title: tumor  81


title: tumor  31 [EXPID10572]

status: Public on May 17 2012

type: RNA

city: Chapel Hill

first: Matthew

middle: D

last: Wilkerson

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description: tumor  31

hyb_protocol: Microarrays were hybridized in an Robbins Scientific hybridization oven with 850ng of labeled Cy3 Reference and 850ng of Cy5 experimental samples using the Agilent hybridization kit as described by the manufacturer. The arrays were incubated overnight and then washed once for 10 minutes in 2X SSC and 0.0005% triton X-102, twice for 5 minutes in 0.1XSSC, and then immersed into Agilent Stabilization and Drying solution for 20 seconds.

scan_protocol: Microarrays were scanned with Agilent Scanner and intensity was recorded using Agilent Feature Extraction Software.

data_processing: Agilent feature extraction output was processed by normexp background correction and loess normalization using Bioconductor library limma.

molecule: total RNA

organism: Homo sapiens

source_name: lung adenocarcinoma tumor RNA

label_protocol: The total RNA labeling and hybridization protocol used is described in the Agilent low RNA input linear amplification kit (http://www.chem.agilent.com/Scripts/PDS.asp?lPage=10003 ), with the following two changes: 1) a Qiagen PCR purification kit was used to clean up the cRNA instead of the LiCl precipitation, and 2) all regents volumes were reduced by one half.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using RNeasy kit from Qiagen following manufacturer's instructions. These total RNA samples were run on an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc) to ensure RNA quality.

treatment_protocol: Not applicable

tag: subtype

value: magnoid

tag: age (90=greater than or equal to 90)

tag: Sex

value: M

value: Smoker

tag: Stage

value: IA

tag: grade

tag: adenosquamous_content (0='no', 1='yes')

tag: egfr (0='wt',1='mutated')

tag: kras (0='wt',1='mutated')

source_name: Stratagene Human Universal Reference

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: tumor  27 [EXPID10564]

description: tumor  27

value: squamoid

value: F


title: tumor  72

type: genomic

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Arrays were scanned using the Affmetrix Gene Chip Scanner.

data_processing: For SNP6 and 250K_Sty platforms separately, probe intensities were processed using CRMAv2 (Bengtsson, et al. PMID: 19535535), converted to log2 values, sample-wise median centered, and divided by the mean of normal samples to make CN values.  CN values were smoothed by circular binary segmentation, sample-wise median centered using autosomes. Finally, CN values were standardized by dividing each sample by its standard deviation. Sex chromosomes were not used in final analysis, so these probesets have NULL for all samples.  SNP6 data were subjected to a within-sample outlier removal process (TCGA Research Network, PMID: 21720365), and struck probesets have 'NULL' values.

label: biotin

molecule: genomic DNA

source_name: lung adenocarcinoma

label_protocol: Followed Affymetrix instructions.

extract_protocol: DNA was extracted using Qiagen’s QIAamp DNA minikit.

tag: tissue type

value: lung

tag: cell type

value: adenocarcinoma


title: tumor  26 [EXPID10563]

description: tumor  26

value: IB


title: tumor  76


title: tumor  73


title: tumor  25 [EXPID10561]

description: tumor  25

value: IIB


title: tumor  79


title: tumor  24 [EXPID10560]

description: tumor  24

value: bronchioid


title: tumor  77


title: tumor  78


title: tumor  59


title: tumor  23 [EXPID10559]

description: tumor  23

value: IIIA


title: tumor  75


title: tumor  58


title: tumor  21 [EXPID10553]

description: tumor  21


title: tumor  20 [EXPID10552]

description: tumor  20


title: tumor  18 [EXPID10545]

description: tumor  18


title: tumor  43


title: tumor  19 [EXPID10551]

description: tumor  19


title: tumor  22 [EXPID10557]

description: tumor  22

tag: sex

value: NeverSmoker

tag: stage


title: tumor  41


title: tumor  17 [EXPID10542]

description: tumor  17

value: IV


title: tumor  40


title: tumor  16 [EXPID10540]

description: tumor  16


title: tumor  37


title: tumor  69


title: tumor  14 [EXPID10536]

description: tumor  14


title: tumor  71


title: tumor  67


title: tumor  15 [EXPID10539]

description: tumor  15


title: tumor  36


title: tumor  35


title: tumor  33


title: tumor  34


title: tumor  13 [EXPID10535]

description: tumor  13


title: tumor  10 [EXPID10523]

description: tumor  10


title: tumor  12 [EXPID10528]

description: tumor  12


title: tumor  66


title: tumor  11 [EXPID10524]

description: tumor  11

value: IIA


title: tumor  65


title: tumor  74


title: tumor  64


title: tumor  61


title: tumor  63


title: tumor  32


title: tumor  9 [EXPID10519]

description: tumor  9


title: tumor  29


title: tumor  39


title: tumor  7 [EXPID10513]

description: tumor  7


title: tumor  27


title: tumor  6 [EXPID10510]

description: tumor  6


title: tumor  57


title: tumor  56


title: tumor  22


title: tumor  55


title: tumor  4 [EXPID10505]

description: tumor  4


title: tumor  28


title: tumor  5 [EXPID10509]

description: tumor  5


title: tumor  3 [EXPID10504]

description: tumor  3


title: tumor  60


title: tumor  23


title: tumor  54


title: IEC day 3 (Cy5) versus IEC day 21 (Cy3) from litter B

city: Hannover

first: Mathias

middle: W.

last: Hornef

address: Carl Neuberg Str. 1

department: Inst. of Medical Microbiology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.0.1”.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings (100 % and 5 %) to increase the dynamic range of the measurements (extended dynamic range mode).

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.5.3.1” by using the recommended default extraction protocol file: GE2-v5_95_Feb07.xml.

organism: Mus musculus

source_name: IEC day 21 from litter B biological replicate 2

label_protocol: 1000ng of total RNA per condition were used to prepare Cy3-, or Cy5-labeled cRNA with the “Low RNA Input Linear Amplification Kit PLUS, Two-Color” (#5188-5340, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: IECs were prepared as described recently (Lotz et al., J. Exp Med. 2006). In brief, mouse intestinal tissue was incubated for 10 min at 37°C in 0.3 M EDTA. shaken vigorously and epithelial cells were separated from the underlying tissue and immune cells by repeated sedimentation at 1 x g at 4°C. Flow cytometric analysis revealed less than 5% and 1% of CD45+ cells in IEC preparations from adult and suckling mice, respectively.

extract_protocol: RNA was isolated using TRIzol (Invitrogen, Darmstadt, Germany) according to the manufacturer’s protocol.

value: small intestinal epithelial cells

tag: age (days)

tag: strain

source_name: IEC day 3 from litter B biological replicate 2


title: tumor  2 [EXPID10500]

description: tumor  2


title: tumor  24


title: IEC day 3 (Cy3) versus IEC day 21 (Cy5) from litter B

source_name: IEC day 3 from litter B biological replicate 1

source_name: IEC day 21 from litter B biological replicate 1


title: tumor  25


title: tumor  8 [EXPID10517]

description: tumor  8


title: tumor  52


title: tumor  53


title: IEC day 3 (Cy5) versus IEC day 21 (Cy3) from litter A

source_name: IEC day 21 from litter A biological replicate 2

source_name: IEC day 3 from litter A biological replicate 2


title: tumor  50


title: tumor  19


title: tumor  20


title: tumor  62


title: IEC day 3 (Cy3) versus IEC day 21 (Cy5) from litter A

source_name: IEC day 3 from litter A biological replicate 1

source_name: IEC day 21 from litter A biological replicate 1


title: PC12_NGF_48h

status: Public on May 16 2012

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

country: Japan

institute: Toyohashi University of Technology

description: miRNA expression after 48hr in NGF-treated PC12

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).

data_processing: The resulting images were processed, and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 11 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.

organism: Rattus norvegicus

source_name: PC12, 48h, 100 ng/ml NGF

label_protocol: One hundred nanograms of total RNA was labeled using the Agilent miRNA Complete Labeling and Hybridization Kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Rat pheochromocytoma PC12 cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% horse serum (HS, Invitrogen, Carlsbad, CA, USA), 5% fetal bovine serum (FBS, MP Biomedicals, Irvine, CA, USA), 100 U/mL penicillin and 100 μg/mL streptomycin at 37ºC under a humidified atmosphere of 5% CO2.

extract_protocol: Total RNA containing miRNA was extracted from cells using the miRNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: Cells seeded on PolyD-lysine-coated plates were treated with 100 ng/ml murine NGF-7S (Invitrogen) in DMEM containing 1% HS and 0.5% FBS for 0, 12, 24 and 48 hr.

tag: cell line

value: pheochromocytoma


title: PC12_NGF_12h

description: miRNA expression after 12hr in NGF-treated PC12

source_name: PC12, 12h, 100 ng/ml NGF


title: tumor  93


title: tumor  17


title: tumor  1 [EXPID10496]

description: tumor  1

value: magnoid

value: M


title: tumor  16


title: PC12_NGF_24h

description: miRNA expression after 24hr in NGF-treated PC12

source_name: PC12, 24h, 100 ng/ml NGF


title: tumor  18


title: tumor  15


title: tumor  13


title: PC12_NGF_0h

description: miRNA expression after 0hr in NGF-treated PC12

source_name: PC12, 0h, 100 ng/ml NGF


title: tumor  10


title: Pioglitazone w0 21-002 R_SFA trt 9 week 0

city: Rahway

first: Oscar

last: Puig

state: NJ

address: 126 East Lincoln Ave

department: Molecular Profiling Research Informatics

institute: Merck Research Laboratories

description: Gene expression profiling of peripheral plaque. LEAP study, pioglitazone armProfiled in the Merck/Agilent 44k v1.1

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

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

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

source_name: Peripheral plaque

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

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: sample type

value: Peripheral plaque. LEAP study. Pioglitazone arm.

tag: treatment

value: Pioglitazone

tag: time

value: Baseline

tag: individual

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Placebo w0 42-001 L_SFA trt 10 week 0

value: Placebo


title: Pioglitazone w0 73-004 L_SFA trt 9 week 0


title: Bifidobacterium breve UCC2003 grown in mMRS (potato galactan/ribose)

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing:
DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 potato galactan/ribose ratios from a single array experiment.
Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in mMRS with potato galactan

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

extract_protocol: RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Bifidobacterium breve UCC2003 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.5% (w/v) of potato galactan solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

tag: growth stage

value: exponential

tag: carbon source

value: potato galactan

source_name: Bifidobacterium breve UCC2003 grown in mMRS with ribose

treatment_protocol: Bifidobacterium breve UCC2003 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 0.5% (w/v) of ribose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

value: ribose


title: tumor  21

value: lung

value: adenocarcinoma


title: tumor  9


title: tumor  12


title: Pioglitazone w6 48-002 L_AT trt 9 week 6

value: Week 6


title: Placebo w6 68-023 R_SFA trt 10 week 6


title: tumor  4


title: tumor  2


title: tumor  3


title: Placebo w0 68-023 R_POP trt 10 week 0


title: Pioglitazone w6 21-002 L_SFA trt 9 week 6


title: Pioglitazone w6 73-004 R_SFA trt 9 week 6


title: Replication timing of 11-015 leukemic patient sample, replicate 2

city: Tallahassee

first: Tyrone

last: Ryba

state: FL

address: 319 Stadium Dr.

