample 135


title: Peripheral blood RNA from InChianti sample 113


title: Peripheral blood RNA from InChianti sample 132


title: Peripheral blood RNA from InChianti sample 122


title: Peripheral blood RNA from InChianti sample 134


title: Peripheral blood RNA from InChianti sample 138


title: Peripheral blood RNA from InChianti sample 120


title: Peripheral blood RNA from InChianti sample 110


title: Peripheral blood RNA from InChianti sample 118


title: Peripheral blood RNA from InChianti sample 102


title: Peripheral blood RNA from InChianti sample 109


title: Peripheral blood RNA from InChianti sample 108


title: Peripheral blood RNA from InChianti sample 100


title: Peripheral blood RNA from InChianti sample 106


title: Peripheral blood RNA from InChianti sample 96


title: Peripheral blood RNA from InChianti sample 93


title: Peripheral blood RNA from InChianti sample 105


title: Peripheral blood RNA from InChianti sample 104


title: Peripheral blood RNA from InChianti sample 97


title: Peripheral blood RNA from InChianti sample 101


title: Peripheral blood RNA from InChianti sample 94


title: Peripheral blood RNA from InChianti sample 98


title: Peripheral blood RNA from InChianti sample 89


title: Peripheral blood RNA from InChianti sample 82


title: Peripheral blood RNA from InChianti sample 88


title: Peripheral blood RNA from InChianti sample 85


title: Peripheral blood RNA from InChianti sample 86


title: Peripheral blood RNA from InChianti sample 99


title: Peripheral blood RNA from InChianti sample 91


title: Peripheral blood RNA from InChianti sample 95


title: Peripheral blood RNA from InChianti sample 103


title: Peripheral blood RNA from InChianti sample 84


title: Peripheral blood RNA from InChianti sample 92


title: Peripheral blood RNA from InChianti sample 83


title: Peripheral blood RNA from InChianti sample 78


title: Peripheral blood RNA from InChianti sample 90


title: Peripheral blood RNA from InChianti sample 79


title: Peripheral blood RNA from InChianti sample 87


title: Peripheral blood RNA from InChianti sample 76


title: Peripheral blood RNA from InChianti sample 74


title: Peripheral blood RNA from InChianti sample 75


title: Peripheral blood RNA from InChianti sample 77


title: Peripheral blood RNA from InChianti sample 71


title: Peripheral blood RNA from InChianti sample 73


title: Peripheral blood RNA from InChianti sample 72


title: Peripheral blood RNA from InChianti sample 70


title: Peripheral blood RNA from InChianti sample 65


title: Peripheral blood RNA from InChianti sample 64


title: Peripheral blood RNA from InChianti sample 67


title: Peripheral blood RNA from InChianti sample 68


title: Peripheral blood RNA from InChianti sample 62


title: Peripheral blood RNA from InChianti sample 69


title: Peripheral blood RNA from InChianti sample 61


title: Peripheral blood RNA from InChianti sample 63


title: Peripheral blood RNA from InChianti sample 55


title: Peripheral blood RNA from InChianti sample 80


title: Peripheral blood RNA from InChianti sample 60


title: Peripheral blood RNA from InChianti sample 54


title: Peripheral blood RNA from InChianti sample 52


title: Peripheral blood RNA from InChianti sample 50


title: Peripheral blood RNA from InChianti sample 56


title: Peripheral blood RNA from InChianti sample 57


title: Peripheral blood RNA from InChianti sample 53


title: Peripheral blood RNA from InChianti sample 59


title: Peripheral blood RNA from InChianti sample 81


title: Peripheral blood RNA from InChianti sample 58


title: Peripheral blood RNA from InChianti sample 51


title: Peripheral blood RNA from InChianti sample 66


title: Peripheral blood RNA from InChianti sample 47


title: Peripheral blood RNA from InChianti sample 45


title: Peripheral blood RNA from InChianti sample 46


title: Peripheral blood RNA from InChianti sample 42


title: Peripheral blood RNA from InChianti sample 36


title: Peripheral blood RNA from InChianti sample 38


title: Peripheral blood RNA from InChianti sample 32


title: Peripheral blood RNA from InChianti sample 39


title: Peripheral blood RNA from InChianti sample 43


title: Peripheral blood RNA from InChianti sample 35


title: Peripheral blood RNA from InChianti sample 41


title: Peripheral blood RNA from InChianti sample 44


title: Peripheral blood RNA from InChianti sample 48


title: Peripheral blood RNA from InChianti sample 34


title: Peripheral blood RNA from InChianti sample 31


title: Peripheral blood RNA from InChianti sample 33


title: Peripheral blood RNA from InChianti sample 107


title: Peripheral blood RNA from InChianti sample 37


title: Peripheral blood RNA from InChianti sample 26


title: Peripheral blood RNA from InChianti sample 40


title: Peripheral blood RNA from InChianti sample 23


title: Peripheral blood RNA from InChianti sample 24


title: Peripheral blood RNA from InChianti sample 30


title: Peripheral blood RNA from InChianti sample 14


title: Peripheral blood RNA from InChianti sample 27


title: PP4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

description: Replicate 4 of 4.

