title: NRVM_24h_aniso_nostretch_02

description: NRVM, aniso FN, 24h, no stretch, harvest2, biological rep2


title: NRVM_24h_iso_stretch_02

status: Public on Jan 30 2013

type: RNA

city: Cambridge

first: Megan

middle: Laura

last: McCain

state: MA

address: 60 Oxford St Room 332

department: Engineering and Applied Sciences

country: USA

institute: Harvard University

description: NRVM, iso FN, 24h, stretch, harvest2, biological rep2

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 17 hours at 45C on Affymetrix GeneChip Rat Gene 1.0 ST Arrays in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe cell intensity data files were loaded into Affymetrix Expression Console Software and normalized using the robust multichip average (RMA) method. Signal values were log2-transformed and analyzed with Bioconductor open source software and the limma package in R. Expression values for each condition were averaged, fit to a linear model, and compared using Bayes statistics.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: NRVMs on iso FN for 1h and stretched for 24h

label_protocol: cDNA was labelled with Affymetrix DNA Labeleing Reagent according to the manufacturer's instructions from 1 ug total RNA.

growth_protocol: NRVMs were seeded on iso and aniso silicone substrates and cultured in supplemented M199 with 10% FBS for the first 48 hours in culture and then supplemented M199 with 2% FBS for the remainder of time in culture.

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

treatment_protocol: Tissues were rinsed with PBS and RNA was extracted using Stratagene Absolutely RNA Miniprep Kit (Agilent Technologies).

tag: background strain

value: Sprague-Dawley

tag: tissue

value: engineered neonatal rat ventricular tissues


title: NRVM_24h_aniso_nostretch_03

description: NRVM, aniso FN, 24h, no stretch, harvest4, biological rep3

source_name: NRVMs on aniso FN for 1h + 24h


title: 42SMU1

city: Vienna

first: Oliver

last: Neubauer

address: Althanstraße 14

country: Austria

institute: University of Vienna

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
42SMU1

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Data were exported after background correction in GenomeStudio software. Analysis was performed in the R (v 2.15.1) statistical environment. Background corrected raw data was quantile normalized using Bioconductor Lumi package (v.2.10.0), and array quality was assessed using ArrayQualityMetrics. The 47.323 transcript probes on the array were non-differentially filtered to remove 18.732 transcript probes that were below the threshold of reliable detection according to the default Illumina scanner software. Differential expression between the baseline values and each post-EXTRI time point was tested using the Bayesian moderated t-statistic available in Limma, in a paired design to account for within-subject correlation. All reported probe p-values were adjusted to control the false discovery rate (FDR) to 0.05 within each comparison, using the Benjamini-Hochberg method in Limma.

organism: Homo sapiens

label_protocol: standard as recommended by illumina

extract_protocol: Neutrophils were isolated from fresh blood plasma by gradient separation followed by two-fold lysis of red blood cells. Muscle biopsies were taken from the vastus lateralis, stored in RNA later (Ambion, Applied Biosystems) overnight, then disrupted and homogenized using RLT lysis buffer and proteinase K (Qiagen). RNA was extracted using the Qiagen RNeasy mini kit according the prescribed protocol with the kit. RNA concentrations and estimation of purity were determined with a Nanodrop spectrophotometer (Thermo Scientific).

tag: subject

value: healthy, endurance-trained individual

tag: subject gender

value: male

tag: subject id

value: skeletal muscle (SMU)

