title: Serum clinical sample 2 with ultracentrifugation and  treated with PMA

type: other

city: St-Hyacinthe

first: Christian

last: Bellehumeur

address: 3200 Sicotte

country: Canada

institute: Université de Montréal

description: Swine serum clinical sample 2 with ultracentrifugation and  treated with PMA

hyb_protocol: Microarray slide were pre-hybridized at 50 Celcius for 1h with DIG easy hyb buffer supplemented with BSA. Then total labeled DNA (typically approximately 3ug of DNA) was hybridized under a coverslip at 50 Celcius for 16 hours. Slides were washed 3 times (5 min) in 0,1x SSC / 0,1% SDS buffer, then 5 min in 0,1x SSC.

scan_protocol: ScanArray software version 1,1. Scanned at a laser intensity of 80 to 100%.

data_processing: Data were evaluated on an excel template. Data normalization was done with this calculation: [(PFL-BFL)/BFL] where PFL represent a PRRSV probe fluorescence intensity and BFL represent the base fluorescence level (negative control probe fluorescence)

molecule: other

organism: Sus scrofa

source_name: serum

label_protocol: Following a first round of random PCR (Wang et al, 2002), DNA was amplified in the presence of amino-allyl dUTP. aaDNA generated was then cleaned with a PCR purification kit and labeled with Cy3 Mono-Reactive dye.

growth_protocol: Not applicable

extract_protocol: Total DNA and RNA was extracted directrly from treated samples with two rounds of Phenol (pH 7.4-7.7) / chloroform / isoamyl alcool extraction. The supernatant was then cleaned with 2 rounds of chloroform extraction. Finally, DNA was precipitated following the addition of Sodium acetate (3M) and addition of Ethanol in combinaison with a 30 min centrifugation step. Total DNA and RNA pellet was resuspended in RNAse free water.

treatment_protocol: treatments assessed on each samples was different combinaison of propidium monoazide (50, 100 or 200 uM) or ethidium monoazide (100, 200 or 400 uM) with or without ultracentrifugation to lower genomic contamination in lung tissue samples spiked with PRRSV (1 000 or 10 000 TCID50/test), serum samples spiked with PRRSV (1 000 TCID50/mL), 3 different lung clinical samples and 2 different serum clinical samples.

tag: sample type

value: serum

tag: molecule

value: Total DNA and RNA


title: Serum clinical sample 1 with ultracentrifugation and  treated with PMA

status: Public on Nov 02 2015

description: Swine serum clinical sample 1 with ultracentrifugation and  treated with PMA


title: Serum clinical sample 2 with ultracentrifugation and not treated

description: Swine serum clinical sample 2 with ultracentrifugation and not treated


title: Rostral.NT3.01d.2

type: RNA

city: Los Angeles

first: Weihong

last: Ge

state: CA

address: 635 Charles E Young Dr South 355

country: USA

institute: UCLA

hyb_protocol: Following fragmentation,  tagged cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array containing 30,000 rat transcripts. The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data was extracted from scanned images using Affymetrix GCOS software. The raw data was normalized using a multi-array (RMA) method using the Expression Console software, followed by log2 transformation.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

label_protocol: BiotinylatedcRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Samples for microarray analysis were homogenized in 1 ml Trizol (Invitrogen, Carlsbad, CA), and RNA extracted using RNEasy miniprep columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: At 1, 3, 10, 20, 30, 60, 90days post surgery, animals were sacrificed, and 5mm segments of spinal cord at the lesion site, as well as immediately caudal or rostral to the lesion segment were collected labeled with R for rostral, C for caudal, and M for lesion site

tag: location

value: Rostral region 5mm tissue

tag: treatment

tag: time (day)

tag: tissue

value: spinal cord


title: Rostral.NT3.01d.3


title: Lung clinical 3 with ultracentrifugation and  treatedm with PMA

description: Swine lung clinical 3 with ultracentrifugation and  treatedm with PMA

source_name: lung

tag: preparation

value: Tissue homogenate

value: lung


title: Middle.LC.60d.1

value: Middle region 5mm tissue

value: Lesion control(LC)


title: Middle.LC.60d.2


title: Middle.LC.90d.2


title: Middle.LC.20d.5


title: Middle.LC.20d.2


title: Serum clinical sample 1 with ultracentrifugation and not treated

description: Swine serum clinical sample 1 with ultracentrifugation and not treated


title: Middle.LC.30d.1


title: Middle.LC.30d.2


title: Middle.LC.20d.3


title: Uninjured .x.1

source_name: Uninjured

value: Uninjured 5mm tissue

value: Uninjured

value: x


title: Lung clinical 3 with ultracentrifugation and not treated

description: Swine lung clinical 3 with ultracentrifugation and not treated


title: Middle.LC.60d.3


title: Middle.LC.10d.2


title: Middle.LC.03d.3


title: Lung clinical 2 with ultracentrifugation and  treatedm with PMA

description: Swine lung clinical 2 with ultracentrifugation and  treatedm with PMA


title: Middle.LC.30d.3


title: Middle.LC.10d.3


title: Middle.LC.90d.1


title: Middle.LC.10d.1


title: Middle.LC.03d.2


title: Middle.ET.03d.2

value: Empty tube(ET)


title: Lung clinical 2 with ultracentrifugation and not treated

description: Swine lung clinical 2 with ultracentrifugation and not treated


title: Middle.ET.03d.3


title: Middle.NT3.90d.2


title: Middle.LC.03d.1


title: Lung clinical 1 with ultracentrifugation and  treatedm with PMA

description: Swine lung clinical 1 with ultracentrifugation and  treatedm with PMA


title: Lung clinical 1 with ultracentrifugation and not treated

description: Swine lung clinical 1 with ultracentrifugation and not treated


title: Serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (2nd expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (2nd experiment)

value: PRRS spiked serum


title: Serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (2nd expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (2nd experiment)


title: Serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (2nd expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (2nd experiment)


title: Serum spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (2nd expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (2nd experiment)


title: Serum spiked with PRRSV (1000 TCID50/test) none treated (2nd expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) none treated (2nd experiment)


title: Middle.NT3.30d.3


title: Middle.NT3.60d.2


title: Middle.NT3.20d.2


title: Middle.NT3.20d.1


title: Middle.NT3.60d.3


title: Middle.NT3.30d.1


title: Middle.NT3.30d.2


title: Middle.NT3.03d.3


title: Middle.NT3.10d.2


title: Serum spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (2nd expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (2nd experiment)


title: Serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (1st expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (1st experiment)


title: Middle.ET.03d.1


title: Middle.NT3.03d.1


title: Serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (1st expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (1st experiment)


title: Middle.NT3.10d.3


title: Caudal.LC.90d.2

value: Caudal region 5mm tissue


title: Middle.NT3.20d.3


title: Serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (1st expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (1st experiment)


title: Caudal.LC.90d.1


title: Middle.NT3.03d.2


title: Caudal.LC.60d.2


title: Serum spiked with PRRSV (1000 TCID50/test) none treated (1st expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) none treated (1st experiment)


title: Caudal.LC.90d.3


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (3rd experiment)

value: PRRS spiked tissue homogenate


title: Caudal.LC.60d.1


title: Caudal.LC.30d.1


title: Caudal.LC.30d.3


title: Serum spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (1st expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (1st experiment)


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and none treated (3rd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and none treated (3rd experiment)


title: Caudal.LC.20d.1


title: Caudal.LC.30d.2


title: Caudal.LC.60d.3


title: Caudal.LC.10d.3


title: Caudal.LC.10d.2


title: Caudal.LC.20d.3


title: Middle.NT3.60d.1


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) treated with EMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) treated with EMA (100uM) (3rd experiment)


title: Middle.NT3.10d.1


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) treated with PMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) treated with PMA (100uM) (3rd experiment)


title: Caudal.LC.20d.2


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) none treated (3rd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) none treated (3rd experiment)


title: Caudal.LC.01d.3


title: Caudal.LC.01d.1


title: Caudal.LC.03d.3


title: Caudal.LC.10d.1


title: Caudal.LC.01d.2


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (2nd experiment)


title: Caudal.ET.90d.2


title: Caudal.LC.03d.1


title: Caudal.ET.90d.3


title: Caudal.ET.60d.2


title: Caudal.ET.90d.1


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (2nd experiment)