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent-026655) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the sandwich firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979), then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulting Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
This experiment used the multiple yellow strategy in which Cy3- and Cy5-labeled biological replicates are cohybridized with a two-color array and similarly labeled samples of different conditions are compared across the arrays.

source_name: Pituitary, peripubertal

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate Cyanine 3 (Cy3) or Cyanine 5 (Cy5)-labeled CTP.

extract_protocol: Total RNA extraction was performed using RNeasy Mini kit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: Hypophyses were removed from adult female mice and and minced.

tag: strain/background

tag: Sex

value: female

value: pituitary

tag: develomental stage

value: adult

value: VD-deficient diet during peripubertal stage


title: Peripheral blood RNA from InChianti sample 15


title: Peripheral blood RNA from InChianti sample 20


title: Peripheral blood RNA from InChianti sample 11


title: Peripheral blood RNA from InChianti sample 29


title: Peripheral blood RNA from InChianti sample 25


title: Peripheral blood RNA from InChianti sample 8


title: Peripheral blood RNA from InChianti sample 9


title: Peripheral blood RNA from InChianti sample 18


title: Peripheral blood RNA from InChianti sample 17


title: Peripheral blood RNA from InChianti sample 21


title: Peripheral blood RNA from InChianti sample 13


title: Peripheral blood RNA from InChianti sample 10


title: PP3

description: Replicate 3 of 4.


title: Peripheral blood RNA from InChianti sample 12


title: Peripheral blood RNA from InChianti sample 6


title: Peripheral blood RNA from InChianti sample 7


title: Peripheral blood RNA from InChianti sample 22


title: Peripheral blood RNA from InChianti sample 28


title: Peripheral blood RNA from InChianti sample 16


title: Peripheral blood RNA from InChianti sample 19


title: PP2

description: Replicate 2 of 4.


title: Peripheral blood RNA from InChianti sample 49


title: PE4

description: Replicate 4 of 4.

source_name: Pituitary, early life

value: VD-deficient diet during early life


title: PaPAO1_pJN105phaF_2

city: AUSTIN

first: Peter

middle: Allan

last: Jorth

state: TEXAS

address: 2506 Speedway Blvd

department: Molecular Genetics and Microbiology

institute: University of Texas at Austin

description: P. aeruginosa PAO1 pJN105-phaF 2

hyb_protocol: GeneChips were washed and stained using an Affymetrix fluidics station at the University of Iowa DNA core facility, followed by manufacturer's guideline.

scan_protocol: GeneChips were scanned using an Affymetrix fluidics station at the University of Iowa DNA core facility, followed by manufacturer's guideline.

data_processing: Microarray .CEL files were processed using the RMA method with the affy package (Version 1.32.1) in R (Version 2.14.1) using default options.

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa PAO1 pJN105-phaF

label_protocol: The cDNA synthesis products were purified and fragmented by brief incubation with DNase I, and the 3' termini of the fragmentation products were labeled with biotin-ddUTP (Schuster M, et al., J. Bacteriol. 185: 2066-2079)).

growth_protocol: Bacteria were grown to exponential phase in morpholinepropanesulfonic acid (MOPS)-buffered medium (50 mM MOPS [pH 7.2], 93 mM NH4Cl, 43 mM NaCl, 3.7 mM KH2PO4, 1 mM MgSO4, and 3.5 μM FeSO4 . 7H2O) supplemented with 0.5% glucose and 0.5% casamino acids.

extract_protocol: Qiagen Rneasy minikit.

treatment_protocol: Cells were mixed with RNA later and saved for RNA isolation.

tag: genotype/variation

value: phaF overexpression (in pJN105-phaF)

tag: growth phase

value: exponential phase


title: PE2

description: Replicate 2 of 4.


title: Peripheral blood RNA from InChianti sample 4


title: PC4

description: Replicate 4 of 4.

source_name: Pituitary, control

value: normal diet


title: Peripheral blood RNA from InChianti sample 5


title: PP1

description: Replicate 1 of 4.


title: Peripheral blood RNA from InChianti sample 3


title: Lymphoblast cell line

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

description: Human lymphoblast cell line

hyb_protocol: Hyb protocol as per manufacturer's instructions, Illumina

scan_protocol: Scan protocol as per manufacturer's instructions, Illumina

data_processing: Raw data was read by the methylumi package in R Development (2.12). The beta scores were calculated from the raw intensity values from each probe, no normalisation was performed.

source_name: Lymphoblast cell line

label_protocol: Label protocol as per manufacturer's instructions, Illumina

extract_protocol: tail lysis buffer, proteinase K digestion, phenol chloroform extraction, ethanol precipitation

value: BEL


title: Peripheral blood RNA from InChianti sample 2

value: peripheral blood leucocyte


title: PE1

description: Replicate 1 of 4.


title: HepG2 AS 5mg/L Jun 12, 2012 rep2

city: Sapporo

first: Toshikazu

last: Fukushima

address: Kita13, Nishi8, Kita-ku

institute: Hokkaido University

hyb_protocol: Hybridization were carried out on Human Genome Focus Array (Affymetrix, Santa Clara, CA) as described in the manufacturer’s instruction.