tag: time point

value: 1; 3 hr post-EXTRI


title: 61PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
61PMN0

value: blood PMN

value: 0; baseline pre-EXTRI


title: NRVM_24h_aniso_longstretch_01

description: NRVM, aniso FN, 24h, long stretch, harvest2, biological rep1

source_name: NRVMs on aniso FN for 1h and stretched longitudinally for 24h


title: 41PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
41PMN0


title: 43SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
43SMU2

value: 2; 48 hr post-EXTRI


title: 44SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
44SMU3

value: 3; 96 hr post-EXTRI


title: 51PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
51PMN0


title: 42PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
42PMN1


title: 41SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
41SMU0


title: 43PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
43PMN2


title: 51SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
51SMU0


title: 44PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
44PMN3


title: 54PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
54PMN3


title: NRVM_24h_iso_nostretch_03

description: NRVM, iso FN, 24h, no stretch, harvest4, biological rep3

source_name: NRVMs on iso FN for 1h + 24h


title: NRVM_6h_aniso_transstretch_01

description: NRVM, aniso FN, 6h, trans stretch, harvest3, biological rep1

source_name: NRVMs on aniso FN for 1h and stretched transversely for 6h


title: NRVM_24h_iso_nostretch_02

description: NRVM, iso FN, 24h, no stretch, harvest2, biological rep2


title: NRVM_6h_aniso_longstretch_03

description: NRVM, aniso FN, 6h, long stretch, harvest5, biological rep3

source_name: NRVMs on aniso FN for 1h and stretched longitudinally for 6h


title: NRVM_6h_aniso_transstretch_02

description: NRVM, aniso FN, 6h, trans stretch, harvest4, biological rep2


title: NRVM_24h_iso_nostretch_01

description: NRVM, iso FN, 24h, no stretch, harvest1, biological rep1


title: NRVM_6h_aniso_longstretch_02

description: NRVM, aniso FN, 6h, long stretch, harvest4, biological rep2


title: 32SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
32SMU1


title: NRVM_6h_iso_stretch_03

description: NRVM, iso FN, 6h, stretch, harvest3, biological rep3

source_name: NRVMs on iso FN for 1h and stretched for 6h


title: 31PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
31PMN0


title: NRVM_6h_iso_stretch_01

description: NRVM, iso FN, 6h, stretch, harvest1, biological rep1


title: NRVM_6h_aniso_transstretch_03

description: NRVM, aniso FN, 6h, trans stretch, harvest5, biological rep3


title: NRVM_6h_iso_stretch_02

description: NRVM, iso FN, 6h, stretch, harvest2, biological rep2


title: NRVM_6h_aniso_nostretch_03

description: NRVM, aniso FN, 6h, no stretch, harvest5, biological rep3

source_name: NRVMs on aniso FN for 1h + 6h


title: 31SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
31SMU0


title: NRVM_6h_aniso_nostretch_02

description: NRVM, aniso FN, 6h, no stretch, harvest2, biological rep2


title: 34PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
34PMN3


title: NRVM_6h_aniso_nostretch_01

description: NRVM, aniso FN, 6h, no stretch, harvest1, biological rep1


title: 33PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
33PMN2


title: 32PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
32PMN1


title: 34SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
34SMU3


title: 24SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
24SMU3


title: 33SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
33SMU2


title: 24PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
24PMN3


title: 22SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
22SMU1


title: 23SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
23SMU2


title: 22PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
22PMN1


title: 23PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
23PMN2


title: 21SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
21SMU0


title: NRVM_0h_01

description: NRVM, iso FN, 0h, no stretch, harvest1, for harvest normalization

source_name: NRVMs on iso FN for 1h


title: NRVM_0h_05

description: NRVM, iso FN, 0h, no stretch, harvest5, for harvest normalization


title: NRVM_6h_iso_nostretch_02

description: NRVM, iso FN, 6h, no stretch, harvest2, biological rep2

source_name: NRVMs on iso FN for 1h + 6h


title: NRVM_0h_03

description: NRVM, iso FN, 0h, no stretch, harvest3, for harvest normalization


title: NRVM_0h_02

description: NRVM, iso FN, 0h, no stretch, harvest2, for harvest normalization