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and none treated (2nd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and none treated (2nd experiment)


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) treated with EMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) treated with EMA (100uM) (2nd experiment)


title: Caudal.ET.60d.3


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) treated with PMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) treated with PMA (100uM) (2nd experiment)


title: Caudal.ET.30d.1


title: Caudal.ET.60d.1


title: Caudal.ET.30d.3


title: Caudal.ET.30d.2


title: Caudal.ET.20d.3


title: Caudal.ET.20d.1


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) none treated (2nd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) none treated (2nd experiment)


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (1st expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (1st experiment)


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and none treated (1st expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and none treated (1st experiment)


title: Caudal.ET.20d.2


title: Caudal.ET.10d.2


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (1st expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (1st experiment)


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) treated with EMA (100uM) (1st expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) treated with EMA (100uM) (1st experiment)


title: Caudal.ET.10d.1


title: Caudal.ET.10d.3


title: Caudal.ET.03d.1


title: Caudal.ET.01d.1


title: Caudal.ET.01d.2


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) treated with PMA (100uM) (1st expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) treated with PMA (100uM) (1st experiment)


title: Caudal.NT3.90d.3


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) none treated (1st expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) none treated (1st experiment)


title: Caudal.ET.03d.3


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (7th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (7th experiment)


title: Caudal.NT3.60d.2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (7th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (7th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (7th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (7th experiment)


title: Caudal.NT3.60d.1


title: Caudal.NT3.90d.2


title: Caudal.NT3.30d.3


title: Middle.NT3.90d.1


title: Caudal.NT3.90d.1


title: Caudal.NT3.20d.3


title: Caudal.ET.03d.2


title: Caudal.NT3.30d.1


title: Middle.NT3.90d.3


title: Caudal.NT3.60d.3


title: Caudal.NT3.10d.3


title: Caudal.NT3.30d.2


title: Caudal.NT3.20d.2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (7th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (7th experiment)


title: Caudal.ET.01d.3


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (7th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (7th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (7th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (7th experiment)


title: Caudal.NT3.20d.1


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (6th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (6th experiment)


title: Caudal.NT3.01d.3


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (6th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (6th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (6th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (6th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (6th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (6th experiment)


title: Caudal.NT3.10d.2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (6th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (6th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (6th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (6th experiment)


title: Caudal.NT3.03d.3


title: Caudal.NT3.01d.2


title: Caudal.NT3.03d.1


title: Caudal.NT3.03d.2


title: Caudal.NT3.01d.1


title: Caudal.NT3.10d.1


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (5th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (5th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (5th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (5th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (5th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (5th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (5th expt)

description:
Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (5th experiment)
Rejected data - high background in PRRSV probes


title: Tat-Scr 1µM 24hr #2

city: Stirling

first: Kevin

last: Petrie

state: Stirling

address: Stirling

department: Biological and Environmental Sciences

country: United Kingdom

institute: University of Stirling

hyb_protocol: The quality and quantity of labeled cRNA was checked and 750 ng of labeled cRNA were hybridized to a GeneChip Human Gene 1.0 ST Arrays using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization using RMA algorithm. Secondary analysis of the data was performed by Transcriptome analysis console (Affymetrix).

organism: Homo sapiens

source_name: MDA-MB-231 breast cancer cell line

label_protocol: All samples were normalized to 200ng and processed according to standard Affymetrix protocols using GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) and WT Expression Kit (Ambion).

growth_protocol: MDA-MB-231 cell lines were maintained in DMEM supplemented with 10% FBS, 1% GlutaMAX (Invitrogen), 10mM HEPES, 1mM sodium pyruvate, non-essential amino acids and 1% antibiotic-antimycotic solution.

extract_protocol: Total RNA was isolated using the ZR RNA MiniPrep Kit (Zymo Research). The concentration and quality of the total RNA was assessed on an Agilent 2100 BioAnalyzer (Agilent Technologies).

treatment_protocol: MDA-MB-231 cells were treated with 1µM Tat-SID peptide or 1µM Tat-Scr scrambled control peptide for 24hr.

tag: cell line


title: Tat-Scr 1µM 24hr #1


title: Tat-Scr 1µM 24hr #3


title: Serum spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (1st expt)

description: Swine serum spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (1st experiment)


title: ATH1 meristematic zone BLJ biological replicate 3

city: Durham

first: Rosangela

last: Sozzani

address: 124 Science Dr

institute: Duke

description:
Gene expression data from meristematic cells under standard conditions for 5 days
Affy one-cycle labeling protocol

hyb_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

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 250.

organism: Arabidopsis thaliana

source_name: Meristematic region dissection

label_protocol: Affy two-cycle labeling (raw 21-26) and one-cycle (everything else) labeling protocol

growth_protocol: Growth Media: Standard media for 5 days

extract_protocol: Quiagen MicroRNAesy kit (total RNA was extracted according to the manufacturer's instruction

treatment_protocol: Seedling roots, 5 days after germination, either protoplasted cells or tissue

value: meristematic zone

tag: genotype/variation

value: BLJ

tag: ecotype

value: :Columbia

tag: age

tag: growth media

value: :Standard media for 5 days


title: Lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (10000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (3rd experiment)

value: Total DNA and RNA


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (5th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (5th experiment)


title: Tat-SID 1µM 24hr #1


title: ATH1 meristematic zone BLJ biological replicate 2

scan_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

value: Seedling roots, 5 days after germination


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (4th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (4th experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (4th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (4th experiment)


title: ATH1 cortex marker meristematic zone WT biological replicate 2

source_name: CO2 sorted cells

value: cortex

value: WT


title: Tat-SID 1µM 24hr #2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (5th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (5th experiment)

value: lung


title: Caudal.LC.03d.2

value: Lesion control(LC)

value: spinal cord


title: hUtSMC_P4+RU_3

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

hyb_protocol: All hybridizations were carried out using the OpArray (Operon) hybridization and wash solutions as recommended by the manufacturer.

scan_protocol: Slides were scanned three times successively (i.e. 3 .gpr files per sample) at 543 nm (Cy3) with a ScanArray Express HT scanner (Perkin Elmer). PMT settings were optimal at 70 %. Resolution was 10 micrometeres.

data_processing: Images were processed using GenePix Pro 6.1.0.4. Only the median value of the three successive scans (provided in the 'Median Table_InputRAW.xlsx') was used generating a tabdelimited text file. This file was imported into GeneSpring GX 12.0 (Agilent Technologies). Data was log transformed and normalised by the Percentile Shift Method using the 75th percentile. Subsequently all normalised data was baseline transformed to the median of all samples.

label_protocol: All samples were prepared for microarray hybridization using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion) according to the manufacturer’s recommendations. Probes were hybridized against the Operon Human Genome Array-Ready Oligo Set Microarrays™ ((AROS) Version 4.0).

growth_protocol: hUtSMCs (Lonza) were cultured in complete Dulbecco’s modified essential medium (DMEM), supplemented with 10 % (v/v) fetal bovine serum (FBS), 100 units/ml penicillin and 0.1 mg/ml streptomycin (Sigma-Aldrich) until cells reached 90 % confluence.