scan_protocol: After hybridization, the array was washed, stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Station 450 (Affymetrix), and scanned on a GeneChip Scanner 3000 7G (Affymetrix). The raw data files [cell intensity (CEL) files] were created from scanned images by AGCC (GeneChip Command Console Software, Affymetrix).

data_processing: For microarray analysis, probe-level data in CEL files were normalized by MAS5 using AGCC and transferred to Avadis 4.3 prophetic software.

source_name: human hepatoma cell line, HepG2

label_protocol: Target preparation were carried out as described in the manufacturer’s instruction.

growth_protocol: Cells were grown in Eagle’s minimal essential medium (MEM) (Nissui, Tokyo, Japan), supplemented with 10% fetal bovine serum (FBS) and 60 mg/mL kanamycin. Cells were maintained at 37 °C in the 5% CO2 humidified incubator.

extract_protocol: Cells were lysed on the 60 mm culture dishes, and total RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Water samples were extracted by solid phase extraction (SPE) and dissolved in DMSO.  Prior to exposure, SPE fraction (maximum content is 1%) was mixed with ×1MEM, and supplemented with 1% fetal bovine serum (FBS) and 60 mg/mL kanamycin.  Cells were seeded onto culture vessels in 105 cell/mL and incubated overnight to grow 40-50% confluent. The normal culture medium was replaced by the sample-containing MEM and incubated for 48 h.

tag: cell bank no

value: male

tag: age of sampling

value: 15 years

tag: tissue derived

value: liver

tag: case history

value: hepatocyte carcinoma

tag: life span

value: infinite

tag: classification

value: transformed

value: exposed to SEP concentrated effluent from activated sludge process (AS) chlorinated with 5mg/L sodium hypochlorite

tag: sample preparation

value: extracted by solid phase extraction (SPE) and mixed with culture medium

tag: sampling date


title: After Hoxb8 Induction

description: AML Model Mouse Cell Line

source_name: After Hoxb8 Induction

tag: strain

tag: cell line

value: HTT


title: PaPAO1_pJN105phaF_1

description: P. aeruginosa PAO1 pJN105-phaF 1


title: PE3

description: Replicate 3 of 4.

value: female

tag: tissue

value: pituitary

value: adult

tag: treatment


title: Before Hoxb8 Induction

description: AML Model Mouse Cell Line

source_name: Before Hoxb8 Induction


title: OP3

description: Replicate 3 of 4.

source_name: Ovary, peripubertal

treatment_protocol: Ovaries were removed from adult female mice and minced.

tag: strain/background

value: ovary

value: VD-deficient diet during peripubertal stage


title: PC3

description: Replicate 3 of 4.

tag: Sex

value: normal diet


title: HepG2 AS 2mg/L Jun 12, 2012 rep1

value: exposed to SEP concentrated effluent from activated sludge process (AS) chlorinated with 2mg/L sodium hypochlorite


title: HepG2 AS 2mg/L Jun 12, 2012 rep2


title: PC1

description: Replicate 1 of 4.

tag: develomental stage


title: OP2

description: Replicate 2 of 4.


title: HepG2 AS 5mg/L Jun 12, 2012 rep1


title: HepG2 AS 0mg/L Jun 12, 2012 rep2

value: exposed to SEP concentrated effluent from activated sludge process (AS) chlorinated with 0mg/L sodium hypochlorite


title: PaPAO1_pJN105_1

description: P. aeruginosa PAO1 pJN105 1

source_name: P. aeruginosa PAO1 pJN105

tag: genotype/variation

value: empty vector control (pJN105)

value: exponential phase


title: HepG2 AS 0mg/L Jun 12, 2012 rep1

value: male

value: 15 years

value: liver


title: PaPAO1_pJN105_2

description: P. aeruginosa PAO1 pJN105 2

tag: growth phase


title: Peripheral blood RNA from InChianti sample 1

value: peripheral blood leucocyte


title: OP4

description: Replicate 4 of 4.


title: PC2

description: Replicate 2 of 4.


title: OE4

description: Replicate 4 of 4.

source_name: Ovary, early life

value: VD-deficient diet during early life


title: HepG2 S-MBR B 5mg/L Apr 12, 2012 rep2

tag: cell bank no

value: hepatocyte carcinoma

value: infinite

value: transformed

value: exposed to SEP concentrated effluent from submerged membrane bioreactor (S-MBR) with higher sludge conc, 8,000 mg/L chlorinated with 5mg/L sodium hypochlorite

value: extracted by solid phase extraction (SPE) and mixed with culture medium


title: HepG2 S-MBR B 5mg/L Apr 12, 2012 rep1

tag: age of sampling


title: HepG2 control Jun 12, 2012 rep2

tag: tissue derived

value: exposed to SPE concentrated MQ water


title: HepG2 S-MBR B 2mg/L Apr 12, 2012 rep2

tag: case history

value: exposed to SEP concentrated effluent from submerged membrane bioreactor (S-MBR) with higher sludge conc, 8,000 mg/L chlorinated with 2mg/L sodium hypochlorite


title: OE2

description: Replicate 2 of 4.