title: NRVM_0h_06

description: NRVM, iso FN, 0h, no stretch, harvest6, for harvest normalization


title: NRVM_6h_iso_nostretch_01

description: NRVM, iso FN, 6h, no stretch, harvest1, biological rep1


title: 21PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
21PMN0


title: NRVM_6h_iso_nostretch_03

description: NRVM, iso FN, 6h, no stretch, harvest3, biological rep3


title: 13SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
13SMU2


title: 14SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
14SMU3


title: 14PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
14PMN3


title: 13PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
13PMN2


title: NRVM_0h_04

description: NRVM, iso FN, 0h, no stretch, harvest4, for harvest normalization


title: 12PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
12PMN1


title: 11SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
11SMU0


title: 11PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
11PMN0


title: 12SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
12SMU1


title: 54SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
54SMU3


title: Wild Type in LB + shock 15min 2mM Indole, replicate 6

type: mixed

city: Norwich

first: Corinne

last: Appia-Ayme

state: Norfolk

address: UEA

department: BIO

country: United Kingdom

institute: University of East Anglia

description: Indole shock_WT_rep6

hyb_protocol: Hybridisations were carried out in a 50μl volume per array. The volume of CyDye-labeled cDNA was reduced in a SpeedVac and adjusted to 21.5μL, then denatured at 94°C for 2 min, centrifuged 2 min and left to cool at RT for 1 min. the labelled cDNA with 37.5μL of hybridisation buffer (Morpholine-4-ethanesulfonic acid (MES) hydrate (pH 6.5) (Sigma, M2933) 50 mM, Sodium chloride 1 M, 99% Formamide (Sigma, F5786) 20 % (w/v), EDTA 20 mM, Triton X-100 (Sigma, T8532) 1 % (w/v)). 50μl of hybridisation mix was pipetted onto the GASKET slide, and an OGT array slide was placed in contact with the hybridisation mix. In a tight chamber, the arrays were hybridised at 55°C for 60 hours in a light-tight hybridisation oven at 4 to 8 rpm. The slide was removed from the hybridisation chamber and washed with buffer 1 (6XSSPE, 0.005% N-lauryl sarcosine) for 5min under agitation and for 5 min with the wash buffer 2 (0.06X SSPE, 0.18% polyethylene glycol 200), then dried in a centrifuge.

scan_protocol: Scanned on a GenePix 4000A scanner (Axon Instruments, Inc.). Images were quantified using Axon GenePrix Pro7.

data_processing: Data were normalised using the Batch Anti-Banana Algorithm in R (BABAR) algorithm and software package, which uses cyclic loess to normalise across the complete dataset (Alston et al., 2010 (PMID 20128918)).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Wild type in LB + 2mM indole OD600=1 for 15min

label_protocol: Total RNA (10 μg) was converted to cDNA and fluorescently labelled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (StrataScript, Stratagene).

growth_protocol: The media was inoculated with 1/1000 of overnight culture and grown to OD600=1 at 37C upon 200rpm agitation.

extract_protocol: Total RNA was extracted using the Promega SV total RNA extraction kit following the manufacturer's instructions.

treatment_protocol: The cells were treated with cold ethanol 20%, phenol 1% and left 30 min on ice prior to centrifugation.

tag: strain

tag: genotype

value: wild type

tag: growth media

value: LB + 2mM Indole 15 min

molecule: genomic DNA

source_name: Wild type in LB

label_protocol: 2 µg of chromosomal DNA was labelled with Cy3-dCTP using the Gibco Bioprime DNA Labelling System.

extract_protocol: Genomic DNA was extracted using the Qiagen Genomic DNA purification kit following the manufacturer's instructions.

value: LB


title: Wild Type in LB + shock 15min 2mM Indole, replicate 4

description: Indole shock_WT_rep4


title: Wild Type in LB + shock 15min 2mM Indole, replicate 5

description: Indole shock_WT_rep5


title: LNCaP-abl_siControl_2

city: New York

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Robust Median Averaging, and quantile normalization using the espresso function form the affy package of R bioconductor

source_name: cell culture

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA

growth_protocol: LNCaP-abl cells were cultured in RPMI-1640 without phenol red media (Cellgro, Mediatech, Inc.  Manassas, VA) supplemented with 10% Charcoal-stripped fetal bovine serum (cFBS), 1% penicillin-streptomycin and 1% L-Glutamine