extract_protocol: Total RNA was isolated from the cells using a combination of Trizol (Ambion) and Qiagen RNeasy Mini Kit (Qiagen). Cells were lysed in Trizol reagent (1 ml Trizol per 1x107 cells) and 0.2ml chloroform (Sigma-Aldrich) per millilitre of Trizol reagent was added, vortexed for 2 min and incubated at room temperature for 10 min. The mixture was centrifuged (13,000 rpm for 15 min at 4 °C), the upper phase mixed with an equal volume of 70% ethanol and loaded onto the RNeasy column (Qiagen). Total RNA was subsequently isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA was quantified using a NanoDrop ND-1000 spectrophotomer (Thermo Scientific) and quality checked using the Agilent 2100 Bioanalyzer. All RNA yielded RNA integrity numbers (RIN) of greater than 9.0 (average 9.8)

treatment_protocol: At 90% confluence cells were preconditioned overnight with Phenol Red Free DMEM (PRF-DMEM), supplemented with 10% double charcoal-stripped fetal bovine serum (CS-FBS) and containing antibiotics. Cells were starved of endogenous steroids in PRF-DMEM supplemented with 2% CS-FBS and antibiotics until the cells attained 100% confluence. Subsequently, cells  were supplemented with 10 nM 17beta-estradiol (E2) or 100nM progesterone . Control cells were grown in ‘starvation media’ in the absence of E2 until harvest. Cells were harvested after  72 h of treatment along with corresponding controls and total RNA was isolated. The complete experiment was replicated three times

tag: cell type

value: human myometrial smooth muscle cells (hUtSMCs)

tag: cell line source

value: normal, non-pregnant female

tag: passage

value: passage 5-8

tag: smooth muscle markers

value: calponin, smoothelin positive (RT-PCR)

tag: other markers

value: oxytocin receptor and ER-alpha positive (RT-PCR)

tag: estrogen response

value: monitored by CD38 and CX43 gene and protein levels

tag: treated with

value: 100nM progesterone +  RU486 for 72hrs


title: ATH1 cortex marker meristematic zone WT biological replicate 1


title: hUtSMC_P4+RU_2


title: hUtSMC_P4_2

value: 100nM progesterone for 72hrs


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (4th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (4th experiment)

value: PRRS spiked tissue homogenate

tag: sample type

tag: molecule


title: ATH1 meristematic zone WT biological replicate 2

value: meristematic zone

value: :Columbia

value: :Standard media for 5 days


title: ATH1 cortex marker meristematic zone WT biological replicate 3

value: cortex

value: Seedling roots, 5 days after germination


title: ATH1 meristematic zone WT biological replicate 1

value: WT


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (4th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (4th experiment)

value: lung

value: Total DNA and RNA


title: hUtSMC_P4_3

value: human myometrial smooth muscle cells (hUtSMCs)


title: ATH1 meristematic zone BLJ biological replicate 1

value: BLJ


title: ATH1 ground tissue marker SHR UAS driving IME biological replicate 3

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
Affy one-cycle labeling protocol

source_name: J0571 sorted cells

value: ground tissue

value: SHR UAS driving IME


title: hUtSMC_P4_1

value: normal, non-pregnant female

value: passage 5-8

value: calponin, smoothelin positive (RT-PCR)

value: oxytocin receptor and ER-alpha positive (RT-PCR)


title: hUtSMC_E2/P4+RU_3

value: monitored by CD38 and CX43 gene and protein levels

value: 10 nM 17beta-estradiol (E2) + 100nM progesterone +  RU486 for 72hrs


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (4th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (4th experiment)

value: PRRS spiked tissue homogenate


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (4th expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (4th experiment)


title: hUtSMC_P4+RU_1

value: 100nM progesterone +  RU486 for 72hrs


title: ATH1 ground tissue marker SHR UAS driving IME biological replicate 1

value: :Standard media for 5 days


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (3rd experiment)


title: hUtSMC_E2/P4+RU_1


title: ATH1 ground tissue marker SHR UAS driving IME biological replicate 2

value: Seedling roots, 5 days after germination


title: ATH1 ground tissue marker SHR UAS driving SCR biological replicate 3

value: SHR UAS driving SCR


title: hUtSMC_E2+P4_3

value: 10 nM 17beta-estradiol (E2) + 100nM progesterone for 72hrs


title: hUtSMC_E2/P4+RU_2


title: ATH1 ground tissue marker SHR UAS driving SCR biological replicate 2


title: hUtSMC_E2+P4_2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (3rd experiment)

value: lung

value: Total DNA and RNA


title: ATH1 ground tissue marker SHR UAS driving SCR biological replicate 1


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (3rd experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (3rd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (3rd experiment)


title: ATH1 ground tissue marker SHR UAS driving JKD biological replicate 3

value: SHR UAS driving JKD


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (2nd experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (3rd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (3rd experiment)


title: ATH1 ground tissue marker SHR UAS driving JKD biological replicate 2

value: ground tissue


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with EMA (100uM) (2nd experiment)


title: hUtSMC_E2_3

value: human myometrial smooth muscle cells (hUtSMCs)

value: 10 nM 17beta-estradiol (E2) for 72hrs


title: ATH1 ground tissue marker SHR UAS driving JKD biological replicate 1


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (3rd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (3rd experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (2nd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (2nd experiment)


title: hUtSMC_E2+P4_1

value: normal, non-pregnant female

value: passage 5-8


title: hUtSMC_E2_1

value: calponin, smoothelin positive (RT-PCR)

value: oxytocin receptor and ER-alpha positive (RT-PCR)


title: hUtSMC_E2_2

value: monitored by CD38 and CX43 gene and protein levels


title: ATH1 ground tissue marker SHR UAS driving MGP biological replicate 1

value: SHR UAS driving MGP


title: ATH1 ground tissue marker SHR UAS driving MGP biological replicate 3


title: hUtSMC_Con_3

value: starvation media (control)


title: hUtSMC_Con_2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with EMA (100uM) (2nd experiment)

value: PRRS spiked tissue homogenate


title: ATH1 ground tissue marker SHR UAS driving MGP biological replicate 2

value: Seedling roots, 5 days after germination

value: :Standard media for 5 days


title: hUtSMC_Con_1


title: ATH1 ground tissue marker SHR UAS driving NUC biological replicate 3

value: SHR UAS driving NUC


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (2nd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (2nd experiment)

value: lung


title: ATH1 ground tissue marker SHR UAS driving NUC biological replicate 1


title: ATH1 ground tissue marker SHR UAS driving NUC biological replicate 2


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (1st expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and treated with PMA (100uM) (1st experiment)

value: Total DNA and RNA


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (1st expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) treated with PMA (100uM) (1st experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (1st expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (1st experiment)


title: ATH1 ground tissue marker SHR UAS driving BLJ biological replicate 1

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
Affy one-cycle labeling protocol

value: SHR UAS driving BLJ


title: ATH1 ground tissue marker SHR UAS driving BLJ biological replicate 3

value: ground tissue


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (2nd expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) none treated (2nd experiment)


title: Lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (1st expt)

description: Swine lung homogenate spiked with PRRSV (1000 TCID50/test) with ultracentrifugation and none treated (1st experiment)


title: ATH1 ground tissue marker SHR biological replicate 2_3

value: SHR


title: ATH1 ground tissue marker SHR biological replicate 2_2


title: ATH1 ground tissue marker SHR UAS driving BLJ biological replicate 2


title: Posttreatment_Placebo5

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

country: Singapore

institute: DUKE-NUS Graduate Medical School

description: Gene expression data from whole blood from overweight women treated with quercetin or placebo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 1.1 ST Arrays. Arrays were washed and stained in the Affymetrix GeneTitan instrument.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G Plus

data_processing: Background adjusted, quantile normalized gene expression signals were generated by the robust multi-array average method (RMA) using RMAExpress (http://rmaexpress.bmbolstad.com/).

source_name: whole blood, fasted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Fasting whole blood (2.5 ml) was drawn from study subjects by standard venipuncture and directly transferred to PAXgene blood RNA tubes (Qiagen, Santa Clara, CA, USA). Isolation of total RNA was accomplished according to the manufacturer's instructions.

treatment_protocol: Subjects were randomized to either mixed flavonoid-fish oil supplement group (Q-Mix; 1000 mg quercetin, 400 mg isoquercetin, 120 mg EGCG from green tea extract, 400 mg n3-PUFAs (220 mg EPA and 180 mg DHA) from fish oil, 1000 mg vitamin C, 40 mg niacinamide, and 800 µg folic acid) or placebo (total n=29, including pre- and post-treatment samples in Q-Mix and placebo arms).The placebo did not contain quercetin, vitamin C, and niacin. Subjects were instructed to ingest two soft chew supplements twice daily (upon awakening, and between 6:00-7:00 pm) for 70 days.