department: Biological Science

institute: Florida State University

description: submitted as of 5/12/12

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 2.5 kb across the human genome.

scan_protocol: NimbleGen MS200 microarray scanner (Roche NimbleGen, Inc.) and MS200 data collection software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from two independent biological replicates in which early and late replicating DNA were differentially labeled were loess-normalized to remove signal intensity-dependent bias, then scaled to a reference data set to have the same median absolute deviation (limma package, R/Bioconductor).The early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using the loess function in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of 11-015 leukemic patient sample

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

tag: diagnosis

value: ALL (B), Pediatric

tag: age (yrs)

tag: gender

tag: disease stage

value: New Diagnosis

tag: karyotype

value: Unknown

source_name: Late replicating DNA of 11-015 leukemic patient sample


title: Replication timing of 11-132 leukemic patient sample, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-132 leukemic patient sample

value: F

source_name: Late replicating DNA of 11-132 leukemic patient sample


title: Placebo w0 62-004 R_SFA trt 10 week 0


title: Placebo w6 59-007 R_SFA trt 10 week 6


title: Placebo w0 68-005 L_SFA trt 10 week 0


title: Replication timing of 11-064 leukemic patient sample, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 11-064 leukemic patient sample

source_name: Late replicating DNA of 11-064 leukemic patient sample


title: Replication timing of 11-132 leukemic patient sample, replicate 1

description: submitted as of 5/12/12


title: Pioglitazone w0 67-006 L_SFA re-extract trt 9 week 0


title: Replication timing of 10-212 leukemic patient sample, replicate 1

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-212 leukemic patient sample

source_name: Late replicating DNA of 10-212 leukemic patient sample


title: tumor  1

source_name: lung adenocarcinoma

tag: tissue type

tag: cell type


title: Placebo w0 50-003 R_POP trt 10 week 0


title: Placebo w6 44-001 R_SFA re-extract trt 10 week 6


title: Replication timing of 11-015 leukemic patient sample, replicate 1

description: submitted as of 5/12/12


title: Pioglitazone w6 63-001 R_AT de-salt trt 9 week 6


title: Replication timing of NC-NC lymphoblastoid cells, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of NC-NC lymphoblastoid cells

source_name: Late replicating DNA of NC-NC lymphoblastoid cells


title: Replication timing of 10-770 leukemic patient sample, replicate 2

description: submitted as of 5/12/12

source_name: Early-replicating DNA of 10-770 leukemic patient sample

source_name: Late replicating DNA of 10-770 leukemic patient sample


title: Placebo w0 44-001 L_SFA re-extract trt 10 week 0


title: Pioglitazone w6 50-009 R_TPT trt 9 week 6


title: Pioglitazone w0 67-006 L_SFA de-salt trt 9 week 0


title: Pioglitazone w0 42-005 R_SFA trt 9 week 0


title: Pioglitazone w6 42-005 L_SFA trt 9 week 6


title: tumor  8


title: Placebo w0 59-007 L_SFA trt 10 week 0


title: Placebo w6 43-004 L_SFA trt 10 week 6


title: Placebo w6 68-005 R_SFA trt 10 week 6


title: Placebo w0 24-008 R_UNK de-salt trt 10 week 0


title: Placebo w6 50-003 L_SFA trt 10 week 6


title: Placebo w6 24-008 L_UNK de-salt 3 trt 10 week 6


title: Placebo w6 24-008 L_UNK de-salt 2 trt 10 week 6


title: Placebo w6 24-008 L_UNK de-salt 1 trt 10 week 6


title: Pioglitazone w0 26-009 L_TPT trt 9 week 0


title: Pioglitazone w0 26-009 L_AT trt 9 week 0


title: Pioglitazone w0 26-004 L_SFA re-extract trt 9 week 0


title: Pioglitazone w6 26-009 R_AT trt 9 week 6


title: Pioglitazone w6 36-002 R_SFA de-salt trt 9 week 6


title: Pioglitazone w0 24-014 Peri_SFA re-extract trt 9 week 0


title: Placebo w0 44-001 L_SFA de-salt trt 10 week 0


title: Pioglitazone w6 62-015 L_SFA trt 9 week 6


title: Pioglitazone w6 10-002 L_SFA re-extract trt 9 week 6


title: Placebo w0 62-025 L_SFA trt 10 week 0


title: Placebo w6 73-001 R_SFA de-salt trt 10 week 6


title: Pioglitazone w6 24-014 L_SFA re-extract trt 9 week 6


title: Placebo w0 67-008 L_SFA trt 10 week 0


title: Placebo w0 73-001 L_SFA de-salt trt 10 week 0


title: Placebo w6 53-001 L_SFA trt 10 week 6


title: Pioglitazone w0 36-002 L_SFA de-salt trt 9 week 0


title: Pioglitazone w6 59-010 L_SFA trt 9 week 6


title: Pioglitazone w0 59-010 R_SFA trt 9 week 0


title: Pioglitazone w0 43-001 R_SFA trt 9 week 0


title: Placebo w0 39-003 R_SFA de-salt trt 10 week 0


title: Placebo w6 73-001 R_POP de-salt trt 10 week 6


title: Placebo w6 57-003 R_SFA trt 10 week 6


title: Placebo w0 57-003 L_SFA trt 10 week 0


title: Placebo w6 39-003 L_SFA de-salt trt 10 week 6


title: Pioglitazone w6 43-001 L_SFA trt 9 week 6


title: Placebo w0 67-003 R_SFA trt 10 week 0


title: Pioglitazone w0 68-011 L_SFA de-salt trt 9 week 0


title: Placebo w0 24-001 L_SFA trt 10 week 0


title: Placebo w0 24-001 L_POP trt 10 week 0


title: Pioglitazone w6 26-004 R_AT de-salt trt 9 week 6


title: Pioglitazone w0 24-014 Peri SFA de-salt trt 9 week 0


title: Pioglitazone w0 68-010 R_POP trt 9 week 0


title: Pioglitazone w0 24-014 Peri_POP de-salt trt 9 week 0


title: Pioglitazone w0 26-004 L_AT de-salt trt 9 week 0


title: Pioglitazone w0 62-018 R_SFA trt 9 week 0


title: Pioglitazone w6 62-018 L_SFA trt 9 week 6


title: Pioglitazone w0 73-008 L_SFA trt 9 week 0


title: Pioglitazone w0 26-004 L_SFA de-salt trt 9 week 0


title: Placebo w6 62-025 R_SFA trt 10 week 6


title: Pioglitazone w6 68-010 L_SFA trt 9 week 6


title: Pioglitazone w6 10-002 L_SFA de-salt trt 9 week 6


title: Placebo w6 14-003 R_SFA de-salt trt 10 week 6


title: Pioglitazone w6 67-006 R_SFA de-salt trt 9 week 6


title: Pioglitazone w0 10-002 R_AT de-salt trt 9 week 0


title: Placebo w6 57-002 L_SFA trt 6 week 6

description: Gene expression profiling of peripheral plaque. LEAP study, losartan armProfiled in the Merck/Agilent 44k v1.1

value: Peripheral plaque. LEAP study. Losartan arm.


title: Pioglitazone w6 24-014 L_SFA de-salt trt 9 week 6


title: Placebo w0 45-001 L_SFA trt 6 week 0


title: Placebo w6 73-001 R_SFA re-extract trt 10 week 6


title: Placebo w0 73-009 L_POP trt 6 week 0


title: Placebo w0 45-001 Peri_POP trt 6 week 0


title: Placebo w6 59-002 R_SFA trt 6 week 6


title: Placebo w6 10-001 R_SFA trt 10 week 6


title: Losartan w0 67-001 L_SFA trt 5 week 0

value: Losartan


title: Placebo w0 73-001 L_SFA re-extract trt 10 week 0

value: Peripheral plaque. LEAP study. Pioglitazone arm.


title: Placebo w6 26-011 R_AT trt 6 week 6


title: Placebo w0 10-001 L_SFA trt 10 week 0


title: Placebo w0 26-011 L_AT trt 6 week 0


title: Placebo w6 10-001 R_POP trt 10 week 6


title: Placebo w0 59-002 L_SFA trt 6 week 0


title: Placebo w0 73-009 L_SFA trt 6 week 0


title: Losartan w6 67-001 R_SFA trt 5 week 6


title: Placebo w0 57-002 R_SFA trt 6 week 0


title: Placebo w6 45-001 R_SFA trt 6 week 6


title: Pioglitazone w0 62-015 R_SFA trt 9 week 0

value: Pioglitazone


title: Placebo w0 58-002 L_SFA trt 6 week 0

value: Baseline


title: genomic DNA from tumor adjacent tissue_NonTumor 62

city: NY

first: Regina

last: Santella

state: NY

address: 630 West 168th St

department: Environmental Health Sciences

institute: Columbia University

hyb_protocol: Illumina Standard protocol

scan_protocol: Illumina Standard protocol

data_processing: β values were generated using the Illumina BeadStudio software v.3.0 [reference: PMID 16449502]. The non_normalized data matrix contains raw unmethylated/methylated intensities, whereh Signal B is the array intensity value for the methylated allele and Signal A is the nonmethylated allele.

label: Cy5 and Cy3

source_name: tumor adjacent tissue_NonTumor

label_protocol: Illumina Standard protocol

extract_protocol: Phenol/chloroform extraction

tag: age

value: male

tag: tissue

value: liver


title: genomic DNA from tumor adjacent tissue_NonTumor 60


title: genomic DNA from tumor adjacent tissue_NonTumor 61


title: genomic DNA from tumor adjacent tissue_NonTumor 59


title: genomic DNA from tumor adjacent tissue_NonTumor 58


title: Placebo w6 58-002 R_SFA trt 6 week 6

source_name: Peripheral plaque

value: Placebo

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Placebo w6 33-009 L_SFA trt 6 week 6


title: Losartan w6 47-001 R_PT trt 5 week 6


title: Placebo w0 33-009 R_SFA trt 6 week 0


title: Placebo w0 33-014 L_SFA trt 6 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 56


title: genomic DNA from tumor adjacent tissue_NonTumor 54


title: genomic DNA from tumor adjacent tissue_NonTumor 55


title: genomic DNA from tumor adjacent tissue_NonTumor 52


title: Placebo w0 33-007 L_SFA trt 6 week 0


title: Placebo w0 50-008 L_SFA trt 6 week 0


title: Placebo w6 50-008 R_CFA trt 6 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 53


title: genomic DNA from tumor adjacent tissue_NonTumor 57


title: genomic DNA from tumor adjacent tissue_NonTumor 49


title: genomic DNA from tumor adjacent tissue_NonTumor 51

value: female


title: genomic DNA from tumor adjacent tissue_NonTumor 50


title: Placebo w6 50-008 R_SFA trt 6 week 6


title: Losartan w6 77-001 R_SFA trt 5 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 47


title: genomic DNA from tumor adjacent tissue_NonTumor 44


title: Losartan w0 77-001 L_SFA trt 5 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 48


title: genomic DNA from tumor adjacent tissue_NonTumor 42


title: genomic DNA from tumor adjacent tissue_NonTumor 45


title: genomic DNA from tumor adjacent tissue_NonTumor 46


title: genomic DNA from tumor adjacent tissue_NonTumor 41


title: genomic DNA from tumor adjacent tissue_NonTumor 40


title: genomic DNA from tumor adjacent tissue_NonTumor 39


title: Placebo w0 33-007 L_POP trt 6 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 37