value: female

value: ovary

value: adult


title: OP1

description: Replicate 1 of 4.

value: VD-deficient diet during peripubertal stage


title: Pregnant FTDC with PIF

city: New Haven

first: Christina

middle: Maria

last: Duzyj

state: CT

address: 333 Cedar St

department: Ob/Gyn: Maternal Fetal Medicine

institute: Yale University

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Probe Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Optical scanning with GeneChip Scanner 3000 (Affymetrix) at W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, CT.

data_processing: Raw data were analyzed by GeneSpring software (Agilent, Santa Clara, CA, USA), normalized for inter-chip and intra-chip variation to eliminate false-positive results. The Sample data tables include MAS5 values. Fold-change data are linked to the Series record.

source_name: Pooled triplicate FTDC culture with PIF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA per the Affymetrix 3' IVT Express Kit User Manual.

growth_protocol: Discarded endometrial tissue from premenopausal women undergoing hysterectomies for benign indications were collected.  Decidual specimens were collected from women undergoing elective terminations in weeks 6-12 of normal pregnancy.  Endometral and decidual cells were isolated and resuspended in RPMI-1640, grown to confluence and confirmed to be leukocyte free.  Cells were then decidualized using 10^-8mol/L estradiol and 10^-7mol/L synthetic progestin analog for 7 days.

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

treatment_protocol: Cells were switched to a serum-free medium containing insulin, transferrin and selenium, 5umol/L trace elecments and 50ug/mL ascorbic acid, and treated for 24 hours with or without synthetic PIF at 100nmol/L.

tag: cell type

value: FTDC

tag: mimicked developmental phase

value: Embryo implantation

value: PIF stimulation


title: Pregnant FTDC culture without PIF

source_name: Pooled triplicate FTDC culture without PIF

value: Control


title: HepG2 S-MBR B 2mg/L Apr 12, 2012 rep1

value: male

value: 15 years

value: liver

tag: life span

tag: classification

tag: sample preparation


title: OC4

description: Replicate 4 of 4.

source_name: Ovary, control

value: normal diet


title: Non-pregnant HESC culture with PIF

source_name: Pooled triplicate HESC culture with PIF

value: HESC

value: Embryogenesis


title: OE1

description: Replicate 1 of 4.

value: VD-deficient diet during early life


title: SSc6lung

city: Pittsburgh

first: Carol

last: Feghali-Bostwick

state: PA

address: MONF 628NW Pittsburgh

department: Medicine

institute: University of Pittsburgh

description: SSc-PAH

data_processing: The data were normalized using median normalization followed by square root transformation in caGEDA [Patel S, Lyons-Weiler J. caGEDA: a web application for the integrated analysis of global gene expression patterns in cancer. Appl Bioinformatics 2004;3(1):49-62]

source_name: SSc-PAH

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

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

value: Lung


title: OC3

description: Replicate 3 of 4.


title: Non-pregnant HESC culture without PIF

source_name: Pooled triplicate HESC culture without PIF


title: SSc36lung

description: SSc-PAH


title: NSC620358

city: Uppsala

first: Mårten

last: Fryknäs

address: Akademiska sjh ingång 61

department: Medical sciencies

institute: Uppsala university

description: Gene expression data from MCF7 cells treated with NSC620358 for 6 hours.

hyb_protocol: Affymetrix GeneChip® expression arrays (Human Genome U133 Plus 2.0 Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm.

scan_protocol: According to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: Breast cancer cell line MCF7

label_protocol: 2 micrograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA according to the GeneChip® Expression Analysis Technical Manual (Rev. 5, Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of total RNA was performed using Qiagen Rneasy minikit according to the manufacturer's instructions.

treatment_protocol: MCF7 cells treated with 10 microM NSC620358 for 6 hours.

tag: perturbagen

value: small molecule

tag: concentration

tag: vehicle

value: DMSO

tag: duration

value: 6 h

tag: cell line


title: HepG2 S-MBR B 0mg/L Apr 12, 2012 rep2

tag: Sex

value: hepatocyte carcinoma

value: infinite

value: transformed

tag: treatment

value: exposed to SEP concentrated effluent from submerged membrane bioreactor (S-MBR) with higher sludge conc, 8,000 mg/L chlorinated with 0mg/L sodium hypochlorite

value: extracted by solid phase extraction (SPE) and mixed with culture medium

tag: sampling date


title: SSc9lung

description: SSc-PAH

tag: tissue


title: SSc7lung

description: SSc-PAH


title: OC2

description: Replicate 2 of 4.

tag: strain/background

value: female

value: ovary

tag: develomental stage

value: adult


title: HepG2 S-MBR B 0mg/L Apr 12, 2012 rep1

tag: cell bank no

value: male

tag: age of sampling

value: 15 years

tag: tissue derived

value: liver

tag: case history


title: HepG2 control Apr 12, 2012 rep2

tag: life span

tag: classification

value: exposed to SPE concentrated MQ water


title: OE3

description: Replicate 3 of 4.