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Three individual siRNAs (Silencer Select, Ambion; Life Technologies, Grand Island, NY) were pooled and transfected into cells using the HiPerFect transfection reagent (Qiagen, Valencia, CA) following manufacturer’s instructions. Non-silencing siRNAs were used as controls.  siRNAs were used at a final concentration of  30nM per individual siRNA

tag: cell line

value: LNCaP-abl

tag: transfection

value: siControl


title: LNCaP-abl_siMED19_1


title: LNCaP-abl_siHIPK2_2


title: LNCaP-abl_siHIPK2_1


title: LNCaP-abl_siMED19_2


title: A2780-shUCHL1

city: Hangzhou

first: Chengmeng

last: Jin

state: zhejiang

address: 268 kaixuan road

department: SBP

country: China

institute: ZCNI

description:
UCHL1 knocked down A2780
A73.mas5

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hours at 45 ℃ on GeneChip U133_plus 2.0 Array. GeneChips were washed and stained in the Affymetrix fluidics Station 450.

scan_protocol: The chips were scanned with the affymetrix genechip 7G plus, and AGCC is used for the image processing

data_processing: Genespring 10.0 is used for automatically normalizing the chip data and analyzing the fold change

source_name: ovarian cancer cell line A2780-shUCHL1

label_protocol: Start with 250ng total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, GeneChip 3 IVT Express Kit (Lot no.901228) is used in the experiment.

growth_protocol: cells were cultured in RPMI 1640 with 10% FBS

extract_protocol: total RNA was extracted with Trizol according to the manufacturer's protocol

treatment_protocol: UCHL1 was knocked down with shUCHL1 or non-target shRNA in A2780

tag: genotype/variation

value: UCHL1 knockdown


title: A2780-control

description:
A2780 control
A-L.mas5

source_name: ovarian cancer cell line A2780-control

value: control


title: LNCaP-abl_siControl_1


title: Wild Type in LB + shock 15min 2mM Indole, replicate 3

description: Indole shock_WT_rep3


title: Wild Type in LB + shock 15min 2mM Indole, replicate 2

description: Indole shock_WT_rep2


title: PA070810 beta cells card B

city: Miami

first: Ricardo

last: Pastori

state: FL

department: Diabetes Research Institute

institute: University of Miami

description: Test

data_processing:
Data was processed using the software SDS 2.3 and RQ manager 1.2 from Applied Biosystems. Cut off value for Ct was set in 32 cycles taking into account that these samples were preamplified. Therefore, undetermined expression and Ct values higher than 32 cycles were substituted by 32 for RQ calculation. If Cts in alpha and beta cell samples were > 32, the miRNA was considered as non-expressed.
Ct for cycle threshold meaning the cycle in which the specific miRNA starts to be detected. ddCt for delta delta Ct, defined by the formula (Ct of the specific miRNA in the target sample-Ct of the endogenous control RNU48 in the target sample)-(Ct of the specific miRNA in the control sample-Ct of the endogenous control RNU48 in the control sample) for each human pancreas preparation. RQ for relative quantification, defined by the formula 2^-ddCt . Small nuclear RNA (RNU48) was used as endogenous control.

label: FAM

source_name: Beta cells from human pancreatic islets

extract_protocol: Total RNA was isolated using the miRVana microRNA isolation kit (Ambion).

value: pancreas

tag: cell type

value: Beta cells

tag: sample type

value: Test


title: Wild Type in LB + shock 15min 2mM Indole, replicate 1

description: Indole shock_WT_rep1


title: HP1876 beta cells card B

description: Test


title: NRVM_6h_aniso_longstretch_01

description: NRVM, aniso FN, 6h, long stretch, harvest3, biological rep1

value: Sprague-Dawley

value: engineered neonatal rat ventricular tissues


title: Wild Type in LB, replicate 4

source_name: Wild type in LB, OD600=1


title: Wild Type in LB, replicate 3


title: HP1915 beta cells card B

description: Test


title: HSC-3 cells-MHT 0h

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description:
HSC-3-0h
HSC-3 cells treated with heat stress at 41°C and cultured for 0 h.
HSC-3 cells are derived from the tongue of a 64-year-old male.