title: genomic DNA from tumor adjacent tissue_NonTumor 36


title: genomic DNA from tumor adjacent tissue_NonTumor 38


title: genomic DNA from tumor adjacent tissue_NonTumor 33


title: genomic DNA from tumor adjacent tissue_NonTumor 32


title: Losartan w0 50-013 L_SFA trt 5 week 0


title: Losartan w6 24-013 L_SFA trt 5 week 6


title: Placebo w0 30-002 L_POP trt 6 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 35


title: Losartan w6 50-013 R_POP trt 5 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 29


title: genomic DNA from tumor adjacent tissue_NonTumor 34


title: Losartan w6 50-013 R_SFA trt 5 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 31


title: genomic DNA from tumor adjacent tissue_NonTumor 30


title: Placebo w0 30-002 L_CFA trt 6 week 0


title: Losartan w0 33-012 R_SFA trt 5 week 0


title: Placebo w6 50-016 L_PT trt 6 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 28


title: genomic DNA from tumor adjacent tissue_NonTumor 27


title: genomic DNA from tumor adjacent tissue_NonTumor 19


title: genomic DNA from tumor adjacent tissue_NonTumor 26


title: genomic DNA from tumor adjacent tissue_NonTumor 22


title: genomic DNA from tumor adjacent tissue_NonTumor 15


title: Losartan w0 68-016 L_TPT trt 5 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 24


title: genomic DNA from tumor adjacent tissue_NonTumor 20


title: genomic DNA from tumor adjacent tissue_NonTumor 23


title: Losartan w6 62-002 L_SFA trt 5 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 21


title: genomic DNA from tumor adjacent tissue_NonTumor 16


title: genomic DNA from tumor adjacent tissue_NonTumor 25


title: genomic DNA from tumor adjacent tissue_NonTumor 14


title: genomic DNA from tumor adjacent tissue_NonTumor 18


title: genomic DNA from tumor adjacent tissue_NonTumor 13


title: genomic DNA from tumor adjacent tissue_NonTumor 17


title: Losartan w6 33-012 L_SFA trt 5 week 6


title: Losartan w0 62-002 R_SFA trt 5 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 10


title: Losartan w6 59-003 L_SFA trt 5 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 11


title: Placebo w6 33-014 R_PT trt 6 week 6


title: Placebo w0 73-013 L_SFA trt 6 week 0


title: Placebo w6 33-014 R_SFA trt 6 week 6


title: Placebo w0 64-001 L_SFA trt 6 week 0


title: genomic DNA from tumor adjacent tissue_NonTumor 7


title: genomic DNA from tumor adjacent tissue_NonTumor 12


title: Placebo w6 64-001 R_SFA trt 6 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 9


title: genomic DNA from tumor adjacent tissue_NonTumor 43


title: Placebo w6 73-013 R_SFA trt 6 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 5


title: genomic DNA from tumor adjacent tissue_NonTumor 2


title: genomic DNA from liver tumor 62

source_name: liver tumor

tag: disease

value: Hepatocellular carcinoma (HCC)

tag: hbsag status

value: Negative

tag: anti-hcv status


title: genomic DNA from tumor adjacent tissue_NonTumor 8


title: genomic DNA from tumor adjacent tissue_NonTumor 4


title: Losartan w0 13-001 L_SFA trt 5 week 0

tag: sample type

tag: treatment


title: genomic DNA from tumor adjacent tissue_NonTumor 6


title: genomic DNA from liver tumor 56

value: Positive


title: Losartan w6 13-001 R_SFA trt 5 week 6

tag: time

value: Week 6

tag: individual


title: genomic DNA from tumor adjacent tissue_NonTumor 1


title: genomic DNA from liver tumor 60


title: Losartan w0 26-002 R_SFA trt 5 week 0


title: genomic DNA from liver tumor 57


title: genomic DNA from liver tumor 61


title: Losartan w0 68-019 L_SFA trt 5 week 0


title: genomic DNA from liver tumor 59


title: genomic DNA from liver tumor 51


title: Placebo w6 31-001 L_SFA trt 6 week 6


title: genomic DNA from tumor adjacent tissue_NonTumor 3


title: genomic DNA from liver tumor 58


title: Placebo w6 26-005 R_PT de-salt trt 6 week 6


title: genomic DNA from liver tumor 54


title: Placebo w0 31-001 R_SFA trt 6 week 0


title: genomic DNA from liver tumor 53


title: genomic DNA from liver tumor 55


title: Placebo w6 30-002 R_SFA trt 6 week 6


title: genomic DNA from liver tumor 52


title: Placebo w6 29-003 R_SFA trt 6 week 6


title: genomic DNA from liver tumor 49


title: genomic DNA from liver tumor 50


title: Losartan w0 33-001 L_SFA trt 5 week 0


title: genomic DNA from liver tumor 48


title: genomic DNA from liver tumor 47


title: genomic DNA from liver tumor 46


title: genomic DNA from liver tumor 45


title: genomic DNA from liver tumor 42


title: genomic DNA from liver tumor 43


title: genomic DNA from liver tumor 44


title: genomic DNA from liver tumor 41


title: Placebo w6 34-001 L_SFA de-salt trt 6 week 6


title: Losartan w0 30-006 R_POP de-salt trt 5 week 0


title: genomic DNA from liver tumor 40


title: Losartan w6 33-001 R_SFA trt 5 week 6


title: genomic DNA from liver tumor 38


title: genomic DNA from liver tumor 39


title: genomic DNA from liver tumor 36


title: genomic DNA from liver tumor 37


title: genomic DNA from liver tumor 35


title: Placebo w6 33-007 R_SFA trt 6 week 6


title: genomic DNA from liver tumor 32


title: genomic DNA from liver tumor 33


title: genomic DNA from liver tumor 30


title: Placebo w6 37-001 L_SFA trt 6 week 6


title: genomic DNA from liver tumor 31


title: Placebo w0 37-001 R_SFA trt 6 week 0


title: Placebo w0 35-004 R_SFA trt 6 week 0


title: genomic DNA from liver tumor 34


title: genomic DNA from liver tumor 27


title: Losartan w6 52-001 L_SFA trt 5 week 6


title: Placebo w6 35-004 L_SFA trt 6 week 6


title: genomic DNA from liver tumor 29


title: genomic DNA from liver tumor 26


title: Losartan w0 42-004 L_SFA trt 5 week 0


title: Losartan w0 42-003 L_SFA trt 5 week 0


title: genomic DNA from liver tumor 25


title: genomic DNA from liver tumor 22


title: Losartan w0 43-005 L_SFA de-salt trt 5 week 0


title: genomic DNA from liver tumor 23


title: genomic DNA from liver tumor 28


title: genomic DNA from liver tumor 24


title: Losartan w6 43-005 R_SFA de-salt trt 5 week 6


title: genomic DNA from liver tumor 19


title: genomic DNA from liver tumor 20


title: genomic DNA from liver tumor 18


title: Losartan w0 52-001 R_SFA trt 5 week 0


title: genomic DNA from liver tumor 17


title: genomic DNA from liver tumor 21


title: genomic DNA from liver tumor 16


title: genomic DNA from liver tumor 14


title: genomic DNA from liver tumor 15


title: Losartan w0 30-006 R_POP re-extract trt 5 week 0


title: Placebo w6 Trt 2 week 6 42-006 L_SFA - no bad QC

description: Gene expression profiling of peripheral plaque. LEAP study, simvastatin armProfiled in the Merck/Agilent 44k v1.1

value: Peripheral plaque. LEAP study. Simvastatin arm.


title: genomic DNA from liver tumor 12


title: genomic DNA from liver tumor 13


title: Placebo w6 34-001 L_SFA re-extract trt 6 week 6


title: genomic DNA from liver tumor 10


title: Placebo w6 Trt 2 week 6 44-002 L_POP - no bad QC


title: genomic DNA from liver tumor 8


title: genomic DNA from liver tumor 7


title: genomic DNA from liver tumor 3


title: genomic DNA from liver tumor 5


title: Placebo w0 Trt 2 week 0 38-002 L_SFA - no bad QC


title: genomic DNA from liver tumor 9


title: genomic DNA from liver tumor 4


title: genomic DNA from liver tumor 11


title: genomic DNA from liver tumor 6


title: genomic DNA from liver tumor 2


title: genomic DNA from liver tumor 1


title: Placebo w0 Trt 2 week 0 42-006 R_SFA - no bad QC


title: Placebo w6 Trt 2 week 6 55-001 R_SFA - no bad QC


title: Simvastatin w6 Trt 1 week 6 33-011 R_SFA - no bad QC

value: Simvastatin


title: Placebo w0 Trt 2 week 0 63-002 L_CFA de-salt - no bad QC


title: Simvastatin w6 Trt 1 week 6 29-002 R_SFA - no bad QC


title: Simvastatin w0 Trt 1 week 0 39-004 R_SFA de-salt - no bad QC


title: Helicobacter pylori strain SS1∆hpyAVIBM

city: BANGALORE

first: RITESH

last: KUMAR

address: DEPARTMENT OF BIOCHEMISTRY, INDIAN INSTITUTE OF SCIENCE

country: India

institute: INDIAN INSTITUTE OF SCIENCE

hyb_protocol: The labeled cRNA samples were hybridized on to a Custom Gene Expression H. pylori 8x15k (AMADID: 22857).

scan_protocol: 600 ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242).

data_processing: Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327) and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

organism: Helicobacter pylori SS1

source_name: Helicobacter pylori strain SS1∆hpyAVIBM

label_protocol: Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step.

growth_protocol: Cells were grown to an OD of 0.6 and then total RNA is isolated

extract_protocol: Bacterial RNA was stabilized in vivo, by using RNA protect Bacteria Reagent (Qiagen). Total RNA was isolated by using RNeasy Kits for RNA purification (Qiagen) as per the manufacturer’s protocol.

tag: genotype/variation

value: ∆hpyAVIBM


title: Helicobacter pylori strain SS1 Repeat

source_name: Helicobacter pylori strain SS1

value: wildtype


title: Helicobacter pylori strain SS1


title: Helicobacter pylori strain AM5 Repeat

organism: Helicobacter pylori

source_name: Helicobacter pylori strain AM5


title: Helicobacter pylori strain AM5∆hpyAVIBM Repeat

source_name: Helicobacter pylori strain AM5∆hpyAVIBM


title: Helicobacter pylori strain AM5∆hpyAVIBM


title: normal iPS

city: Tokyo

first: Keiki

last: Kumano

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description: Gene expression data from iPS cells

hyb_protocol: Following amplification, 5 ug of cRNA were hybridized to HG-U133 Plus 2.0 GeneChip arrays (Affymetrix).

scan_protocol: Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.  Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.  Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.  Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.  Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).Background subtraction, normalization and expression values of our data were calculated using the rma algorithm, available as a part of the Affymetrix package of the Bioconductor open-source software library for the statistical language R (http://www.bioconductor.org).

source_name: human iPS cells

label_protocol: Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system  Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.  Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.  Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.  Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.  Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.    Biotin labeling of fragmented cDNA was carried out using NuGen Ovation Biotin labeling system.

growth_protocol: iPS cells were maintained on MEF.

extract_protocol: Total RNA was extracted with RNAeasy reagents (QIAGEN, Hilden, Germany) according to the manufacture's instructions. The integrity of RNA was checked by Agilent 2100 Bioanalyzer.

treatment_protocol: DNA was removed by RNAse-freeDNAse treatment using standard procedure.