tag: gender

value: Female

tag: individual condition

value: overweight

tag: individual identifier

tag: agent

value: Placebo

tag: time

value: Posttreatment

value: whole blood


title: ATH1 ground tissue marker SHR biological replicate 2_1

tag: tissue

tag: genotype/variation

tag: ecotype


title: Pretreatment_Quercetin6

value: Quercetin

value: Pretreatment


title: ATH1 ground tissue marker WT biological replicate 2_3

value: WT

tag: age

tag: growth media


title: buccal epithelium, smokeless coal, female 9

city: Boston

first: Teresa

last: Wang

state: MA

address: 72 East Concord St., E-632

department: Computational Biomedicine

institute: Boston University

description:
CQ 1361 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven at 640 at 45 deg. C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: RMA normalization was conducted using custom CDF: HuGene10stv1_Hs_ENTREZG.cdf [Brainarray Version 14]

source_name: RNA from buccal epithelium of smokeless coal-burning female

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA from buccal scrapings was isolated using miRNeasy Mini Kit (Qiagen, Valencia, CA)

value: female

value: buccal epithelium

tag: coal-burning

value: smokeless

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: Posttreatment_Quercetin6

tag: gender

tag: individual condition

tag: individual identifier

tag: agent

tag: time

tag: tissue


title: Pretreatment_Quercetin5


title: buccal epithelium, smokeless coal, female 8

description:
CQ 1356 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: age

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)


title: ATH1 ground tissue marker SHR biological replicate 3

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
Affy two-cycle labeling protocol

tag: genotype/variation

tag: ecotype

value: Seedling roots, 5 days after germination

tag: growth media

value: :Standard media for 5 days


title: Posttreatment_Quercetin5


title: buccal epithelium, smokeless coal, female 6

description:
CQ 1340 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)


title: ATH1 ground tissue marker SHR biological replicate 2

tag: tissue

tag: age


title: buccal epithelium, smokeless coal, female 4

description:
CQ 1192 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: gender

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: pyrene (ng/m3)


title: Pretreatment_Quercetin7

tag: individual condition

tag: individual identifier

tag: agent

tag: time


title: buccal epithelium, smokeless coal, female 7

description:
CQ 1341 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)


title: ATH1 ground tissue marker WT biological replicate 2_1

tag: tissue

tag: genotype/variation

tag: ecotype

tag: growth media


title: buccal epithelium, smokeless coal, female 5

description:
CQ 1338 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: gender

tag: age

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)


title: buccal epithelium, smokeless coal, female 3

description:
CQ 1188 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: pyrene (ng/m3)


title: Pretreatment_Quercetin4

tag: individual condition

tag: individual identifier

tag: agent

tag: time

tag: tissue


title: ATH1 ground tissue marker WT biological replicate 2_2

tag: genotype/variation

tag: ecotype

tag: age

tag: growth media


title: ATH1 ground tissue marker SHR biological replicate 1


title: buccal epithelium, smokeless coal, female 2

description:
CQ 1184 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: gender

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)


title: Pretreatment_Placebo6

tag: individual condition

tag: individual identifier


title: buccal epithelium, smokeless coal, female 1

description:
CQ 1182 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smokeless-coal

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: normal mammary gland, biological rep3

city: Frederick

first: David

last: Salomon

state: MD

address: 1050 Boyles Drive, Bldg. 560 Room 1246

department: NCI

institute: NIH

description: normal mammary gland

hyb_protocol: The assays were performed according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)

data_processing: Normalization was performed using the software nSolver version 1.1 (NanoStrings Technologies). The normalized counts were imported into the MultiExperiment Viewer Version 10.2 (MeV_4_8, http://www.tm4.org) software (Saeed et al 2003; 2006). The gene expression valuesProbe intensities were median-centered and log-transformed. Significant transcripts were selected using a t-test or the ANOVA statistical test with p <0.01 or 0.05. For clustering samples based on gene expression profile, we applied an unsupervised hierarchical clustering using Pearson correlation and average linkage.

organism: Mus musculus

source_name: Normal mammary gland

extract_protocol: Tissue samples were laser captured using the MMI CellCut Plus (Molecular Machines & Industries, Glattbrugg Switzerland) as described in Golubeva et al 2013. Laser microdissected cells were lysed using the lysis buffer RLT from Qiagen Micro RNAeasy Kit (Qiagen Gaithersburg, MD) and total RNA lysates were prepared for NanoStrings analysis (Geiss et al 2008). In vitro JygMC(A) GFP/Luc cells were cultured either as monolayers in plates or 3D spheres on ultra-low adherent plates (third generation spheres). Total RNA from tissue samples was extracted using TRIzol reagent according to the manufacturer's recommendations (Invitrogen, Carlsbad, CA). Total RNA from cells was isolated and purified using the RNeasy Mini Kit and subjected to DNAse treatment (Qiagen, Gaithersburg, MD) in accordance to manufacturer instructions). Following extraction, 1ug of total RNA was reverse transcribed using the RETROscript® kit (Ambion, Carlsbad, CA) in accordance with manufacturer's instructions.

tag: tissue

value: Normal mammary gland

tag: histology

tag: strain

value: BalbC nude


title: normal mammary gland, biological rep2

description: normal mammary gland

scan_protocol: The assays were performed according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)


title: ATH1 ground tissue marker WT biological replicate 1

value: ground tissue

tag: genotype/variation

tag: ecotype

tag: age

tag: growth media


title: Posttreatment_Quercetin4

tag: gender

tag: agent

tag: time


title: buccal epithelium, smoky coal, female 25

description:
CQ 1532 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

source_name: RNA from buccal epithelium of smoky coal-burning female

tag: coal-burning

value: smoky

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)


title: ATH1 ground tissue marker WT biological replicate 2

tag: tissue


title: Pretreatment_Placebo4

value: Female

tag: individual condition

tag: individual identifier


title: normal mammary gland, biological rep1

description: normal mammary gland

label_protocol: The assays were performed according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)

tag: histology

tag: strain


title: buccal epithelium, smoky coal, female 26

description:
CQ 1538 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: gender

tag: age

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: Posttreatment_Placebo4

value: overweight

tag: agent

tag: time


title: Pretreatment_Placebo5

value: Placebo


title: buccal epithelium, smoky coal, female 21

description:
CQ 1516 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)


title: Pretreatment_Placebo3

tag: gender

tag: individual condition

tag: individual identifier

tag: tissue


title: Posttreatment_Quercetin2

value: Posttreatment


title: Posttreatment_Placebo7

value: whole blood


title: HepG2 shTHOC5 versus shControl

city: Hannover

first: Doan Duy Hai

last: Tran

state: Niedersachsen

address: Carl-Neubergsstr. 1

department: Institut of physiological Chemistry

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent). 825ng of each labelled cRNA population (Cy3 and Cy5) were combined and cohybridized onto one 4x180K region.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’. A modified version of the recommended default extraction protocol file ‘GE2_107_Sep09.xml’ in which the ‘Minimal number of replicates used to calculate Population Outliers’ was set to 5.  For inter-array normalization, processed intensity values as generated in the Feature Extraction process, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of normalized PS values to retrieve one resulting value per probe and sample. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5. Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 20. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 20.  Measurements of control Features have been deleted from the Matrix.

source_name: HepG2 cells treated with control sh RNA

label_protocol: Synthesis of Cy3- or Cy5-labeled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Huh7 and HepG2 cells were grown in Dulbecco´s modified Eagle's medium supplemented with 10% (v/v) FCS.

extract_protocol: Total RNAs were isolated with the High Pure RNA Isolation kit (Roche Diagnostics, Mannheim, Germany) according to the manufacturer´s instructions.

treatment_protocol: Huh7 and HepG2 cells were infected with lentiviral THOC5 and control shRNAs.