hyb_protocol: After fragmentation, the biotinylated cRNA was hybridized to arrays at 45°C for 16 h.

scan_protocol: The arrays were washed, stained with streptavidin-phycoerythrin and scanned with a probe array scanner (Affymetrix).

data_processing: Data were processed using RMA using GeneChip Analysis Suite.

source_name: Human oral squamous cell carcinoma cell line HSC-3, MHT, 0h

label_protocol: 500 ng of total RNA was used to synthesize cRNA with a GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: HSC-3 cells were cultured in Eagle's Minimum Essential Medium supplemented with 10% fetal bovine serum at 37°C in humidified air with 5% CO2 and 95% air.

extract_protocol: Total RNA was extracted from cells using an RNeasy Total RNA Extraction kit (Qiagen), and treated with DNase I (Qiagen) for 15 min at room temperature to remove residual genomic DNA. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies), producing RIN values between 9.5 and 10.

treatment_protocol: MHT treatment was carried out by immersing plastic culture vessels containing the attached cells in a water bath at 41°C for 30 min. After heat treatment, the cells were incubated for 0-3 h at 37°C.

value: oral squamous cell carcinoma cells

tag: morphology

value: epithelial-like

tag: life span

value: infinite

tag: treatment

value: heat stress

value: 0 hr


title: normal skin 10

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: normal skin epidermal cells

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: patient

value: healthy volunteer 10

value: normal epidermis


title: HSC-3 cells-MHT 1h

description:
HSC-3-1h
HSC-3 cells treated with heat stress at 41°C and cultured for 1 h.
HSC-3 cells are derived from the tongue of a 64-year-old male.

source_name: Human oral squamous cell carcinoma cell line HSC-3, MHT, 1h

value: 1 hr


title: normal skin 9

value: healthy volunteer 9


title: HSC-3 cells-control

description:
HSC-3-C
HSC-3 cells (control).
HSC-3 cells are derived from the tongue of a 64-year-old male.

source_name: Human oral squamous cell carcinoma cell line HSC-3, control


title: HSC-3 cells-MHT 3h

description:
HSC-3-3h
HSC-3 cells treated with heat stress at 41°C and cultured for 3 h.
HSC-3 cells are derived from the tongue of a 64-year-old male.

source_name: Human oral squamous cell carcinoma cell line HSC-3, MHT, 3h

value: 3 hr


title: normal skin 7

value: healthy volunteer 7


title: normal skin 8

value: healthy volunteer 8


title: HP1908 beta cells card B

description: Test

tag: tissue

value: pancreas


title: Wild Type in LB, replicate 2

value: wild type

value: LB


title: HP1914 beta cells card B

description: Test

value: Beta cells

value: Test


title: Wild Type in LB, replicate 1


title: HP1901 beta cells card B

description: Test


title: PA070810 alpha cells card B

description: Control

source_name: Alpha cells from human pancreatic islets

value: Alpha cells

value: Control


title: normal skin 6

value: healthy volunteer 6


title: Adipose tissue, normal diet

city: Hidaka

first: Yasushi

last: Okazaki

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

description: Gene expression data from adipose tissue obtained from mice fed a normal diet (ND) as a control

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 45

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing:
The intensity data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al. Nucleic Acids Res 31(4): e15, 2003) via R/Bioconductor affy 2.13.1 package using default analysis settings.
The values of matrix table are logarithmic (log2) values

organism: Mus musculus

source_name: The adipose tissue of mice fed a normal diet (CE-2)

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

growth_protocol: Healthy grown C57BL/6 mice were used for high fat diet treatment to induce obesity.

extract_protocol: At 18 week-old, total RNAs from adipose tissues were prepared by using Nucleospin RNA II Isolation Kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: Mice were fed a normal diet CE-2 or high fat diet HFD32 (Clea, Tokyo, Japan) from 6 week-old to 18 week-old.