value: iPS cells

tag: disease status

value: normal cord blood


title: Helicobacter pylori strain SS1∆hpyAVIBM Repeat


title: Helicobacter pylori strain AM5


title: Young  HUVEC 1

city: Ancona

first: Fabiola

last: Olivieri

state: Ancona

address: Via Tronto

department: Dept of clinical and molecular sciences

country: Italy

institute: Università Politecnica delle Marche

description: HUVEC II passage

data_processing: The relative amount of each miRNA was calculated using the comparative threshold (Ct) method with ΔCt = Ct(miRNA)-Ct(RNU44). We used median  normalization method for array data. Relative quantification of miRNA expression was calculated with the 2-ΔΔCt method. ΔΔCt was calculated as CT  microRNA- median Ct values obtained in the sample profiling.

label: FAM

source_name: Umbilical Vein Endothelial Cells

label_protocol: About 150-200 ng of total RNA were converted to cDNA by priming with a mixture of looped primers using manufacturer’s instructions (MegaPlex kit, Applied Biosystems, Foster City, CA). Pre-amplification was performed using 3 microliters of input RNA with PreAmp kit (Applied Biosystem, Foster City, CA). 9 microliters of pre-amplified cDNA were used for mature miRs profiling by real-time PCR instrument equipped with a 348 well reaction plate (7900 HT, Applied Biosystem, Foster City CA) and human MiR Array pool A

growth_protocol: HUVEC cells were purchased from Clonetics Corporation (Lonza, Basel, Switzerland) and cultured in endothelial growth medium EGM-2 (Lonza)

extract_protocol: Total RNA was extracted with RNA purification kit (Norgen Biotek Corporation, Thorold, ON, Canada)

treatment_protocol: Endothelial cell replicative senescence was studied by subjecting endothelial cells to subsequent passages until XIII

value: young (II passage)

value: HUVEC


title: Young  HUVEC 3

description: HUVEC II passage


title: CML-iPS1

description: Gene expression data from iPS cells

value: CML


title: Helicobacter pylori strain 26695∆ hpyAVIBM

organism: Helicobacter pylori 26695

value: ∆ hpyAVIBM


title: Placebo w6 Trt 2 week 6 67-007 R_POP - no bad QC

value: Placebo


title: Helicobacter pylori strain 26695

source_name: Helicobacter pylori strain 26695


title: CML-iPS 2

description: Gene expression data from iPS cells


title: Simvastatin w0 Trt 1 week 0 67-002 L_SFA - no bad QC

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Helicobacter pylori strain 26695∆ hpyAVIBM Repeat


title: Senescent HUVEC 2

description: HUVEC XIII passage

value: senescent (XIII passage)


title: Senescent HUVEC 1

description: HUVEC XIII passage


title: Placebo w6 Trt 2 week 6 29-002 R_POP - no bad QC


title: Placebo w0 Trt 2 week 0 68-004 R_SFA - no bad QC


title: Helicobacter pylori strain 26695 Repeat


title: Simvastatin w6 Trt 1 week 6 68-006 R_SFA - no bad QC


title: Senescent HUVEC 3

description: HUVEC XIII passage


title: Simvastatin w6 Trt 1 week 6 33-010 R_SFA re-extract - no bad QC


title: Placebo w6 Trt 2 week 6 33-003 R_SFA - no bad QC


title: Simvastatin w0 Trt 1 week 0 62-027 L_POP - no bad QC


title: Young  HUVEC 2

description: HUVEC II passage


title: Simvastatin w0 Trt 1 week 0 10-003 R_SFA - no bad QC


title: RF_LDM_rep1, mRNA

city: Ya'an

first: Mingzhou

last: Li

state: Sichuan

address: No.46  Xinkang Road

department: College of Animal Science and Technology

country: China

institute: Sichuan Agricultural University

description: Rongchang pig (R), longissimus doris muscle

hyb_protocol: Fragmentation was carried out by incubation at 60°C for 30 min in fragmentation buffer (Agilent Technologies), and the process was stopped by the addition of an equal volume of hybridization buffer (Agilent Technologies). The fragmented target was applied to an Agilent Pig Gene Expression Oligo Microarray. Hybridization was carried out at 60°C for 17 h in a hybridization oven (Robbins Scientific).

scan_protocol: The hybridized single-channel array was scanned with an Agilent microarray scanner.

data_processing: The TIFF image generated was loaded into Feature Extraction Software (Agilent Technologies) for feature data extraction, and data analysis was performed with MultiExperiment Viewer (MeV).

organism: Sus scrofa

source_name: Rongchang pig, longissimus doris muscle

label_protocol: The labeling procedure was carried out using an RNA Fluorescent Linear Amplification Kit (Agilent Technologies). The sample was labeled with Cy-3 dye only.

growth_protocol: Three pig breeds with distinguished fat levels were analyzed: Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous, Chinese breed that has not undergone artificial selection).

extract_protocol: The total RNA (10 µg) of the 180 samples was extracted with TRIzol (Invitrogen) and further purified using an RNeasy column (Qiagen). The total RNA quantity and purity passed the analysis of a NanoDrop ND-1000 spectrophotometer (Nano Drop) at 260/280 nm (ratio > 2.0). The integrity of the total RNA also passed the analysis of a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent Technologies) with RIN number > 6.0.

tag: breed

value: Rongchang

value: female

value: 210 days

value: muscle:longissimus doris muscle


title: RF_ULB_rep1, mRNA

description: Rongchang pig (R), ULB: upper layer of backfat

source_name: Rongchang pig, upper layer of backfat

tag: gender

value: adipose:upper layer of backfat


title: RF_ULB_rep3, mRNA


title: RF_PMM_rep3, mRNA

description: Rongchang pig (R), psoas major muscle

source_name: Rongchang pig, psoas major muscle

value: muscle:psoas major muscle


title: RF_PMM_rep2, mRNA

description: Rongchang pig (R), psoas major muscle


title: RF_RAD_rep1, mRNA

description: Rongchang pig (R), RAD: retroperitoneal adipose

source_name: Rongchang pig, retroperitoneal adipose

value: adipose:retroperitoneal adipose


title: RF_MAD_rep1, mRNA

description: Rongchang pig (R), MAD: mesenteric adipose

source_name: Rongchang pig, mesenteric adipose

value: adipose:mesenteric adipose


title: RF_LDM_rep3, mRNA


title: RF_PAD_rep2, mRNA

description: Rongchang pig (R), PAD: pericardial adipose

source_name: Rongchang pig, pericardial adipose

value: adipose:pericardial adipose


title: RF_LDM_rep2, mRNA


title: RF_ULB_rep2, mRNA


title: Simvastatin w0 Trt 1 week 0 29-002 L_SFA - no bad QC

value: Peripheral plaque. LEAP study. Simvastatin arm.

value: Simvastatin


title: RF_RAD_rep3, mRNA


title: Simvastatin w0 Trt 1 week 0 29-002 L_POP - no bad QC


title: RF_PMM_rep1, mRNA

description: Rongchang pig (R), psoas major muscle


title: RF_PAD_rep1, mRNA


title: Placebo w6 Trt 2 week 6 68-004 L_SFA - no bad QC

value: Week 6


title: Simvastatin w0 Trt 1 week 0 68-006 L_SFA - no bad QC


title: RF_RAD_rep2, mRNA


title: RF_ILB_rep3, mRNA

description: Rongchang pig (R), ILB: inner layer of backfat

source_name: Rongchang pig, inner layer of backfat

value: adipose:inner layer of backfat


title: RF_PAD_rep3, mRNA


title: Simvastatin w0 Trt 1 week 0 68-006 L_POP - no bad QC


title: Simvastatin w6 Trt 1 week 6 10-003 L_SFA - no bad QC


title: Simvastatin w6 Trt 1 week 6 62-027 R_SFA - no bad QC


title: RF_MAD_rep2, mRNA


title: Placebo w0 Trt 2 week 0 63-002 L_SFA de-salt - no bad QC

value: Placebo


title: RF_MAD_rep3, mRNA


title: Placebo w6 Trt 2 week 6 33-006 L_POP - no bad QC


title: Simvastatin w6 Trt 1 week 6 29-002 R_POP - no bad QC


title: RF_GOM_rep1, mRNA

description: Rongchang pig (R), GOM: greater omentum

source_name: Rongchang pig, greater omentum

value: adipose:greater omentum


title: RF_ILB_rep2, mRNA


title: RF_GOM_rep3, mRNA

description: Rongchang pig (R), GOM: greater omentum


title: RF_IAD_rep1, mRNA

description: Rongchang pig (R), IAD: intermuscular adipose

source_name: Rongchang pig, intermuscular adipose

value: adipose:intermuscular adipose


title: RF_IAD_rep2, mRNA


title: RF_GOM_rep2, mRNA

description: Rongchang pig (R), GOM: greater omentum


title: RF_IAD_rep3, mRNA


title: RF_ASA_rep3, mRNA

description: Rongchang pig (R), ASA: abdominal subcutaneous adipose

source_name: Rongchang pig, abdominal subcutaneous adipose

value: adipose:abdominal subcutaneous adipose


title: Placebo w0 Trt 2 week 0 68-003 L_SFA - no bad QC

source_name: Peripheral plaque

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Simvastatin w0 Trt 1 week 0 59-009 L_SFA - no bad QC


title: RF_ILB_rep1, mRNA

value: Rongchang

value: female

value: 210 days


title: RF_ASA_rep1, mRNA


title: Simvastatin w0 Trt 1 week 0 75-003 R_SFA de-salt - no bad QC


title: RM_LDM_rep2, mRNA

value: male

value: muscle:longissimus doris muscle


title: RM_PMM_rep3, mRNA

description: Rongchang pig (R), psoas major muscle

value: muscle:psoas major muscle


title: Simvastatin w6 Trt 1 week 6 59-009 R_SFA - no bad QC


title: RM_PMM_rep1, mRNA

description: Rongchang pig (R), psoas major muscle


title: RM_ULB_rep2, mRNA

value: adipose:upper layer of backfat


title: RM_LDM_rep1, mRNA


title: RM_LDM_rep3, mRNA


title: RM_PMM_rep2, mRNA

description: Rongchang pig (R), psoas major muscle


title: RM_ULB_rep3, mRNA


title: Placebo w0 Trt 2 week 0 33-006 R_POP - no bad QC

value: Peripheral plaque. LEAP study. Simvastatin arm.