tag: cell line

tag: cell type

value: hepatocellular carcinoma

source_name: HepG2 cells treated with THOC5 sh RNA


title: buccal epithelium, smoky coal, female 17

description:
CQ 1421 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: buccal epithelium, smoky coal, female 19

description:
CQ 1512 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)


title: buccal epithelium, smoky coal, female 18

description:
CQ 1501 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: gender

tag: tissue

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)


title: Posttreatment_Placebo2

description: Gene expression data from whole blood from overweight women treated with quercetin or placebo

tag: individual condition

tag: individual identifier

tag: agent

tag: time


title: Pretreatment_Placebo2

value: Pretreatment


title: buccal epithelium, smoky coal, female 23

description:
CQ 1521 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)


title: Pretreatment_Quercetin3

value: Quercetin


title: buccal epithelium, smoky coal, female 24

description:
CQ 1522 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

value: female

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: buccal epithelium, smoky coal, female 22

description:
CQ 1518 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: gender

tag: tissue

value: buccal epithelium

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)


title: ATH1 ground tissue marker WT biological replicate 3

description:
Gene expression data from J0571 sorted cells under standard conditions for 5 days
Affy two-cycle labeling protocol

tag: genotype/variation

value: WT

tag: ecotype

tag: age

tag: growth media


title: Posttreatment_Placebo3

tag: individual condition

tag: individual identifier

tag: agent

tag: time


title: buccal epithelium, smoky coal, female 20

description:
CQ 2514 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)


title: Posttreatment_Placebo6

tag: gender

tag: tissue


title: Huh7 shTHOC5 versus shControl

source_name: Huh7 cells treated with control sh RNA

tag: cell line

tag: cell type

source_name: Huh7 cells treated with THOC5 sh RNA


title: normal lung parenchyma, biological rep2

description: normal lung parenchyma

source_name: Normal lung parenchyma

value: Normal lung parenchyma

tag: histology

tag: strain


title: normal lung parenchyma, biological rep3

description: normal lung parenchyma


title: Pretreatment_Quercetin2

tag: individual condition

tag: individual identifier

tag: agent


title: buccal epithelium, smoky coal, female 16

description:
CQ 1420 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: normal lung parenchyma, biological rep1

description: normal lung parenchyma

tag: tissue


title: Pretreatment_Placebo1

tag: gender

tag: time


title: buccal epithelium, smoky coal, female 15

description:
CQ 1411 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)


title: mammary tumors metastasis to lungs, biological rep9

description: Lung metastasis

source_name: Lung metastasis

value: Lung metastasis

tag: histology

tag: strain


title: mammary tumors metastasis to lungs, biological rep8

description: Lung metastasis


title: mammary tumors metastasis to lungs, biological rep5

description: Lung metastasis


title: mammary tumors metastasis to lungs, biological rep6

description: Lung metastasis


title: mammary tumors metastasis to lungs, biological rep4

description: Lung metastasis


title: mammary tumors metastasis to lungs, biological rep7

description: Lung metastasis


title: buccal epithelium, smoky coal, female 13

description:
CQ 1370 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)


title: buccal epithelium, smoky coal, female 12

description:
CQ 1366 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: tissue

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: Posttreatment_Quercetin8

tag: gender

tag: individual condition

tag: individual identifier

tag: agent

tag: time


title: Posttreatment_Placebo1


title: buccal epithelium, smoky coal, female 14

description:
CQ 1401 0253
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)


title: mammary tumors metastasis to lungs, biological rep3

description: Lung metastasis

tag: tissue

tag: histology

tag: strain


title: buccal epithelium, smoky coal, female 8

description:
CQ 1322 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: phenanthrene (ng/m3)


title: Posttreatment_Quercetin7

tag: gender

tag: individual condition

tag: individual identifier

tag: agent

tag: time


title: Posttreatment_Quercetin1


title: Pretreatment_Quercetin1


title: Pretreatment_Placebo7


title: buccal epithelium, smoky coal, female 10

description:
CQ 2332 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)

tag: pyrene (ng/m3)


title: buccal epithelium, smoky coal, female 11

description:
CQ 1362 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: tissue

tag: coal-burning

tag: acenaphthylene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)


title: 1A_Rep2

city: Edmonton

first: Kathryn

last: Graham

state: Alberta

address: 11560 University Ave

department: Oncology

institute: University of Alberta

description: gene expression in transfected HCT116 cell line

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  The data was them imported into GeneSpring 10, default normalization to the 75th percentile was used. The normalized data is in a Log2 format.

source_name: HCT 116 Cell line xenograft

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

extract_protocol: RNA was isolated an Rneasy kit (Qiagen) according to the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: human cell line in a mouse xenograft

tag: cell line

value: HCT116 cell line transfected with pCDNA3-HA tagged RASSF1A (wild type)


title: buccal epithelium, smoky coal, female 9

description:
CQ 2328 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: gender

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: phenanthrene (ng/m3)


title: 1A_Rep3


title: 1A_Rep1


title: buccal epithelium, smoky coal, female 6

description:
CQ 2181 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)


title: mammary tumors metastasis to lungs, biological rep2

description: Lung metastasis

tag: histology

tag: strain

value: BalbC nude


title: mammary tumors metastasis to lungs, biological rep1

description: Lung metastasis

tag: tissue


title: mammary tumors EMT, biological rep11

description: Primary tumor

source_name: Primary tumor

value: Mammary Primary tumor

value: Mammary Primary tumor EMT


title: mammary tumors EMT, biological rep10

description: Primary tumor


title: mammary tumors EMT, biological rep8

description: Primary tumor


title: mammary tumors EMT, biological rep9

description: Primary tumor


title: Posttreatment_Quercetin3

description: Gene expression data from whole blood from overweight women treated with quercetin or placebo

value: Female

tag: individual condition

value: overweight

tag: individual identifier

tag: agent

tag: time


title: mammary tumors EMT, biological rep5

description: Primary tumor


title: Vector_Rep3

tag: cell type

value: HCT116 cell line transfected with pCDNA3 vector

value: Empty Vector


title: mammary tumors EMT, biological rep7

description: Primary tumor


title: buccal epithelium, smoky coal, female 3

description:
CQ 2121 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: coal-burning

value: smoky

tag: acenaphthylene (ng/m3)

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)

tag: naphthalene (ng/m3)

tag: pyrene (ng/m3)


title: buccal epithelium, smoky coal, female 2

description:
CQ 1111 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: gender

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: phenanthrene (ng/m3)


title: buccal epithelium, smoky coal, female 4

description:
CQ 1144 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: age

tag: tissue


title: buccal epithelium, smoky coal, female 5

description:
CQ 2146 0252
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: coal-burning

tag: acenaphthylene (ng/m3)


title: mammary tumors EMT, biological rep3

description: Primary tumor

tag: histology

tag: strain


title: mammary tumors EMT, biological rep6

description: Primary tumor


title: mammary tumors EMT, biological rep4

description: Primary tumor


title: buccal epithelium, smoky coal, female 1

description:
CQ 1110 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

tag: benzo(k)fluoranthene (ng/m3)

tag: chrysene (ng/m3)

tag: dibenz(a,h)anthracene (ng/m3)

tag: indeno(1,2,3-cd)pyrene (ng/m3)


title: mammary tumors EMT, biological rep2

description: Primary tumor


title: normal mammary gland, biological rep2

description: New Sample- 16MG4

data_processing: Nanostring RCC files uploaded on Nanostring v1.1 and annotated with NanoString miRv1.3. Raw data were subjected to geometric mean normalization and average background subtraction using Partek GS v6.6.

source_name: normal mammary gland

extract_protocol: Tissue samples were laser captured using the MMI CellCut Plus (Molecular Machines & Industries, Glattbrugg Switzerland) as described in Golubeva et al 2013. Laser microdissected cells and cell line (in vitro JygMC(A) GFP/Luc cells cultured either as monolayers in plates or 3D spheres on ultra-low adherent plates third generation spheres) were lysed using the lysis buffer RLT from Qiagen Micro RNAeasy Kit (Qiagen Gaithersburg, MD) and total RNA lysates were prepared for mRNA NanoStrings analysis (Geiss et al 2008). For miRNA analysis, total RNA lysates from cells was purified using the miRNeasy Micro Kit (Qiagen, Gaithersburg, MD) in accordance to manufacturer instructions.