value: VD-deficient diet during early life


title: SSc33lung

description: SSc-PAH

value: Lung


title: HepG2 control Jun 12, 2012 rep1

tag: sample preparation


title: HepG2 control Apr 12, 2012 rep1


title: OC1

description: Replicate 1 of 4.

value: normal diet


title: Liver_Replicate_3

city: Madrid

first: Paula

last: Martinez

state: Madrid

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on a G2505C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.7).

data_processing: Microarray background subtraction was carried out using normexp method. Normalization was performed using lowess for within array normalization and quantiles for between array normalization. Differentially expressed genes were obtained by applying linear models with R limma package (Smyth, 2005) (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p-value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

source_name: Liver, wild-type mouse, 30 weeks

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

extract_protocol: Total RNA was extracted with Trizol. The QIAGEN kit was employed for purification. RNA Integrity Numbers were in the range 6.6 to 8.7 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

tag: genotype/variation

value: wild-type

tag: age

value: 30 weeks

source_name: Liver, Rap1 knockout mouse -/-, 30 weeks


title: Liver_Replicate_2


title: Liver_Replicate_1


title: Untreated control, 13 week_old, biological rep3

city: Berkeley

first: Cyrus

middle: Farrokh

last: Khambatta

state: CA

address: 309 Morgan Hall

department: Nutritional Sciences

institute: University of California at Berkeley

description: Gene expression data from untreated ZDF rat at 13 weeks of age.

hyb_protocol: Labeled cRNA (15.0 ug) was fragmented by Magnesium ion-mediated hydrolysis and hybridized for 16hr at 45oC to Affymetrix GeneChip Rat Genome 230 2.0 arrays, which contain probes for over 31,000 transcripts representing approximately 28,700 annotated rat genes and expressed sequence tags (ESTs) (Affymetrix, Santa Clara, CA).  Arrays were washed and stained using a Fluidics Station 450 (Affymetrix).  The arrays were stained with phycoerythrein-conjugated streptavidin (Invitrogen, Carlsbad, CA).

scan_protocol: Fluorescence intensities were determined using a GCS 3000 7G high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using programs resident in AGCC and Expression Console (Affymetrix). Quality control metrics for cRNA integrity, sample loading, and variations in staining were determined by MAS 5.0 statistical algorithms.

data_processing: Signal values were generated by the RMA method and Detection p-values were generated by MAS 5.0.  Probe sets exhibiting significant differential expression were identified using GeneMaths XT (Applied Maths, Austin TX), based on the following criteria: 1) MAS5.0 detection p-values ≤ 0.05 for all samples in at least one experimental group, 2) ANOVA p-value ≤ 0.05, 3) Absolute Signal log ratio ≥ 1.0 and independent t-test p-value ≤ 0.05 for at least one pair wise comparison versus the control group. Unsupervised hierarchical clustering and heat map generation were performed in GeneMaths XT following row mean centering of log2 transformed RMA signal values; probe set clustering was performed by the Unweighted Pair Group Method using Arithmetic averages (UPGMA) using Pearson correlation as the similarity metric.  Gene annotation, gene ontology information and biochemical pathway information were obtained from the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 from the National Institute of Allergy and Infectious Diseases (NIAID), at the National Institutes of Health (NIH).

organism: Rattus norvegicus

source_name: Untreated control ZDF rat islets at 13 weeks of age

label_protocol: cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription using the T7 promoter-coupled double stranded cDNA as template and the Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.).

extract_protocol: Total RNA was isolated from 20-30 mg of islets using the RNEasy kit according to the manufacturer’s instructions (Qiagen, Valencia, CA).  Equal amounts of RNA from each of 3 replicates were reverse transcribed to cDNA after the purity and concentration of RNA samples were determined from OD260/280 readings using a dual beam UV spectrophotometer and RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Five-week old ZDF (fa/fa) animals (n=24) were purchased from Charles River Laboratories (Wilmington, MA).  Following 48 hours of acclimation, animals were randomized into one of three groups: rosiglitazone treated (RT), rosiglitazone withdrawal (RW), or untreated controls (UC) and sacrificed at either 9, 11, 13, or 15 weeks of age.  All animals were fed the Purina 5008 diet.  Rosiglitazone was administered in the diet as powdered Avandia tablets (3mg rosiglitazone/kg body weight).

tag: strain

value: Zucker Diabetic Fatty Rat

tag: gender

value: 13 weeks

value: pancreatic islets


title: Wild-type white fat, rep 4

hyb_protocol: Total RNA samples were analyzed on Agilent's Mouse Genome DNA microarray by following manufacturer instructions. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1).

data_processing: Microarray background subtraction was carried out using normexp method. Normalization was performed using quantiles. Differentially expressed genes were obtained by applying linear models with R limma package (Smyth, 2005) (Bioconductor project, http://www.bioconductor.org). To account for multiple hypotheses testing, the estimated significance level (p-value) was adjusted using Benjamini & Hochberg False Discovery Rate (FDR) correction.

source_name: White fat, wild-type mouse, 10 weeks

label_protocol: Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore.