title: Placebo w6 Trt 2 week 6 68-003 R_SFA - no bad QC


title: RF_ASA_rep2, mRNA


title: Simvastatin w6 Trt 1 week 6 74-003 R_SFA - no bad QC

value: Simvastatin


title: Placebo w6 Trt 2 week 6 30-003 L_POP - no bad QC

value: Week 6


title: Simvastatin w0 Trt 1 week 0 62-028 R_SFA - no bad QC


title: RM_ULB_rep1, mRNA


title: RM_RAD_rep2, mRNA

value: adipose:retroperitoneal adipose


title: Simvastatin w6 Trt 1 week 6 75-003 L_POP de-salt - no bad QC


title: RM_RAD_rep3, mRNA


title: RM_MAD_rep1, mRNA

value: adipose:mesenteric adipose


title: Placebo w0 Trt 2 week 0 30-003 R_SFA - no bad QC

value: Placebo


title: RM_RAD_rep1, mRNA


title: Simvastatin w6 Trt 1 week 6 62-029 R_POP - no bad QC


title: RM_MAD_rep2, mRNA


title: RM_PAD_rep2, mRNA

value: adipose:pericardial adipose


title: Simvastatin w0 Trt 1 week 0 62-029 L_POP - no bad QC


title: Simvastatin w0 Trt 1 week 0 62-029 L_SFA - no bad QC


title: Placebo w6 Trt 2 week 6 30-003 L_SFA - no bad QC


title: RM_PAD_rep3, mRNA


title: RM_PAD_rep1, mRNA


title: RM_IAD_rep3, mRNA

value: adipose:intermuscular adipose


title: RM_MAD_rep3, mRNA


title: RM_ILB_rep3, mRNA

value: adipose:inner layer of backfat


title: RM_ILB_rep1, mRNA


title: Simvastatin w0 Trt 1 week 0 62-028 R_POP - no bad QC

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: RM_IAD_rep1, mRNA

value: Rongchang


title: Placebo w6 Trt 2 week 6 50-017 R_SFA - no bad QC


title: Placebo w6 Trt 2 week 6 59-001 L_SFA de-salt - no bad QC


title: RM_ILB_rep2, mRNA

value: 210 days


title: RM_IAD_rep2, mRNA

value: male


title: RM_ASA_rep3, mRNA

value: adipose:abdominal subcutaneous adipose


title: RM_GOM_rep2, mRNA

description: Rongchang pig (R), GOM: greater omentum

value: adipose:greater omentum


title: RM_ASA_rep1, mRNA


title: RM_GOM_rep1, mRNA

description: Rongchang pig (R), GOM: greater omentum


title: TF_PMM_rep2, mRNA

description: Tibetan pig (T), psoas major muscle

source_name: Tibetan pig, psoas major muscle

value: Tibetan

value: female

value: muscle:psoas major muscle


title: Placebo w6 Trt 2 week 6 59-001 L_POP de-salt - no bad QC

value: Peripheral plaque. LEAP study. Simvastatin arm.

value: Week 6


title: RM_GOM_rep3, mRNA

description: Rongchang pig (R), GOM: greater omentum


title: Placebo w0 Trt 2 week 0 40-001 L_SFA - no bad QC


title: TF_PMM_rep1, mRNA

description: Tibetan pig (T), psoas major muscle


title: Placebo w0 Trt 2 week 0 59-001 R_SFA re-extract - no bad QC


title: TF_LDM_rep1, mRNA

description: Tibetan pig (T), longissimus doris muscle

source_name: Tibetan pig, longissimus doris muscle

value: muscle:longissimus doris muscle


title: TF_LDM_rep3, mRNA


title: TF_ULB_rep3, mRNA

description: Tibetan pig (T), ULB: upper layer of backfat

source_name: Tibetan pig, upper layer of backfat

value: adipose:upper layer of backfat


title: TF_ULB_rep1, mRNA


title: TF_LDM_rep2, mRNA


title: TF_ULB_rep2, mRNA


title: TF_RAD_rep3, mRNA

description: Tibetan pig (T), RAD: retroperitoneal adipose

source_name: Tibetan pig, retroperitoneal adipose

value: adipose:retroperitoneal adipose


title: Placebo w6 Trt 2 week 6 48-013 R_SFA - no bad QC

value: Placebo


title: RM_ASA_rep2, mRNA


title: Placebo w6 Trt 2 week 6 35-003 L_SFA - no bad QC


title: Placebo w6 Trt 2 week 6 59-001 L_SFA re-extract - no bad QC


title: TF_PAD_rep3, mRNA

description: Tibetan pig (T), PAD: pericardial adipose

source_name: Tibetan pig, pericardial adipose

value: adipose:pericardial adipose


title: TF_PMM_rep3, mRNA

description: Tibetan pig (T), psoas major muscle


title: Simvastatin w6 Trt 1 week 6 12-001 R_SFA - no bad QC

value: Simvastatin


title: TF_RAD_rep1, mRNA


title: TF_RAD_rep2, mRNA


title: TF_PAD_rep2, mRNA


title: Simvastatin w0 Trt 1 week 0 62-012 L_SFA - no bad QC

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: TF_MAD_rep2, mRNA

description: Tibetan pig (T), MAD: mesenteric adipose

source_name: Tibetan pig, mesenteric adipose

value: 210 days

value: adipose:mesenteric adipose


title: TF_ILB_rep2, mRNA

description: Tibetan pig (T), ILB: inner layer of backfat

source_name: Tibetan pig, inner layer of backfat

value: adipose:inner layer of backfat


title: Simvastatin w6 Trt 1 week 6 62-028 L_SFA - no bad QC


title: TF_MAD_rep1, mRNA


title: TF_MAD_rep3, mRNA


title: Placebo w6 Trt 2 week 6 40-001 R_SFA - no bad QC


title: TF_ILB_rep1, mRNA


title: TF_PAD_rep1, mRNA


title: Simvastatin w6 Trt 1 week 6 62-029 R_SFA - no bad QC


title: TF_ILB_rep3, mRNA


title: TF_GOM_rep2, mRNA

description: Tibetan pig (T), GOM: greater omentum

source_name: Tibetan pig, greater omentum

value: adipose:greater omentum


title: TF_IAD_rep3, mRNA

description: Tibetan pig (T), IAD: intermuscular adipose

source_name: Tibetan pig, intermuscular adipose

value: Tibetan

value: adipose:intermuscular adipose


title: TF_IAD_rep2, mRNA

value: female


title: TF_IAD_rep1, mRNA


title: TF_GOM_rep3, mRNA

description: Tibetan pig (T), GOM: greater omentum


title: TF_ASA_rep3, mRNA

description: Tibetan pig (T), ASA: abdominal subcutaneous adipose

source_name: Tibetan pig, abdominal subcutaneous adipose

value: adipose:abdominal subcutaneous adipose


title: Simvastatin w0 Trt 1 week 0 75-003 R_POP de-salt - no bad QC

description: Gene expression profiling of peripheral plaque. LEAP study, simvastatin armProfiled in the Merck/Agilent 44k v1.1

value: Peripheral plaque. LEAP study. Simvastatin arm.


title: Placebo w0 Trt 2 week 0 35-003 R_SFA - no bad QC


title: Simvastatin w0 Trt 1 week 0 62-027 L_SFA - no bad QC


title: Placebo w0 Trt 2 week 0 33-003 L_POP - no bad QC


title: Simvastatin w0 Trt 1 week 0 33-008 R_SFA - no bad QC


title: TF_GOM_rep1, mRNA

description: Tibetan pig (T), GOM: greater omentum


title: Placebo w6 Trt 2 week 6 62-013 L_SFA de-salt - no bad QC

value: Week 6


title: TF_ASA_rep1, mRNA


title: Placebo w6 Trt 2 week 6 38-002 R_SFA - no bad QC


title: Placebo w0 Trt 2 week 0 48-013 L_SFA - no bad QC


title: Simvastatin w6 Trt 1 week 6 42-002 R_SFA - no bad QC


title: TF_ASA_rep2, mRNA


title: TM_PMM_rep2, mRNA

description: Tibetan pig (T), psoas major muscle

value: male

value: muscle:psoas major muscle


title: TM_ULB_rep3, mRNA

value: adipose:upper layer of backfat


title: TM_PMM_rep3, mRNA

description: Tibetan pig (T), psoas major muscle


title: TM_RAD_rep2, mRNA

value: adipose:retroperitoneal adipose


title: Placebo w0 Trt 2 week 0 67-007 L_SFA - no bad QC

value: Placebo


title: TM_LDM_rep2, mRNA

value: muscle:longissimus doris muscle


title: TM_PMM_rep1, mRNA

description: Tibetan pig (T), psoas major muscle


title: TM_ULB_rep2, mRNA


title: TM_LDM_rep1, mRNA


title: TM_RAD_rep3, mRNA


title: TM_ULB_rep1, mRNA


title: Simvastatin w0 Trt 1 week 0 42-002 L_SFA - no bad QC

value: Simvastatin

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Simvastatin w0 Trt 1 week 0 68-008 L_SFA - no bad QC


title: TM_PAD_rep2, mRNA

value: 210 days

value: adipose:pericardial adipose


title: TM_RAD_rep1, mRNA

value: Tibetan


title: TM_MAD_rep2, mRNA

value: adipose:mesenteric adipose


title: TM_PAD_rep3, mRNA


title: TM_MAD_rep3, mRNA


title: TM_PAD_rep1, mRNA


title: TM_MAD_rep1, mRNA


title: Simvastatin w0 Trt 1 week 0 74-003 L_SFA - no bad QC


title: Placebo w6 Trt 2 week 6 73-012 R_PT - no bad QC


title: Placebo w0 Trt 2 week 0 73-012 L_PT - no bad QC


title: TM_LDM_rep3, mRNA


title: TM_ILB_rep3, mRNA

value: adipose:inner layer of backfat


title: TM_ILB_rep2, mRNA


title: TM_GOM_rep3, mRNA

description: Tibetan pig (T), GOM: greater omentum

value: adipose:greater omentum


title: TM_IAD_rep1, mRNA

value: adipose:intermuscular adipose


title: Placebo w0 Trt 2 week 0 59-001 R_SFA de-salt - no bad QC

value: Peripheral plaque. LEAP study. Simvastatin arm.


title: Simvastatin w0 Trt 1 week 0 64-003 R_SFA - no bad QC


title: Placebo w0 Trt 2 week 0 29-001 R_SFA - no bad QC


title: TM_IAD_rep3, mRNA

value: male


title: Placebo w6 Trt 2 week 6 44-002 L_SFA - no bad QC

value: Week 6


title: TM_ILB_rep1, mRNA


title: Placebo w0 Trt 2 week 0 59-004 L_SFA de-salt - no bad QC


title: Simvastatin w6 Trt 1 week 6 33-008 L_SFA - no bad QC


title: TM_GOM_rep2, mRNA

description: Tibetan pig (T), GOM: greater omentum


title: TM_ASA_rep1, mRNA

value: adipose:abdominal subcutaneous adipose


title: TM_ASA_rep3, mRNA


title: TM_ASA_rep2, mRNA


title: TM_IAD_rep2, mRNA


title: Placebo w0 Trt 2 week 0 62-023 R_SFA - no bad QC


title: LF_PMM_rep1, mRNA

description: Landrace pig (L), psoas major muscle

source_name: Landrace pig, psoas major muscle

value: Landrace

value: female

value: muscle:psoas major muscle


title: LF_PMM_rep2, mRNA

description: Landrace pig (L), psoas major muscle


title: TM_GOM_rep1, mRNA

description: Tibetan pig (T), GOM: greater omentum


title: LF_LDM_rep1, mRNA

description: Landrace pig (L), longissimus doris muscle

source_name: Landrace pig, longissimus doris muscle

value: muscle:longissimus doris muscle


title: LF_PMM_rep3, mRNA

description: Landrace pig (L), psoas major muscle


title: LF_LDM_rep2, mRNA


title: LF_LDM_rep3, mRNA


title: Placebo w6 Trt 2 week 6 29-001 L_SFA - no bad QC

value: Placebo


title: Simvastatin w0 Trt 1 week 0 77-003 R_SFA - no bad QC

value: Simvastatin

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: LF_ULB_rep2, mRNA

description: Landrace pig (L), ULB: upper layer of backfat

source_name: Landrace pig, upper layer of backfat

value: 210 days

value: adipose:upper layer of backfat


title: Placebo w6 Trt 2 week 6 30-005 R_SFA de-salt - no bad QC


title: LF_ULB_rep3, mRNA


title: Placebo w6 Trt 2 week 6 63-004 L_SFA - no bad QC


title: LF_RAD_rep3, mRNA

description: Landrace pig (L), RAD: retroperitoneal adipose

source_name: Landrace pig, retroperitoneal adipose

value: adipose:retroperitoneal adipose


title: LF_ULB_rep1, mRNA


title: LF_RAD_rep1, mRNA


title: LF_RAD_rep2, mRNA


title: Placebo w0 Trt 2 week 0 63-004 R_SFA - no bad QC


title: LF_MAD_rep3, mRNA

description: Landrace pig (L), MAD: mesenteric adipose

source_name: Landrace pig, mesenteric adipose

value: adipose:mesenteric adipose


title: LF_PAD_rep2, mRNA

description: Landrace pig (L), PAD: pericardial adipose

source_name: Landrace pig, pericardial adipose

value: adipose:pericardial adipose


title: Placebo w6 Trt 2 week 6 63-002 R_POP de-salt - no bad QC

source_name: Peripheral plaque

value: Peripheral plaque. LEAP study. Simvastatin arm.