value: normal mammary gland


title: MOAP-1_Rep1

tag: cell type

tag: cell line

value: HCT116 cell line transfected with a wild type MOAP-1

value: MOAP-1, wild type


title: mammary tumors EMT, biological rep1

description: Primary tumor


title: normal lung parenchyma, biological rep2

description: New Sample- 16 Lung

source_name: normal lung parenchyma

value: normal lung parenchyma


title: K278R_Rep3

value: HCT116 cell line transfected with a K278R mutation

value: K278R mutation


title: K278R_Rep2


title: MOAP-1_Rep3


title: Vector_Rep2


title: K278R_Rep1


title: K264R_Rep2

value: HCT116 cell line transfected with a K264R mutation

value: K264R mutation


title: Vector_Rep1

value: human cell line in a mouse xenograft


title: K264R_Rep3


title: mammary tumors carcinoma, biological rep7

description: Primary tumor

value: Mammary Primary tumor Carcinoma

value: BalbC nude


title: normal mammary gland, biological rep1

description: New Sample- 15MG4


title: mammary tumors carcinoma, biological rep8

description: Primary tumor

value: Mammary Primary tumor


title: mammary tumors carcinoma, biological rep6

description: Primary tumor


value: Lung metastasis


title: normal lung parenchyma, biological rep1

description: New Sample- 15 Lung


title: K264R_Rep1

value: HCT116 cell line transfected with a K(lysine) at position 264 mutated to an R (arginine)


title: MOAP-1_Rep2


title: mammary tumors carcinoma, biological rep4

description: Primary tumor


title: mammary tumors carcinoma, biological rep3

description: Primary tumor


title: mammary tumors EMT, biological rep6

value: Mammary Primary tumor EMT


title: PVD3

city: Tomioka Urayasu

first: Ayumi

last: Ouchi

state: Chiba

department: Ophthalmology

country: Japan

institute: Juntendo University Urayasu Hospital

data_processing: Data were normalized to the average Ct value of the endogenous control(U6 snRNA). Fold change values were calculated by standard deltadeltaCt methods using MH1 value as a denominator.

label: Fam

label_protocol: TaqMan miRNA Reverse Transcription Kit

extract_protocol: miRNeasy Serum/Plasma Kit

value: vitreous

tag: diagnosis

value: proliferative vitreoretinal disease (PVD)


title: mammary tumors carcinoma, biological rep2

description: Primary tumor


title: mammary tumors EMT, biological rep5


title: PVD1


title: PVD2


title: Cell line

description: Monolayer cell line

source_name: Monolayer cell line

value: Cell line


title: MH3

source_name: vitreous_macular hole

value: macular hole


title: mammary tumors carcinoma, biological rep5

description: Primary tumor


title: MH2


title: mammary tumors EMT, biological rep4


title: MH1


title: mammary tumors EMT, biological rep3


description: GA 76


title: mammary tumors EMT, biological rep2

description: GB 71


title: Control Rectosigmoid area (R_C)

city: New Delhi

first: Raju

last: Ranjha

state: Delhi

address: Lab. No.441, School of Life Sciences,

department: School of Life Sciences

country: India

institute: Jawaharlala Nehru University

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: rectosigmoid colon remission Ulcerative colitis

label_protocol: 150 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA extracted using miRvana miRNa isolation kit following manufacturers instruction.

value: Colon Biopsy

tag: phenotype

value: Healthy Control

source_name: reference: Total RNA from Human Colon Biopsy


description: GB 71


description: GB 70/GB 72/GA75


title: reduced diet 25679

city: Portland

first: Alina

last: Maloyan

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Medicine

institute: Oregon Health and Science University

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Papio hamadryas

source_name: left ventricle

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 0.5 µg total RNA per sample.These RNA samples were first subject to dephosphorylation reaction to remove 5’ phosphate groups of miRNA molecules. Then an oligonucleotide adapter was added to 3’ end of sample (3’OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contained a tag segment for capturing fluorescent dye during a later dye staining process. .

growth_protocol: Six control pregnant baboons ate ad libitum, and six nutrient restricted pregnant baboons ate a reduced diet (70% of control) from 0.16 gestation (G) through pregnancy resulting in fetal IUGR. Fetuses (3 males and 3 females per group) were euthanized at C-section at 0.9G.

extract_protocol: Total RNA was isolated from fetal hearts

treatment_protocol: Two dietary regimen: regular or reduced (70% of control) diet

tag: gender

value: female

value: left ventricle

tag: treatment

value: reduced diet


title: reduced diet 26690

value: male


title: reduced diet 26699


title: UC remission Rectosigmoid area (R_R)

value: Remission UC patient


title: mammary tumors carcinoma, biological rep1

description: Primary tumor

value: Mammary Primary tumor Carcinoma


title: reduced diet 27365


title: reduced diet 9085


title: mammary tumors EMT, biological rep1

description: GB 70/GB 72/GA75

value: BalbC nude


title: 3D sphere cell line

description: 3D spheres cell line

source_name: 3D spheres cell line


title: Active UC Ascending Colon (R_A)

source_name: rectosigmoid colon Active Ulcerative colitis

value: Active UC patient


description: GB 70/GB 72/GA75

value: Mammary Primary tumor


title: Control Ascending Colon (N_C)

source_name: ascending colon Control individuals


title: UC remission Ascending Colon (N_R)

source_name: ascending colon remission Ulcerative colitis


title: control diet 8001

value: control diet


title: 3D sphere cell line, biological rep2

description: Jyg MC (A) GFP/Luc spheres-2

value: JygMC(A)


title: control diet 27188


title: Cell line, biological rep2

description: Jyg MC (A) GFP/Luc cells-2


title: control diet 9129


title: Active UC Ascending Colon (N_A)

source_name: ascending colon Active Ulcerative colitis


title: reduced diet 25680


title: control diet 26201


title: control diet 27049


title: Cell line, biological rep1

description: Jyg MC (A) GFP/Luc cells-1


title: control diet 26246


title: 3D sphere cell line, biological rep1

description: Jyg MC (A) GFP/Luc spheres-1


title: compare WT/mutant NC-B

status: Public on Nov 01 2015

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: NCTC parental strain

hyb_protocol: A mixture of cDNA obtained from reverse transcription of RNA from WT or mutant strains were diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. Per chip and per spot normalisation wee performed in GeneSpring (7.3)

label: cyanine 3

organism: Staphylococcus aureus subsp. aureus NCTC 8325

source_name: NCTC mutant R

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grownup to OD600=0.8 in MHB (Becton Dickinson) enriched with 1.25 mM CaCl2

extract_protocol: Briefly, bacteria were stabilized in RNA protect for 5 minutes, then harvested. Cells were lysed in the presence of 600 µg/ml lysostaphin and total RNA was extracted using the PrestoSpin R bug Kit including DNase I treatment (Molzym). Quantity and absence of contaminating DNA was measured by using the Nanodrop spectrophotometer (Nanodrop Technologies), and by qPCR, respectively.

treatment_protocol: RNA Protect (Qiagen)

tag: genotype/variation

value: dapto R

value: wildtype

label: cyanine 5

source_name: NCTC wild type


title: compare WT/mutant NC-A

description: NCTC parental strain


title: compare WT/mutant SG-B

description: SG511 parental strain

organism: Staphylococcus aureus

source_name: SG511 mutant R

source_name: SG511 wild type


title: Fc-Eda-A1 treated (4hours), Eda null E13.5 mammary buds, biological replicate 3

city: Helsinki

first: Maria

last: Voutilainen

address: Viikinkaari 9

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

description: Approximately 20 mammary buds pooled together from 5-6 embryos

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute  • Transfer 200μl of hybridization solution to each array, then tape holes • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Probes were re-annotated using CustomCDF annotations. Data were quantile normalized and summarized by using RMA-Cybert-package as applied in statistical environment R. Data were analyzed with the Custom CDF  ENSG 14.1.0.

source_name: mammary buds, Eda null, treated

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

growth_protocol: Mammary buds were isolated from E13.5 Eda-/- embryos. Mammary buds from the other half of an embryo were used as a control and the other half was treated with recombinant Fc-Eda-A1 protein. Samples were incubated for 4 hours either in the presence (treated) or absence (non-treated control) of recombinant Fc-Eda-A1 protein.

extract_protocol: Approximately 20 Eda-/- mammary buds from 5-6 embryos were pooled together. Epithelial mammary buds were microdissected from the embryos and majority of the surrounding mesenchyme was removed manually. Samples were snap frozen and RNA was extracted using the RNeasy mini kit (Qiagen).