extract_protocol: Total RNA was extracted with Trizol. The QIAGEN kit was employed for purification. RNA Integrity Numbers were in the range 6.5 to 8.5 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

value: white fat

value: 10 weeks


title: SSc16lung

description: SSc-PAH


title: Untreated control, 13 week_old, biological rep2


title: SSc28lung

description: SSc-PAH


title: Untreated control, 13 week_old, biological rep1


title: Liver_dye_swap_experiment

description:
LIVER_DYE-SWAP_1
Dye-swap experiment.


title: Rosiglitazone 2 week withdrawal, 11 week_old, biological rep2

description: Gene expression data from Rosiglitazone treated (weeks 5-9) then withdrawal (weeks 9-11) ZDF rat at 11 weeks of age.

source_name: Rosiglitazone withdrawal ZDF rat islets at 11 weeks of age

value: 11 weeks


title: SSc8lung

description: SSc-PF

source_name: SSc-PF


title: SSc17lung

description: SSc-PAH


title: Rosiglitazone 2 week withdrawal, 11 week_old, biological rep3


title: SSc3lung

description: SSc-PAH


title: SSc32lung

description: SSc-PAH


title: Wild-type white fat, rep 2


title: Wild-type white fat, rep 3


title: Wild-type white fat, rep 1


title: Lymphoblast cell line

data_processing: Raw data was read by the minfi package in R Development (2.12). The beta scores were calculated from the raw intensity values from each probe, no normalisation was performed.

source_name: Human lymphoblast cell line

tag: cell line

value: JWL

tag: cell type

value: Human lymphoblast


title: SSc5lung

description: SSc PF

source_name: SSc PF


title: After Hoxb8 Induction

source_name: AML Model Mouse Cell Line

value: HTT

value: AML


title: Rosiglitazone treated, 9 week_old, biological rep3

description: Gene expression data from Rosiglitazone treated (weeks 5-9) ZDF rat at 9 weeks of age.

source_name: Rosiglitazone treated ZDF rat islets at 9 weeks of age

value: male

value: 9 weeks


title: SSc29lung

description: SSc-PF


title: CHA011_L2*T654I

city: Trieste

first: Paola

last: Roncaglia

state: TS

address: via Bonomea 265

department: Neurobiology

country: Italy

institute: SISSA/ISAS (International School for Advanced Studies)

hyb_protocol: Labeled cRNA was hybridized on Affymetrix GeneChip Human Genome U133A 2.0 Arrays. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).

scan_protocol: Arrays were scanned  with the GeneChip Scanner 3000 7G. Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Further data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Prior to statistical analysis, normalized data were then filtered based on Affymetrix detection call so that only probes that had a present call in at least one of the arrays were retained. Probes with intensity values <100 in all arrays were also excluded. Statistical analysis was performed with Rank Product and Significance Analysis of Microarray.

label_protocol: A 6μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).

growth_protocol: Cell lines were thawed on the same date, and grown with the same batch of RPMI-1640 media supplemented with 10% Fetal Calf Serum, 2 mM L-glutamine,  0.1 mg/ml streptomycin and 100 U/ml penicillin, under identical conditions (5% CO2, 37°C) to approximately the same cell density (10^6 cells/ml).

extract_protocol: Total RNA was extracted from 5x10^6 lymphoblastoid cells using the Qiaquick RNA Easy plus extraction kit (Qiagen, Mannheim, Germany) according to manufacturer's instructions.

treatment_protocol: No treatment

tag: group

value: patient

value: Epstein–Barr Virus transformed lymphocytes


title: SSc27lung

description: SSc PF

tag: tissue

value: Lung


title: Rosiglitazone treated, 9 week_old, biological rep2


title: Rap1 -/- white fat, rep 4

source_name: White fat, Rap1 knockout mouse -/-, 10 weeks

tag: strain/background


title: SSc38lung

description: SSc PF


title: NZB3LPS

city: Cambridge

first: Yingting

last: Mok

address: Hills Road

department: Cambridge Institute for Medical Research

institute: University of Cambridge

description: miRNA profiling

hyb_protocol: Oligonucleotide probes were coupled to color-coded polystyrene beads, allowing the simultaneous detection of about 90 different target oligonucleotides. To obtain expression profiles for 309 miRNAs, we created four distinct sets of bead-coupled miRNA probes. Each sample was hybridized to the four bead sets to generate a complete miRNA profile. Oligos were 5´-amino modified with a 6-carbon linker and conjugated to carboxylated xMAP beads (Luminex, Austin, TX, USA) in 96-well formats following the standard manufacturer's protocol. To generate bead set pools, 3 μl of each oligo-bead conjugate was mixed into 1 ml 1.5× TMAC buffer (4.5 M tetramethylammonium chloride, 0.15% sarkosyl, 75 mM Tris-HCl pH 8.0, 6 mM EDTA). Samples were hybridized in a 96-well format with two water-only blanks and at least three bead blanks containing water instead of the labeled sample for use as a background control. We included replicate probes and technical replicate samples across bead sets and sample plates, respectively, to aid quality control and data preprocessing. Hybridization was carried out overnight at 50°C with 33 μl of the bead pool and 15 μl of labeled sample.  Unbound sample was removed from beads by washing with 1 × TE and re-suspending in 1× TMAC buffer. SAPE, streptavidin-phycoerythrin, premium grade (Invitrogen) was added to the beads (1:100 dilution) and incubated for 10 minutes at 50°C to bind to biotin moieties on the cDNA. S

scan_protocol: Samples were processed on a Luminex 100 machine and median fluorescence intensity (MFI) values acquired using the StarStation software (ACS, Sheffield, UK).