title: Simvastatin w0 Trt 1 week 0 33-011 L_SFA - no bad QC


title: primary cultured RDEB cSCC fibroblasts RDEB3SCC1F

city: Dundee

first: Andrew

last: South

address: Ninewells Hopsital and Medical School

department: Division of Cancer Research

country: United Kingdom

institute: University of Dundee

description: Primary fibroblast culture

hyb_protocol: standard Agilent Protocol

scan_protocol: standard Agilent Protocol

data_processing: Agilent Feature Extraction Software

source_name: RDEB cSCC fibroblasts

label_protocol: standard Agilent Protocol

extract_protocol: Trizol

tag: body site

value: Forearm

value: primary cultured RDEB cSCC fibroblasts

tag: disease state

value: recessive dystrophic epidermolysis bullosa, cutaneous squamous cell carcinoma


title: Simvastatin w0 Trt 1 week 0 33-010 L_SFA de-salt - no bad QC


title: LF_PAD_rep3, mRNA

value: Landrace


title: LF_PAD_rep1, mRNA

value: female


title: LF_MAD_rep2, mRNA


title: primary cultured RDEB cSCC fibroblasts RDEB7SCC2F

description: Primary fibroblast culture

value: Ankle


title: Placebo w6 Trt 2 week 6 57-005 L_SFA - no bad QC

value: Week 6


title: Simvastatin w6 Trt 1 week 6 77-003 L_SFA - no bad QC


title: primary cultured RDEB cSCC fibroblasts RDEB2SCC1F

description: Primary fibroblast culture


title: primary cultured RDEB dermal fibroblasts RDEB48F

description: Primary fibroblast culture

source_name: RDEB dermal fibroblasts

value: Axilla

value: recessive dystrophic epidermolysis bullosa


title: primary cultured RDEB dermal fibroblasts RDEB23F

description: Primary fibroblast culture


title: Simvastatin w6 Trt 1 week 6 33-010 R_SFA de-salt - no bad QC

value: Simvastatin


title: LF_MAD_rep1, mRNA


title: LF_ILB_rep1, mRNA

description: Landrace pig (L), ILB: inner layer of backfat

source_name: Landrace pig, inner layer of backfat

value: adipose:inner layer of backfat


title: primary cultured RDEB dermal fibroblasts RDEB27F

description: Primary fibroblast culture


title: primary cultured RDEB dermal fibroblasts RDEB26F

description: Primary fibroblast culture


title: LF_ILB_rep3, mRNA

value: 210 days


title: LF_IAD_rep3, mRNA

description: Landrace pig (L), IAD: intermuscular adipose

source_name: Landrace pig, intermuscular adipose

value: adipose:intermuscular adipose


title: LF_IAD_rep1, mRNA


title: LF_ILB_rep2, mRNA


title: Placebo w0 Trt 2 week 0 55-001 L-SFA - no bad QC

value: Placebo

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Simvastatin w0 Trt 1 week 0 33-010 L_SFA re-extract - no bad QC

value: Peripheral plaque. LEAP study. Simvastatin arm.


title: Simvastatin w6 Trt 1 week 6 62-012 R_SFA - no bad QC


title: LF_IAD_rep2, mRNA


title: LF_GOM_rep2, mRNA

description: Landrace pig (L), GOM: greater omentum

source_name: Landrace pig, greater omentum

value: adipose:greater omentum


title: Placebo w6 Trt 2 week 6 62-023 L_SFA - no bad QC


title: primary cultured cSCC fibroblasts SCCIC16

description: Primary fibroblast culture

source_name: cSCC fibroblasts

value: Ear

value: primary cultured cSCC fibroblasts

value: cutaneous squamous cell carcinoma


title: LF_GOM_rep1, mRNA

description: Landrace pig (L), GOM: greater omentum

value: Landrace

value: female


title: Placebo w0 Trt 2 week 0 57-005 R_SFA - no bad QC


title: primary cultured cSCC fibroblasts SCCT7F

description: Primary fibroblast culture

value: Finger


title: primary cultured cSCC fibroblasts SCCIC15

description: Primary fibroblast culture

value: Penis


title: primary cultured cSCC fibroblasts SCCIC17

description: Primary fibroblast culture

value: Scalp


title: Simvastatin w0 Trt 1 week 0 68-001 R_SFA de-salt - no bad QC

value: Simvastatin


title: Simvastatin w6 Trt 1 week 6 68-001 L_POP de-salt - no bad QC

value: Week 6


title: primary cultured cSCC fibroblasts SCCT6F

description: Primary fibroblast culture

value: Hand


title: LF_GOM_rep3, mRNA

description: Landrace pig (L), GOM: greater omentum

value: 210 days


title: primary cultured normal human dermal fibroblasts NHF66

description: Primary fibroblast culture

source_name: normal human dermal fibroblasts

value: Reduction surgery N/A

value: normal


title: KD_2 to Rh30_2_DS

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
SHH_toRHH_2_DS
Compare KD_2 to Rh30_2
Biological replicate 2 of 2, knockdown clone cells to Rh30 wild type cells, dye swap
US83903566_251485051229_4.txt

hyb_protocol: Microarray hybridization was performed at 65°C for 18 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 3μm resolution, and the array data was extracted with Agilent feature extraction software using the GE2_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used along with LOWESS normalization

source_name: Rh30 cells

label_protocol: 500ng of total RNA were labeled (Cy3, control sample; Cy5, test sample) according to Agilent's labeling protocol

growth_protocol: 2 million cells were plated into a T75 flask with DMEM medium containing 10% FBS  either with (for CON and KD clones) or without (for Rh30 cells) 1 μg/ml puromycin and allowed to grow at 37°C for 24 hours  before RNA extraction.

extract_protocol: Total RNA extracted using Qiagen Rneasy kit following manufacturer's instructions

tag: cell line

value: alveolar rhabdomyosarcoma cell line Rh30

value: Rh30 wild type sample 2

value: PAX3-FOXO1 knockdown clone sample 2


title: Placebo w0 Trt 2 week 0 44-002 R_POP - no bad QC

value: Peripheral plaque. LEAP study. Simvastatin arm.

value: Placebo

value: Baseline

value: Total RNA from a pool of 14 human carotid atherosclerotic plaques


title: Placebo w6 Trt 2 week 6 30-005 R_SFA re-extract - no bad QC


title: primary cultured normal human dermal fibroblasts NHF88

description: Primary fibroblast culture

tag: cell type


title: LF_ASA_rep3, mRNA

description: Landrace pig (L), ASA: abdominal subcutaneous adipose

source_name: Landrace pig, abdominal subcutaneous adipose

value: Landrace

value: female

tag: age

value: adipose:abdominal subcutaneous adipose


title: KD_2 to Rh30_2

description:
SHH_toRHH_2
Compare KD_2 to Rh30_2
Biological replicate 2 of 2, knockdown clone cells to Rh30 wild type cells
US83903566_251485051229_3.txt


title: primary cultured normal human dermal fibroblasts NHF2

description: Primary fibroblast culture


title: LF_ASA_rep2, mRNA

tag: tissue


title: LF_ASA_rep1, mRNA


title: LM_PMM_rep1, mRNA

description: Landrace pig (L), psoas major muscle

value: male

value: muscle:psoas major muscle


title: KD_1 to Rh30_1_DS

description:
SHH_toRHH_1_DS
Compare KD_1 to Rh30_1
Biological replicate 1 of 2, knockdown clone cells to Rh30 wild type cells, dye swap
US83903566_251485051227_2.txt

value: Rh30 wild type sample 1

value: PAX3-FOXO1 knockdown clone sample 1


title: BL vs. 8CB rep. 1

city: Bonn

first: Eva

last: Held

address: Endenicher Allee 15

department: Animal Science

institute: University of Bonn

description: Analysis  was performed by comparing the gene expression 2-cell stage biopsies that  developed to blastocyst ansd those blocked at 4-cell stage

hyb_protocol: A total of 825 ng of each labeled sample were incubated in a solution containing 2X blocking agent and 1X fragmentation buffer in a volume of 55 μl at 65 °C for 15 min, and were then put on ice. Fifty-five microliters of 2X GEx Hybridization Buffer HI-RPM was added for a final volume of 110 μl. The hybridization mix was added onto the array and hybridization was performed at 65 °C for 17 hr using an Agilent Hybridization chamber in a rotating oven

scan_protocol: Array scanning and image analysis was performed using Axon GenePix 4000B scanner and GenePix Pro analysis software (version 4.0) (Axon Instruments, Foster City, CA), respectively

data_processing:
Data analysis was perfomed using R programme and  bioconductor packages. The values from each channel were log2 transformed and normalized using the LOESS algorithm to remove intensity dependent effects within the calculated values.  Differentially expressed genes were obtained using linear models for microarray data (LIMMA)
Loess normalized log2 ratio (Cy5/Cy3):A mean log2-transformed value of (Cy5/Cy3) was calculated for each probeset

organism: Bos taurus

source_name: BL

label_protocol: Labelling aRNA was performed using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Embryos were developed in vitro until day 7

extract_protocol: Total RNA was extracted from three independent pools consisting of 15 blastomeres, whose sister-blastomeres 1. blocked at 2 cell stage, 2. blocked at 4 cell stage, 3. developed to blastocyst using the PicoPureTM RNA isolation kit according to the manufacturer's instruction. Genomic DNA contamination was removed by performing on column DNA digestion using RNase-free DNase set (Qiagen, Hilden, Germany).

treatment_protocol: Gene expression comparison was done between embryos developed to Blastocyst and those blocked at 2- Cell stage

value: Biopsies of 2-Cell embryo developed to blastocyst

treatment_protocol: Blastomeres of 2-cell stage embryos were cultured individually, the corresponding half retained for transcriptome analysis. After 7 days of culture frozen samples were pooled according to the subsequent development of individual cultured sister blastomeres.