tag: age

value: embryonic mammary bud

tag: genotype

value: Eda-/-

value: Fc-Eda-A1 treated (4hours)


title: buccal epithelium, smoky coal, female 7

description:
CQ 1311 0251
buccal epithelial RNA from nonsmoking, healthy female exposed to smoky-coal

source_name: RNA from buccal epithelium of smoky coal-burning female

tag: tissue

value: buccal epithelium

tag: coal-burning

value: smoky

tag: benz(a)anthracene (ng/m3)

tag: benzo(a)pyrene (ng/m3)

tag: benzo(b)fluoranthene (ng/m3)

tag: benzo(g,h,i)perylene (ng/m3)

tag: fluoranthene (ng/m3)

tag: fluorene (ng/m3)

tag: naphthalene (ng/m3)

tag: phenanthrene (ng/m3)

tag: pyrene (ng/m3)


title: Fc-Eda-A1 treated (4hours), Eda null E13.5 mammary buds, biological replicate 2


title: RND_39B

city: NANTES

first: Gwenola

last: LE DREAN

address: CHU Hôtel Dieu

country: France

institute: INRA

description:
sentrixID: 4562019056
sentrixPosition: I

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio (Illumina)

source_name: IUGR_Normal Chow diet

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

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

treatment_protocol: Colonic epithelial cells were isolated immediately after tissue collection. Proximal and distal colon were mechanically-disrupted by vortexing following 1h-incubation (30 rpm, 4°C) in 1mM EGTA and 1mM EDTA Ca++/Mg++ free (CMF)-Hank's Buffered Salt Solution (HBSS).

tag: strain

value: Sprague Dawley

value: 8 months

tag: birth status

value: intra-uterine growth retardation (IUGR)

tag: diet

value: Normal Chow diet (ND)

value: colon

tag: cell type

value: colonic epithelial cells


title: Non-treated control, Eda null E13.5 mammary buds, biological replicate 1

source_name: mammary buds, Eda null, non-treated

tag: age

tag: treatment


title: RND_37B

description:
sentrixID: 4562019056
sentrixPosition: L

tag: tissue


title: RND_35B

description:
sentrixID: 4562019056
sentrixPosition: B


title: compare WT/mutant SG-A

description: SG511 parental strain

tag: genotype/variation


title: RHFD_3A2

description:
sentrixID: 4562019056
sentrixPosition: D

source_name: IUGR_High-Fat diet

value: High-Fat diet (HFD)


title: RND_19B

description:
sentrixID: 4562019012
sentrixPosition: F


title: Non-treated control, Eda null E13.5 mammary buds, biological replicate 2

tag: genotype


title: RND_33B

description:
sentrixID: 4562019012
sentrixPosition: J


title: RND_17B

description:
sentrixID: 4562019012
sentrixPosition: B


title: RHFD_25B2

description:
sentrixID: 4562019056
sentrixPosition: K


title: RHFD_21B2

description:
sentrixID: 4562019056
sentrixPosition: G


title: CND_36B

description:
sentrixID: 4562019056
sentrixPosition: E

source_name: control_Normal Chow diet

value: control


title: CND_32B

description:
sentrixID: 4562019056
sentrixPosition: A


title: RHFD_3A1

description:
sentrixID: 4562019012
sentrixPosition: D


title: Non-treated control, Eda null E13.5 mammary buds, biological replicate 3


title: Fc-Eda-A1 treated (4hours), Eda null E13.5 mammary buds, biological replicate 1


title: CND_20A

description:
sentrixID: 4562019012
sentrixPosition: I


title: RHFD_25B1

description:
sentrixID: 4562019012
sentrixPosition: L


title: RHFD_21B1

description:
sentrixID: 4562019012
sentrixPosition: H


title: CND_38B

description:
sentrixID: 4562019056
sentrixPosition: H


title: CHFD_22B

description:
sentrixID: 4562019056
sentrixPosition: J

source_name: control_High-Fat diet


title: CHFD_28B

description:
sentrixID: 4562019012
sentrixPosition: C


title: CND_18A

description:
sentrixID: 4562019012
sentrixPosition: E


title: CHFD_10B1

description:
sentrixID: 4562019012
sentrixPosition: K


title: CHFD_10B2

description:
sentrixID: 4562019056
sentrixPosition: C


title: Wt_2

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

description:
Sample name: TK2010121059 (398)
398-Ctrl2
Control wild-type

hyb_protocol: Affymetrix starndard protocol, performed by the microarray core facility at the Dana Farber Cancer Institute (DFCI)

data_processing: dChiP software (DFCI)

source_name: chondrocytes

growth_protocol: Primary overnight culture of isolated rib chondrocytes in DMEM with 10% FCS.

extract_protocol: Sureprep (Fisher)

value: mixed background C57B6/129Sv

value: new born mice (P0.5-day old)

value: WT

value: primary rib chondrocytes


title: CHFD_8B

description:
sentrixID: 4562019012
sentrixPosition: G


title: CND_14A

description:
sentrixID: 4562019012
sentrixPosition: A


title: hiPSC (1a)

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

description: Biotin

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16hr (overnight) hybridization at 45degC at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing:
Data were processed using dChip software. Background correction was applied and normalization to the median array intensity was performed, gene level expression were summarized from the corrected intensities.
probe group file: HuGene-1_0-st-v1.r3.cdf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: Human iPSC

label_protocol: Ambion WT Expression kit  was used to generate ssDNA performed using Afymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: iPSC were differentiated into chondrocytes using sequential growth factor treatment as described in the manuscript.

extract_protocol: QIAGEN RNeasy.

treatment_protocol: Treatment with growth factors for 14 days.

value: iPSC


title: Adult chondrocyte (35M) (5a)

description: Biotin

source_name: Human adult chondrocyte

value: adult chondrocyte


title: hiChondrocytes p3 (4a)

description: Biotin

source_name: iPSC-derived chondrocytes (passage 3)

value: iPSC-derived chondrocytes (passage 3)


title: Adult chondrocyte (27F) (5)

description: Biotin


title: CHFD_4A

description:
sentrixID: 4562019056
sentrixPosition: F


title: hiChondrocytes Day 9 (3)

description: Biotin

source_name: iPSC differentiated to chondrocyte for 9 days


title: hiChondrocytes p3 (4)

description: Biotin


title: hiChondrocytes Day 4 (2)

description: Biotin

source_name: iPSC differentiated to chondrocyte for 4 days


title: hiPSC (1)

description: Biotin


title: Type 1 diabetes subject 9

first: Linda

last: Yip

address: 269 Campus Drive West, CCSR Building Rm. 2240

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 9

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) and data were extracted using Feature Extraction software.

data_processing: Data were processed using Genespring 12.6.  Samples were filtered for detected entities.

source_name: pancreas

label_protocol: 1 ug of total RNA was labeled with Cy3 using the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Trizol Reagent combined with the Qiagen Rneasy Mini Kit.

treatment_protocol: Frozen pancreas tissues were obtained from the network of pancreatic organ donors with diabetes (JDRF nPOD) and homogenized in Trizol reagent according to manufacturer's instructions.