data_processing: For the miRNA profiling of B cells across C57BL/6 and autoimmune strains of mice, well-to-well scaling was performed such that the total MFI of the post-labeling controls in each well was equal to the median value across all wells. Sample scaling was performed such that total MFI of the pre-labeling controls in each sample was equal to the median value across all samples. A threshold of 1 was applied and the data was log2-transformed. Filtering for ‘expressed’ miRNAs was performed by employing a cutoff value of three standard deviations above the median MFI of all readings. Differential gene expression between sample pairs was analysed by carrying out 1-way ANOVAs (1 way Analysis of Variance) for all combinations of sample pairs using Graphpad Prism. Combinations with p value <0.05 were then filtered to show only within-strain comparisons. Differential gene expression across all samples was analysed using GEPAS T-rex multi-class comparison (ANOVA) tool (Montaner et al, 2006), which provided P-values adjusted for multiple testing, with control of family-wise error rate  and false-discovery rate (Storey & Tibshirani, 2003).

label_protocol: After purification of 18-26 bp RNAs, adaptors were ligated at the 3´ and 5´ ends using T4 RNA ligase (Fermentas, Burlington, OT, CA), a RNA-DNA hybrid 5´-pUUUaaccgcgaattccagt-idT-3´ (Dharmacon; X = RNA, x = DNA, p = phosphate, idT = inverted [3´-3´ bond] deoxythymidine) was ligated to the 3´ end and 5´-acggaattcctcactAAA-3´ (Dharmacon) was ligated to the 5´ end using T4 RNA ligase. These bi-ligated products underwent reverse transcription using an adaptor specific primer (M37, 5´-pTACTGGAATTCGCGGTTA-3´) and then amplified and labeled using PCR (M37 and M33, 5´-biotin-CAACGGAATTCCTCACTAAA-3´). Amplification was performed on an Eppendorf thermal cycler at 95°C for 30 s, 50°C for 30 s and 72°C for 40 s for 18 cycles. PCR products were precipitated without glycogen and redissolved in 66 μl 1 × TE buffer containing 1 μl of three biotinylated post labeling controls (100 fmols each, FVR506, PTG20210, MRC677).

extract_protocol: MiRNAs were extracted from 5 μg of sample total RNA using denaturing PAGE.

value: NZB

tag: autoimmune strain

value: yes

value: splenic B-cell

tag: treatment

value: LPS


title: SSc26lung

description: SSc PF


title: Rosiglitazone 2 week withdrawal, 11 week_old, biological rep1

value: Zucker Diabetic Fatty Rat

value: pancreatic islets


title: TEF006_L2*M666T

value: female


title: NZB1LPS

description: miRNA profiling


title: SSc30lung

description: SSc PF


title: Rap1 -/- white fat, rep 1

value: white fat

value: 10 weeks


title: Heart

source_name: Heart Tissue from Mouse 88

value: Heart


title: MAR021_L2*M666V


title: NZB3Fab

description: miRNA profiling

value: Fab


title: Rap1 -/- white fat, rep 2


title: Liver

source_name: Liver Tissue from Mouse 88

value: Liver


title: Rosiglitazone treated, 9 week_old, biological rep1

value: male


title: Spleen

source_name: Spleen Tissue from Mouse 88

value: Spleen


title: SSc24lung

description: SSc PF


title: Before Hoxb8 Induction

value: HTT

value: AML


title: NZB2Fab

description: miRNA profiling


title: Wild-type liver, rep 4

source_name: Liver, wild-type mouse, 10 weeks

value: wild-type

value: liver


title: Wild-type liver, rep 3


title: SSc19lung

description: SSc PF

value: Lung


title: BoneMarrowBisulfite1

source_name: Bone Marrow from Mouse 87

value: Bone Marrow


title: NZB1Fab

description: miRNA profiling

value: NZB

value: yes

value: splenic B-cell


title: BoneMarrowBisulfite1_rep2

source_name: Bone Marrow from Mouse 88


title: LymphNode_Mouse 88

source_name: Lymph Node from Mouse 88

value: Lymph Node


title: Rap1 -/- white fat, rep 3

value: white fat


title: CTRL_mal_39yrs

value: healthy control

value: Epstein–Barr Virus transformed lymphocytes


title: LymphNode_Mouse 87

source_name: Lymph Node from Mouse 87


title: NZB3rest

description: miRNA profiling

value: rest


title: SSc23lung

description: SSc PF


title: BOR057_L2*G671R

value: patient

value: female


title: Wild-type liver, rep 1

value: 10 weeks


title: Wild-type liver, rep 2


title: BoneMarrowBisulfite2


title: NZB1rest

description: miRNA profiling


title: NZB2rest

description: miRNA profiling


title: SSc14lung

description: SSc-PF


title: CTRL_mal_34yrs

value: male


title: CTRL_mal_26yrs


title: SSc11lung

description: SSc PF


title: NOD3Fab

description: miRNA profiling

value: NOD

value: Fab


title: PPH8lung

description: IPAH (PPH)