tag: species

value: Bos taurus

value: Biopsies of 2-Cell embryo blocked at 4 cell stage


title: KD_1 to Rh30_1

description:
SHH_toRHH_1
Compare KD_1 to Rh30_1
Biological replicate 1 of 2, knockdown clone cells to Rh30 wild type cells
US83903566_251485051227_1.txt

value: alveolar rhabdomyosarcoma cell line Rh30


title: LM_PMM_rep2, mRNA

description: Landrace pig (L), psoas major muscle

source_name: Landrace pig, psoas major muscle

value: 210 days


title: LM_PMM_rep3, mRNA

description: Landrace pig (L), psoas major muscle


title: KD_1 to CON_1

description:
SHH_toCON_1
Compare KD_1 to CON_1
Biological replicate 1 of 2, knockdown clone cells to control clone cells
US83903566_251485051227_3.txt

value: Control clone sample 1


title: LM_LDM_rep3, mRNA

source_name: Landrace pig, longissimus doris muscle

value: muscle:longissimus doris muscle


title: 8CB vs. BL rep. 2

description: Analysis  was performed by comparing the gene expression 2-cell stage biopsies that  blocked in 4CB and those developed to Blastocyst


title: 8CB vs. BL rep. 3


title: LM_LDM_rep1, mRNA


title: KD_2 to CON_2_DS

description:
SHH_toCON_2_DS
Compare KD_2 to CON_2
Biological replicate 2 of 2, knockdown clone cells to control clone cells, dye swap
US83903566_251485051229_2.txt

value: Control clone sample 2

value: PAX3-FOXO1 knockdown clone sample 2


title: KD_1 to CON_1_DS

description:
SHH_toCON_1_DS
Compare KD_1 to CON_1
Biological replicate 1 of 2, knockdown clone cells to control clone cells, dye swap
US83903566_251485051227_4.txt


title: LM_ULB_rep3, mRNA

source_name: Landrace pig, upper layer of backfat

value: adipose:upper layer of backfat


title: BL vs. 8CB rep. 3


title: 8CB vs. BL rep. 1


title: Rh30_2 to CON_2_DS

description:
RHH_toCON_2_DS
Compare Rh30_2 to CON_2
Biological replicate 2 of 2, Rh30 wild type cells to control clone cells, dye swap
US83903566_251485051228_3.txt

value: Rh30 wild type sample 2


title: BL vs. 2CB rep. 2

description: Analysis  was performed by comparing the gene expression 2-cell stage biopsies that  developed to blastocyst ansd those blocked at 2-cell stage

value: Biopsies of 2-Cell embryo blocked at 2 cell stage


title: KD_2 to CON_2

description:
SHH_toCON_2
Compare KD_2 to CON_2
Biological replicate 2 of 2, knockdown clone cells to control clone cells
US83903566_251485051229_1.txt


title: BL vs. 2CB rep. 1


title: LM_LDM_rep2, mRNA

description: Landrace pig (L), longissimus doris muscle

value: Landrace


title: BL vs. 2CB rep. 3


title: Rh30_2 to CON_2

description:
RHH_toCON_2
Compare Rh30_2 to CON_2
Biological replicate 2 of 2, Rh30 wild type cells to control clone cells
US83903566_251485051228_4.txt


title: LM_ULB_rep2, mRNA

description: Landrace pig (L), ULB: upper layer of backfat

value: male


title: BL vs. 8CB rep. 2


title: Rh30_1 to CON_1_DS

description:
RHH_toCON_1_DS
Compare Rh30_1 to CON_1
Biological replicate 1 of 2, Rh30 wild type cells to control clone cells, dye swap
US83903566_251485051228_1.txt


title: 2CB vs. BL rep. 3

description: Analysis  was performed by comparing the gene expression 2-cell stage biopsies that  blocked in 2CB and those developed to Blastocyst

treatment_protocol: Gene expression comparison was done between embryos developed zo Blastocyst and those blocked at 2- Cell stage


title: Rh30_1 to CON_1

description:
RHH_toCON_1
Compare Rh30_1 to CON_1
Biological replicate 1 of 2, Rh30 wild type cells to control clone cells
US83903566_251485051228_2.txt


title: 2CB vs. BL rep. 2


title: 2CB vs. BL rep. 1


title: HUVECs (miR-181b/miR negative CTL)-rep4

city: Boston

first: Mark

last: Feinberg

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and women's hospital

description: Biological replicate 4 of 4. comparison of microRNA negative control VS. miR-181b

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) (v 8.5.1.1) was used to read out and process the microarray image files. FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).

source_name: HUVECs-Passage 3 human Umbilical Vein Endothelial Cells

label_protocol: To produce Cy3- and Cy5-labeled cRNA, 1 μg of each total RNA sample was amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: HUVECs were obtained from Lonza (cc-2159) and cultured in endothelial cell growth medium EGM®-2 (cc-3162). Cells passaged less than five times were used for all experiments. Lipofectamine™ 2000 transfection reagent from Invitrogen was used for transfection following manufacturer’s instructions. MiRNA negative control or miR-181b mimics were transfected at 10 nM concentration, and cells were allowed to grow for 36 h before treatment of 10 ng/ml recombinant human TNF-α from R&D Systems (210-TA/CF) for 4 h.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Primary cells

tag: passage

tag: transfection

value: microRNA negative control


title: LM_ULB_rep1, mRNA


title: LM_RAD_rep1, mRNA

description: Landrace pig (L), RAD: retroperitoneal adipose

source_name: Landrace pig, retroperitoneal adipose

value: adipose:retroperitoneal adipose


title: HUVECs (miR-181b/miR negative CTL)-rep2

description: Biological replicate 2 of 4. comparison of microRNA negative control VS. miR-181b


title: LM_RAD_rep2, mRNA


title: LM_PAD_rep3, mRNA

description: Landrace pig (L), PAD: pericardial adipose

source_name: Landrace pig, pericardial adipose

value: adipose:pericardial adipose


title: murine bone marrow CCR9+ pDC replicate 2

city: Singapore

first: Pavandip Singh

last: Wasan

address: 8A Biomedical Grove, #03-06, Immunos

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description: murine bone marrow, Mus Musculus, C57BL/6,CCR9+ pDC, total RNA, biotin, cy3

hyb_protocol: Hybridized onto Mouse WG-6 v2 Beadchips (Illumina inc.)

scan_protocol: scanned with a BeadArray Scanner 500GX (Illumina inc.), chip images were analyzed using GenomeStudio Gene expression Version 1.8

data_processing: Array data were extracted at the probeset level with no background correction using Illumina's BeadStudio software. These raw data were normalised according using the Loess method within the LUMI package in R/Bioconductor v2.13.1. Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate, and probesets with corrected p-value less than 0.05 were considered. Matrix non-normalized contains the murine (GPL6887) raw Illumina data. Matrix normalized contains the murine (GPL6887) data post normalization using Loess normalization within the Lumi package of R/Bioconductor.

label: biotin, cy3

source_name: murine bone marrow

label_protocol: TargetAmp-Nano Labelling Kit protocol (Illumina inc.)

extract_protocol: murine bone marrow isolation, FACS sorting of CCR9- pDC-like DC precursors and CCR9+ pDC, total RNA isolation using the Ambion mirVana miRNA isolation kit

value: female

value: 7 weeks

tag: strain

tag: cell subtype

value: CCR9+ pDC


title: murine bone marrow CCR9+ pDC replicate 1


title: LM_MAD_rep2, mRNA

description: Landrace pig (L), MAD: mesenteric adipose

source_name: Landrace pig, mesenteric adipose

value: 210 days

value: adipose:mesenteric adipose


title: HUVECs (miR-181b/miR negative CTL)-rep3

description: Biological replicate 3 of 4. comparison of microRNA negative control VS. miR-181b


title: HUVECs (miR-181b/miR negative CTL)-rep1

description: Biological replicate 1 of 4. comparison of microRNA negative control VS. miR-181b


title: LM_MAD_rep1, mRNA


title: murine bone marrow CCR9- pDC-like DC precursor replicate 1

description: murine bone marrow, Mus Musculus, C57BL/6,CCR9- pDC, total RNA, biotin, cy3

value: CCR9- pDC


title: LM_RAD_rep3, mRNA


title: LM_MAD_rep3, mRNA


title: LM_PAD_rep2, mRNA


title: murine bone marrow CCR9- pDC-like DC precursor replicate 3


title: LM_PAD_rep1, mRNA


title: murine bone marrow CCR9+ pDC replicate 3


title: MUT+Rosi 3

city: Houston

first: Philippe

middle: M

last: Campeau

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were normalized using the Rank Invariant method.

source_name: NIH-3T3 + PPARγ2 E157D + Rosi

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

growth_protocol: Cells were grown in high-glucose DMEM with 10% FBS and 2 µg/mL blasticidin.

extract_protocol: Total RNA was isolated with TRI Reagent (Sigma) and purified with isopropanol and ethanol as in the manufacturer's instructions. An additional purification step was done using the RNeasy columns (Qiagen).

treatment_protocol: 24 hours of 20 µM or an equal volume of DMSO as vehicle control.

value: fibroblast

tag: transgene

value: E157D PPARγ2

tag: treatment

value: 20 µM Rosiglitazone


title: LM_ILB_rep2, mRNA

description: Landrace pig (L), ILB: inner layer of backfat

source_name: Landrace pig, inner layer of backfat

value: adipose:inner layer of backfat


title: WT 3

description: replicate 3

source_name: NIH-3T3 + PPARγ2 WT

value: WT PPARγ2

value: DMSO


title: WT+Rosi 3

description: replicate 3

source_name: NIH-3T3 + PPARγ2 WT + Rosi


title: MUT 3

description: replicate 3

source_name: NIH-3T3 + PPARγ2 E157D


title: LM_IAD_rep3, mRNA

description: Landrace pig (L), IAD: intermuscular adipose

source_name: Landrace pig, intermuscular adipose

value: Landrace

value: male

value: adipose:intermuscular adipose


title: LM_ILB_rep3, mRNA


title: LM_GOM_rep1, mRNA

description: Landrace pig (L), GOM: greater omentum

source_name: Landrace pig, greater omentum

value: adipose:greater omentum


title: LM_IAD_rep1, mRNA


title: LM_ASA_rep3, mRNA

description: Landrace pig (L), ASA: abdominal subcutaneous adipose

source_name: Landrace pig, abdominal subcutaneous adipose

value: adipose:abdominal subcutaneous adipose


title: MUT 2

description: replicate 2


title: WT+Rosi 2

description: replicate 2


title: LM_GOM_rep3, mRNA

description: Landrace pig (L), GOM: greater omentum


title: MUT+Rosi 1

description: replicate 1


title: WT 2

description: replicate 2


title: LM_IAD_rep2, mRNA


title: murine bone marrow CCR9- pDC-like DC precursor replicate 2

value: female


title: MUT+Rosi 2

description: replicate 2


title: WT+Rosi 1

description: replicate 1


title: MUT 1

description: replicate 1


title: LM_GOM_rep2, mRNA

description: Landrace pig (L), GOM: greater omentum


title: wt-starved-1-a

status: Public on May 15 2012

city: Utrecht

first: Patrick

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009. The limma R package version 2.12.0 is used for final gene expression analysis. P-values are Benjamini-Hochberg FDR corrected.