tag: tissue region

value: body

tag: Sex

value: M

tag: serum autoantibody

value: Negative

tag: c-peptide (ng/ml)

tag: npod id


title: hiChondrocytes Day 4 (2a)

description: Biotin

value: iPSC differentiated to chondrocyte for 4 days


title: Type 1 diabetes subject 6

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 6

value: mIAA+


title: Wt_1

description:
Sample name: TK2010121058 (397)
397-Ctrl-1
Control wild-type

scan_protocol: Affymetrix starndard protocol, performed by the microarray core facility at the Dana Farber Cancer Institute (DFCI)


title: hiChondrocytes Day 9 (3a)

description: Biotin

value: iPSC differentiated to chondrocyte for 9 days


title: Type 1 diabetes subject 8

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 8

value: F


title: Type 1 diabetes subject 7

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 7

value: GADA+ IA-2A+

value: 22 (7 with T1D)


title: Type 1 diabetes subject 5

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 5

value: GADA+ IA-2A+ ZnT8A+ mIAA+


title: Type 1 diabetes subject 2

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 2

value: head

value: IA-2A+ mIAA+

value: 32 (7 with T1D)


title: Type 1 diabetes subject 3

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 3

value: GADA+ mIAA+

value: 17 (7 with T1D)


title: mammary tumors EMT, biological rep7

source_name: Primary tumor

value: Mammary Primary tumor

tag: histology

value: Mammary Primary tumor EMT

value: BalbC nude


title: Type 1 diabetes subject 4

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 4

value: 19 (7 with T1D)


title: Type 1 diabetes subject 1

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 1

value: M

value: 31(5 with T1D)


title: Auto-antibody positive subject 4

description: Gene expression in the pancreas of an auto-antibody positive individual - subject 4

value: GADA+


title: Auto-antibody positive subject 5

description: Gene expression in the pancreas of an auto-antibody positive individual - subject 5

value: body


title: Auto-antibody positive subject 3

description: Gene expression in the pancreas of an auto-antibody positive individual - subject 3

value: F


title: Healthy human control 7

description: Gene expression in the pancreas of healthy human control - subject 7

value: Negative


title: Healthy human control 4

description: Gene expression in the pancreas of healthy human control - subject 4


title: 15-08-042-0 [expression]

city: Aurora

last: Schwartz

state: CO

address: Anschutz Medical Campus

institute: University of Colorado, Anschutz Medical Campus

hyb_protocol: Agilent version 6.6

scan_protocol: Agilent GE1_1105_Oct12

data_processing: limma was used to backgroundCorrect(method=”normexp”, offset=8) → normalizeBetweenArrays(method=”quantile”) → keep only probes where half of the samples had a 10% higher signal than the 95th pctile of the control probes

source_name: nasal-epithelium

label_protocol: Low Input Quick Amp (Agilent)

extract_protocol: AllPrep kit (Qiagen)

tag: asthma

value: FALSE

tag: lnige

tag: gender

value: Female

value: No

value: Yes

tag: site

value: Washington D.C.


title: Type 1 diabetes subject 10

description: Gene expression in the pancreas of a Type 1 diabetic individual- subject 10

value: GADA+ IA-2A+ mIAA+ ZnT8A+


title: Healthy human control 2

description: Gene expression in the pancreas of healthy human control - subject 2

value: tail


title: Healthy human control 3

description: Gene expression in the pancreas of healthy human control -subject 3


title: 15-08-028-9 [expression]

value: TRUE

value: Male


title: 15-08-026-2 [expression]


title: 15-08-035-5 [expression]


title: Healthy human control 1

description: Gene expression in the pancreas of healthy human control - subject 1


title: 15-08-025-8 [expression]


title: Auto-antibody positive subject 1

description: Gene expression in the pancreas of an auto-antibody positive individual - subject 1


title: Healthy human control 5

description: Gene expression in the pancreas of healthy human control - subject 5


title: 15-08-034-0 [expression]


title: 15-08-020-4 [expression]


title: 15-08-018-4 [expression]


title: 15-08-023-6 [expression]


title: 15-08-012-1 [expression]


title: 15-08-024-3 [expression]


title: 15-08-008-1 [expression]


title: Auto-antibody positive subject 2

description: Gene expression in the pancreas of an auto-antibody positive individual - subject 2

value: head


title: Healthy human control 6

description: Gene expression in the pancreas of healthy human control - subject 6


title: 15-08-011-3 [expression]


title: 15-08-017-8 [expression]


title: 15-08-013-2 [expression]


title: 15-07-021-6 [expression]

value: New York


title: 15-07-020-0 [expression]


title: 15-07-030-2 [expression]


title: 15-07-023-7 [expression]


title: 15-08-002-3 [expression]


title: 15-07-034-1 [expression]


title: 15-07-005-3 [expression]


title: 15-08-003-4 [expression]


title: 15-07-018-0 [expression]


title: 15-06-004-6 [expression]

value: Detroit


title: 15-06-007-9 [expression]


title: 15-07-029-2 [expression]


title: 15-08-007-5 [expression]


title: 15-06-006-7 [expression]


title: 15-06-008-0 [expression]


title: 15-07-013-3 [expression]


title: 15-05-031-0 [expression]

value: Denver


title: 15-05-022-0 [expression]


title: 15-05-024-9 [expression]


title: 15-05-032-3 [expression]


title: 15-05-037-5 [expression]


title: 15-05-017-4 [expression]


title: 15-05-006-4 [expression]


title: 15-05-012-6 [expression]


title: 15-06-002-2 [expression]


title: 15-05-004-0 [expression]


title: 15-05-005-5 [expression]


title: 15-04-006-0 [expression]

value: Dallas


title: 15-04-009-4 [expression]


title: 15-04-005-6 [expression]


title: 15-02-053-1 [expression]

value: Boston


title: 15-04-003-9 [expression]


title: 15-02-040-6 [expression]


title: Auto-antibody positive subject 6

description: Gene expression in the pancreas of an auto-antibody positive individual - subject 6

value: M

value: GADA+ IA-2A+


title: 15-02-038-9 [expression]


title: 15-02-035-8 [expression]

value: FALSE


title: 15-04-001-8 [expression]

value: Female


title: 15-02-041-0 [expression]

value: No


title: 15-02-049-9 [expression]

value: Yes


title: 15-02-047-5 [expression]


title: 15-02-019-5 [expression]


title: 15-02-039-1 [expression]


title: Eed cKO_2

description:
Sample name: TK2010121061 (400)
400-EED cKO-2
Conditional Eed knockout in chondroctes

label_protocol: Affymetrix starndard protocol, performed by the microarray core facility at the Dana Farber Cancer Institute (DFCI)

tag: strain

value: mixed background C57B6/129Sv

value: new born mice (P0.5-day old)

value: Eed cKO

value: primary rib chondrocytes


title: Eed cKO_1

description:
Sample name: TK2010121060 (399)
399-EED cKO-1
Conditional Eed knockout in chondroctes

tag: cell type


title: 15-02-016-9 [expression]

value: Male

tag: age


title: 15-02-015-3 [expression]

value: TRUE


title: 15-02-030-4 [expression]


title: 15-02-028-7 [expression]


title: 15-02-017-6 [expression]


title: 15-02-026-0 [expression]


title: 15-02-020-2 [expression]


title: 15-02-013-0 [expression]


title: 15-02-010-7 [expression]


title: 15-02-014-8 [expression]


title: 15-02-011-1 [expression]


title: 15-02-008-4 [expression]


title: 15-02-005-0 [expression]


title: T22_Obese_Normalized

city: Tempe

first: Samantha

middle: Elaine

last: Day

state: AZ

address: University Dr. and Mill Ave.

institute: Arizona State University

description: Gene expression of obese participant

hyb_protocol: Cy3-labeled cRNA was fragmented using Agilent Gene Expression Hybridization kit and hybridized to the SurePrint G3 Human Gene Expression 8x60K v2 Microarray  at 65C for 17 hours.

scan_protocol: After washing using Agilent's protocol (see manufacturer's instruction), slides were scanned with an Agilent C scanner.

data_processing: Feature extraction software version 12.0.1.1  (Agilent) was used for analysis.

source_name: Vastus lateralis muscle

label_protocol: Total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent) and quantified for Cy3 dye labeled cRNA concentration.

extract_protocol: Muscle biopsy specimens were homogenized in TRIzol solution using a Polytron. Total RNA was purified with RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Participants underwent euglycemic hyperinsulinemic clamps with muscle biopsies. The biopsies were immediately frozen in liquid nitrogen.

value: Vastus lateralis muscle

tag: obese status

value: obese


title: T21_Obese_Normalized

description: Gene expression of obese participant

tag: tissue


title: T19_Obese_Normalized

description: Gene expression of obese participant


title: 60389_532

city: Rennes

first: carlos

last: blanco

address: 263 avenue Général Leclerc

department: SVE

institute: université rennes 1

description: replicate 1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) 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: Dickeya dadantii 3937

source_name: D.dadantii 3937_0.3M NaCl M63

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Dickeya dadantii 3937 was grown to mild exponential growth phase (OD 600nm 0.4) in M63 medium containing 03 M NaCl .

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: growth media

value: 0.3 M NaCl M63 medium


title: T13_Obese_Normalized

description: Gene expression of obese participant


title: T17_Obese_Normalized

description: Gene expression of obese participant