tag: diet

value: normal diet (CE-2, as a control)

value: adipose tissue


title: Adipose tissue, high fat diet

description: Gene expression data from the adipose tissue obtained from mice fed a high fat diet (HFD).

source_name: The adipose tissue of mice fed a high fat diet (HFD32)

value: high fat diet (HFD32)


title: Low treatment 18 days recovery

type: genomic

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: 5mC profile in L18d sample

hyb_protocol: standard protocol according to NimbleGen Kit

scan_protocol: NimbleScan's default protocol using Agilent Scanner

data_processing: For each array, Loess normalization was applied excluding top 5% probes with the largest original Cy5/Cy3 log2 ratio. Quantile normalization was then applied across all the arrays.

source_name: Low treatment 18 days recovery 5mC (MIRA) enriched samples

label_protocol: standard protocol according to standard NimbleGen Protocol

extract_protocol: MinElute PCR Purification Kit (Qiagen; Valencia, CA). Genomic DNA was fragmented by sonication to an average size of ~400 bp using a Sonifier cell disruptor 350 (Branson; Danbury, CT).

value: Normal human epidermal keratinocytes (NHEK)

value: 5mC (MIRA)

tag: antibody

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: 11x 130j/m^2 UV-B treatment and harvest after a recovery time of 18 days

source_name: L18 input DNA

value: input DNA


title: HP1876 alpha cells card B

description: Control


title: Wild Type in LB + 2mM Indole, replicate 4

source_name: Wild type in LB + 2mM indole, OD600=1

value: LB + 2mM Indole


title: Wild Type in LB + 2mM Indole, replicate 3

source_name: Wild type in LB


title: Wild Type in LB + 2mM Indole, replicate 2


title: Wild Type in LB + 2mM Indole, replicate 1


title: normal skin 5

value: healthy volunteer 5

value: normal epidermis


title: normal skin 3

value: healthy volunteer 3


title: normal skin 4

value: healthy volunteer 4


title: No treatment control 18 days

description: 5mC profile in N18d sample

source_name: No treatment control 18 days 5mC (MIRA) enriched samples

value: no treatment and harvest at the same time like H18d

source_name: N18d input DNA


title: normal skin 2

value: healthy volunteer 2


title: High treatment 18 days recovery

description: 5mC profile in H18d sample

source_name: High treatment 18days recovery 5mC (MIRA) enriched samples

value: 11x 260j/m^2 UV-B treatment and harvest after a recovery time of 18 days

source_name: H18d input DNA


title: Low treatment control

description: 5mC profile in Lcon sample

source_name: Low treatment control 5mC (MIRA) enriched samples

value: 1x 130j/m^2 UV-B treatment and directly harvest

source_name: Lcon input DNA


title: HP1915 alpha cells card B

description: Control

value: pancreas

value: Alpha cells

value: Control


title: HP1914 alpha cells card B

description: Control


title: HP1908 alpha cells card B

description: Control


title: HP1901 alpha cells card B

description: Control


title: sdiA Mutant in LB + 2mM Indole, Replicate 4

hyb_protocol: Hybridisations were carried out in a 50μl volume per array. The volume of CyDye-labeled cDNA was reduced in a SpeedVac and adjusted to 21.5μL, then denatured at 94°C for 2 min, centrifuged 2 min and left to cool at RT for 1 min. the labelled cDNA with 37.5μL of hybridisation buffer (Morpholine-4-ethanesulfonic acid (MES) hydrate (pH 6.5) (Sigma, M2933) 50 mM, Sodium chloride 1 M, 99% Formamide (Sigma, F5786) 20% (w/v), EDTA 20 mM, Triton X-100 (Sigma, T8532) 1% (w/v)). 50μl of hybridisation mix was pipetted onto the GASKET slide, and an OGT array slide was placed in contact with the hybridisation mix. In a tight chamber, the arrays were hybridised at 55°C for 60 hours in a light-tight hybridisation oven at 4 to 8 rpm. The slide was removed from the hybridisation chamber and washed with buffer 1 (6XSSPE, 0.005% N-lauryl sarcosine) for 5min under agitation and for 5 min with the wash buffer 2 (0.06X SSPE, 0.18% polyethylene glycol 200), then dried in a centrifuge.