molecule: nuclear RNA

organism: Saccharomyces cerevisiae

source_name: refpool

label_protocol: robot amplification and labeling v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0

value: refpool

source_name: wt-starved

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: wt-starved


title: LM_ASA_rep2, mRNA

value: 210 days


title: wt-rite-H3-HA-1-b


title: wt-rite-H3-HA-1-a


title: wt-starved-1-b


title: wt-rite-H3-T7-1-a


title: WT 1

description: replicate 1


title: wt-rite-2-a

source_name: wt-rite

value: wt-rite


title: hif1-del-2-a


title: hif1-del-starved-1-a


title: hhf2-mut-K5R-K12R-starved-1-b


title: hif1-del-2-b


title: hif1-del-starved-1-b


title: hhf2-mut-K5Q-K12Q-starved-1-b


title: hat2-del-starved-1-a


title: hhf2-mut-K5R-K12R-starved-1-a


title: LM_ASA_rep1, mRNA


title: hat2-del-2-a


title: hat2-del+hif1-del-1-a


title: hat2-del+hif1-del-starved-1-a


title: hat1-del-starved-1-b


title: hat2-del-starved-1-b


title: hat2-del-2-b


title: hhf2-mut-K5Q-K12Q-starved-1-a


title: hat1-del-2-b


title: hat2-del+hif1-del-1-b


title: hat2-del+hif1-del-starved-1-b


title: hat1-del-starved-1-a


title: hat1-del-2-a


title: wt-rite-2-b


title: kidneys pooled from six female MRL/lpr mice_1

city: Shanghai

last: Shen

address: 145 Shan Dong Middle Road

department: Department of Rheumatology

institute: Renji Hospital, JiaoTong University School of Medicine

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous housekeeping MammU6. [delta] CT =  CT,sample - CT,reference.

label_protocol: Individual TaqMan® MicroRNA Assays cards were performed for miRNA profiling following the Manufacturer’s instructions .Reverse transcription was performed from 50ng total RNA per sample using Megaplex™ RT Pools(Applied Biosystems). Then add Megaplex™ PreAmp Primers(Applied Biosystems) for additional assay sensitivity. Quantitative real-time PCR were performed on an AbiPrism 7900 HT cycler (Applied Biosystems) with 1 cycle at 50℃ for 2 minutes and 95℃ for 10 minutes and 40 cycles at 94℃ for 15 seconds and 60℃ for 60 seconds.

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

value: MRL/Lpr

value: kidney


title: kidneys pooled from six female MRL/lpr mice_2


title: kidneys pooled from three control mice_2

source_name: kidneys pooled from three control mice

value: control


title: spinal cords pooled from six EAE mice_1

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous housekeeping MammU6. [delta] CT =  CTsample - CTreference.

source_name: spinal cord from EAE mice

tag: genotype/variation

value: experimental autoimmune encephalomyelitis (EAE) mice

value: spinal cord


title: spinal cords pooled from six EAE mice_2


title: kidneys pooled from three control mice_1


title: spinal cords pooled from six naïve control mice_2

source_name: spinal cord from naïve control mice

value: naive control


title: spinal cords pooled from six naïve control mice_1


title: joint samples pooled from six CIA mice_1

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the average of RNU24 and RNU6B value. [delta]CT =  CTsample - CTreference.

source_name: joint samples pooled from six CIA mice

value: joint tissues


title: joint samples pooled from six CIA mice_2


title: joint samples pooled from six naïve control mice_2


title: synovial tissues from RA individual_1

description:
Test
RA-1

data_processing: TLDA were run in the 7900 HT Sequence Detection system. The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. Automatic baseline and manual CT were set to 0.2 for all samples. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous housekeeping MammU6.  [delta] CT =  CTsample - CTreference.

source_name: synovial tissues from RA individual

tag: tissue source

value: rheumatoid arthritis (RA) patient

value: synovial tissues


title: synovial tissues from RA individual_3

description:
Test
RA-3


title: LM_ILB_rep1, mRNA

tag: breed

value: Landrace

value: male

value: adipose:inner layer of backfat


title: synovial tissues from RA individual_2

description:
Test
RA-2


title: joint samples pooled from six naïve control mice_1


title: synovial tissues from RA individual_4

description:
Test
RA-4


title: hat1-del+hat2-del-1-b


title: hat1-del+hat2-del-1-a


title: synovial tissues from OA individual_2

description:
Control
OA-2

source_name: synovial tissues from OA individual

value: osteoarthristis (OA) patient


title: hat1-del+hat2-del+hif1-del-1-a

value: refpool


title: hat1-del+hif1-del-starved-1-a


title: synovial tissues from OA individual_1

description:
Control
OA-1


title: hat1-del+hat2-del+hif1-del-1-b


title: synovial tissues from normal individual_2

description:
Control
Nor-2

source_name: synovial tissues from normal individual

value: normal individual (victims of accidental injury)


title: hat1-del+hif1-del-starved-1-b


title: hat1-del+hif1-del-1-a


title: hat1-del+hif1-del-1-b


title: synovial tissues from normal individual_1

description:
Control
Nor-1


title: Flp-FBXO25-∆F_48 h _ rep2

city: Ribeirão Preto

first: Ana

middle: Carolina

last: Humanes

state: SP

address: Avenida Bandeirantes, 3900

department: Bioquímica e Imunologia

country: Brazil

institute: Universidade de São Paulo

description:
252665213785_GE2-v5_95_Feb07_1_4
Biological replicate 2 of 2.  Flp-In-293-∆F-FBXO25 , untreated or treated with tetracyclin for 48 hours.

hyb_protocol: 825 ng of each labeled cRNA was mixed with Agilent Fragmentation Mix and incubated at 60 °C for 30 minutes. The fragmentation was interrupted by adding 55 µL of 2X GE Hybridization Buffer HI-RPM. Finally, 110 µL of sample was placed down onto the microarray slide, which was mounted into the Agilent™ Microarray Hybridization Chamber Kit. The hybridization was carried out in Agilent G2545A Hybridization Oven set to 65 °C for 17 hours. Microarray slides were washed according to Agilent’s instruction.

scan_protocol: Scanned on GenePix 4000B microarray scanner (Molecular Devices, USA

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction. Data were processed using TIGR platform. Data were visualized and statistically analysed (t test) using TMeV from TIGR.

source_name: Flp-FBXO25-∆F_48 h treated

label_protocol: cDNA was synthesized from 1 µg of total RNA using Agilent's cDNA Master Mix. cRNA amplification and labeling were performed by adding to the samples the Agilent Transcription Master Mix plus Cyanine-3 (for untreated samples) or Cyanine-5 (for tetracycline treated samples) for 2 hours at 40 ºC.

growth_protocol: Flp-In-293-WT-FBXO25 and Flp-In-293-∆F-FBXO25 cells were grown in DMEM supplemented with 10% fetal bovine serum and the antibodies  Hygromicin and Blasticidin (for clonal selection) at 37ºC in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted using Rnaeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Flp-In-293-WT-FBXO25 and Flp-In-293-∆F-FBXO25 cells were treated with tetracycline for 24 and 48 hours to induce Fbxo25 (wild type or mutant) expression


title: Flp-FBXO25-∆F_24 h _ rep2

description:
252665213785_GE2-v5_95_Feb07_1_2
Biological replicate 2 of 2.  Flp-In-293-∆F-FBXO25 , untreated or treated with tetracyclin for 24 hours.

source_name: Flp-FBXO25-∆F_24 h treated


title: Flax_outer_rep3_60-mers arrays

city: Villeneuve d'Ascq

first: Lucau

last: Anca

address: Cité scientifique

country: France

institute: University Lille 1

description: This sample is of flax stem outer tissues. It is the third of three technical replicates used in this experiment. Hybridization was on 60-mers arrays.

hyb_protocol: Microarrays were hybridized at 38°C (25-mers arrays) and at 42°C (60-mers arrays) during 16 to 18h with 6µg of Cy3 labelled ds-cDNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5µm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA, USA) piloted by GenePix Pro 6.0 software (Axon).

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Linum usitatissimum

source_name: Flax stem outer tissues

label_protocol: Double-stranded cDNA (ds-cDNA) was synthesized from 10 µg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 250 ng random hexamer primers. ds-cDNA was cleaned and labeled in accordance with the Nimblegen Gene Expression Analysis protocol (Nimblegen Systems, Inc., Madison, WI, USA).

growth_protocol: Linum usitatissimum (var. Diane) plants were grown in a growth chamber (light/night cycles 16h (22°C)/8h (19°C), 50% humidity and light intensity of 400 µE s-1 m-2) and harvested after nine weeks of grown. The outer fiber-bearing tissues were peeled off and inner tissues (xylem) from a 15 cm long stem section were cut into short fragments before both tissues were frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated from the collected tissues. 100 mg of frozen stem tissues were ground in liquid nitrogen using the Trizol method (Invitrogen, Carlsbad, CA). Total RNAs were purified using the RNeasy Plant kit (Qiagen) according to the manufacturer's instructions. The genomic DNA was eliminated after treatment with Dnase I for 20 min at 37°C using the DNA-free kit (Ambion, Austin, TX, USA). RNA was checked for purity and degradation by capillary electrophoresis using the Bio-Analyzer Experion (Bio-Rad; RNA Standard Sens kit; RNA StdSens chips).

tag: tissues

value: outer stem tissues

tag: array type

value: Nimblegen 60-mers


title: Flp-FBXO25-∆F_48 h _ rep1

description:
252665213785_GE2-v5_95_Feb07_1_3
Biological replicate 1 of 2.  Flp-In-293-∆F-FBXO25 , untreated or treated with tetracyclin for 48 hours.


title: Flp-FBXO25-WT_48 h _ rep1

description:
252665213786_GE2-v5_95_Feb07_1_3
Biological replicate 1 of 2.  Flp-In-293-WT-FBXO25 , untreated or treated with tetracyclin for 48 hours.

source_name: Flp-FBXO25-WT_48 h treated


title: Flp-FBXO25-∆F_24 h _ rep1

description:
252665213785_GE2-v5_95_Feb07_1_1
Biological replicate 1 of 2.  Flp-In-293-∆F-FBXO25 , untreated or treated with tetracyclin for 24 hours.


title: Flax_outer_rep1_60-mers arrays

description: This sample is of flax stem outer tissues. It is the first of three technical replicates used in this experiment. Hybridization was on 60-mers arrays.


title: Flax_inner_rep2_60-mers arrays

description: This sample is of flax stem inner tissues. It is the second of three technical replicates used in this experiment. Hybridization was on 60-mers arrays.

source_name: Flax stem inner tissues

value: inner stem tissues


title: Flax_outer_rep2_60-mers arrays

description: This sample is of flax stem outer tissues. It is the second of three technical replicates used in this experiment. Hybridization was on 60-mers arrays.


title: Flp-FBXO25-WT_24 h _ rep2

description:
252665213786_GE2-v5_95_Feb07_1_2
Biological replicate 2 of 2.  Flp-In-293-WT-FBXO25 , untreated or treated with tetracyclin for 24 hours.

source_name: Flp-FBXO25-WT_24 h treated

source_name: Flp-FBXO25-WT_ untreated


title: Flp-FBXO25-WT_48 h _ rep2

description:
252665213786_GE2-v5_95_Feb07_1_4
Biological replicate 2 of 2.  Flp-In-293-WT-FBXO25 , untreated or treated with tetracyclin for 48 hours.


title: Flax_inner_rep1_60-mers arrays

description: This sample is of flax stem inner tissues. It is the first of three technical replicates used in this experiment. Hybridization was on 60-mers arrays.


title: Flax_inner_rep3_60-mers arrays

description: This sample is of flax stem inner tissues. It is the third of three technical replicates used in this experiment. Hybridization was on 60-mers arrays.