source_name: IPAH (PPH)


title: NOD3LPS

description: miRNA profiling

value: LPS


title: PPH4lung

description: IPAH (PPH)

value: Lung


title: PPH9lung

description: IPAH (PPH)


title: PPH18lung

description: IPAH (PPH)


title: NOD2Fab

description: miRNA profiling


title: CTRL_fem_37yrs


title: NOD2LPS

description: miRNA profiling


title: CTRL_fem_51yrs


title: Rap1 -/- liver, rep 3

source_name: Liver, Rap1 knockout mouse -/-, 10 weeks

value: liver


title: Rap1 -/- liver, rep 4


title: NOD1Fab

description: miRNA profiling


title: NOD1LPS

description: miRNA profiling


title: PPH17lung

description: IPAH (PPH)


title: NZB2LPS

description: miRNA profiling

value: NZB


title: Pre-transformed DP thymocytes mouse #23

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

description:
Sample name: Mouse #23
purified CD8+CD4+ thymocytes, R26-βcat mouse #2
gene expression data from DP pre-transformed thymocytes from a young R26-βcat mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 7G System

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. Target intensity was set at 100.

label_protocol: cRNA were prepared according to MessageAmp™ Premier RNA Amplification Kit (Ambion) protocol from 0.1 ug total RNA.

extract_protocol: RNAs were extracted with the RNAeasy kit, following the manufacturer's instructions (including DNAse I treatment)

treatment_protocol: Thymus were dissected from euthanized mice and cells collected after tissue disruption.Thymocytes were stained with CD4 and CD8 conjugated antibodies and CD8+CD4+ DP cells were sorted and purified on FACSAriaII (purity>98%).

value: R26NC/NC CD4Cre+

value: 6 weeks

value: purified CD8+CD4+ thymocytes

value: Thymus


title: Pre-transformed DP thymocytes mouse #20

description:
Sample name: Mouse #20
purified CD8+CD4+ thymocytes, R26-βcat mouse #1
gene expression data from DP pre-transformed thymocytes from a young R26-βcat mouse


title: NOD3rest

description: miRNA profiling

value: yes

value: splenic B-cell


title: R26-βcat transformed thymocytes mouse #11

description:
Sample name: Mouse #11
Total thymic tumor (CD8+CD4+ cells ≥ 95%), R26-βcat mouse #4
gene expression data from a thymic tumor from a leukemic R26-βcat mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Thymic lymphomas were dissected from euthanized sick mice and cells collected after tissue disruption.

value: 21 weeks

value: tumoral thymocytes


title: NOD2rest

description: miRNA profiling

value: rest


title: NOD1rest

description: miRNA profiling


title: PPH11lung

description: IPAH (PPH)


title: Rap1 -/- liver, rep 2

value: 10 weeks


title: R26-βcat transformed thymocytes mouse #31

description:
Sample name: Mouse #31
Total thymic tumor (CD8+CD4+ cells ≥ 95%), R26-βcat mouse #3
gene expression data from a thymic tumor from a leukemic R26-βcat mouse

value: 23 weeks


title: NL8lung

description: NL

source_name: NL


title: PPH14lung

description: IPAH (PPH)


title: Control DP thymocytes mouse #22

description:
Sample name: Mouse #22
purified CD8+CD4+ thymocytes, control mouse #2
gene expression data from DP thymocytes from a control mouse

value: R26NC/NC CD4Cre-


title: LPR3LPS

description: miRNA profiling

value: MRL-lpr


title: Rap1 -/- liver, rep 1


title: LPR2LPS

description: miRNA profiling

value: LPS


title: LPR1LPS

description: miRNA profiling


title: NL41lung

description: NL

value: Lung


title: PPH1lung

description: IPAH (PPH)


title: R26-βcat transformed thymocytes mouse #96

description:
Sample name: Mouse #96
Total thymic tumor (CD8+CD4+ cells ≥ 95%), R26-βcat mouse #2
gene expression data from a thymic tumor from a leukemic R26-βcat mouse

value: 26 weeks


title: NL37lung

description: NL


title: R26-βcat transformed thymocytes mouse #94

description:
Sample name: Mouse #94
Total thymic tumor (CD8+CD4+ cells ≥ 95%), R26-βcat mouse #1
gene expression data from a thymic tumor from a leukemic R26-βcat mouse

value: 28 weeks


title: Pre-transformed DP thymocytes mouse #24

description:
Sample name: Mouse #24
purified CD8+CD4+ thymocytes, R26-βcat mouse #3
gene expression data from DP pre-transformed thymocytes from a young R26-βcat mouse

value: R26NC/NC CD4Cre+


title: NL35lung

description: NL


title: LPR3Fab

description: miRNA profiling

value: Fab


title: NL31lung

description: NL


title: LPR2Fab

description: miRNA profiling