source_name: sdiA mutant in LB + 2mM indole, OD600=1

label_protocol: Total RNA (10 μg) was converted to cDNA and fluorescently labeled by random priming to incorporate Cy5-dCTP (Amersham) using reverse transcriptase (StrataScript, Stratagene).

growth_protocol: The media was inoculated with 1/1000 of overnight culture and grown to OD600=1 at 37 C upon 200rpm agitation.

treatment_protocol: The cells were treated with cold ethanol 20%, phenol 1% and left 30min on ice prior to centrifugation.

value: sdiA mutant

value: LB + 2mM indole

label_protocol: 2 µg of chromosomal DNA was labeled with Cy3-dCTP using the Gibco Bioprime DNA Labeling System.

value: wild type

value: LB


title: sdiA Mutant in LB + 2mM Indole, Replicate 3


title: sdiA Mutant in LB + 2mM Indole, Replicate 2


title: sdiA Mutant in LB + 2mM Indole, Replicate 1


title: normal skin 1

source_name: normal skin epidermal cells

value: healthy volunteer 1


title: Splenocyte 2month TG Biologic Replicate 2

city: Baltimore

first: Linda

last: Resar

state: MD

address: 720 Rutland Ave

department: Hematology

institute: Johns Hopkins University

description: Hybridization was performed by the Johns Hopkins Medical Institutions Microarray Core Facility.

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual, 2004.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual, 2004.

data_processing: Image analysis using GCOS 1.4, using MAS 5.0 algorithm and manufacturer’s specifications. Global scaling of images to a target intensity of 150.

label: Biotin

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter oligo dT primer for cDNA synthesis, and ENZO IVT kit (www.affymetrix.com, GeneChip Expression Analysis, Technical Manual, 2003).

growth_protocol: Mice were maintained in the Johns Hopkins Broadway Research Building Animal Facility.

extract_protocol: RNeasy Kit (QIAGEN)

tag: sex

value: Male

tag: age

value: 2 months

tag: cell source

value: Spleen

value: splenocyte

value: HMGA1a transgenic


title: No treatment control 8 days

description: 5mC profile in N8d sample

source_name: No treatment control 8 days 5mC (MIRA) enriched samples

value: Normal human epidermal keratinocytes (NHEK)

value: 5mC (MIRA)

value: In Lab purified His-MBD3L1 & GST-MBD2b

value: no treatment and harvest at the same time like H8d

source_name: N8d input DNA

value: input DNA


title: High treatment 8 days recovery

description: 5mC profile in H8d sample

source_name: High treatment 8 days recovery 5mC (MIRA) enriched samples

value: 11x 260j/m^2 UV-B treatment and harvest after a recovery time of 8 days

source_name: H8d input DNA


title: P3 - reticular dermis

description: laser capture microdissection tissue

source_name: reticular dermis cells

value: reticular dermis cells


title: Splenocyte 12month TG Biologic Replicate 2

value: 12 months

tag: strain

tag: genotype


title: Splenocyte 12month WT Biologic Replicate 2


title: Wild Type in LB + 2mM Indole, Replicate 4

tag: growth media

value: LB + 2mM indole


title: High treatment control

description: 5mC profile in Hcon sample

source_name: High treatment control 5mC (MIRA) enriched samples

value: 1x 260j/m^2 UV-B treatment and directly harvest

source_name: Hcon input DNA

value: 1x260j/m^2 UV-B treatment and directly harvest


title: P3 - basal

description: laser capture microdissection tissue

source_name: basal cells

value: basal cells


title: P3 - suprabasal

description: laser capture microdissection tissue

source_name: suprabasal cells

value: suprabasal cells


title: Splenocyte 2month WT Biologic Replicate 2

value: Male

value: 2 months

value: wild type


title: Splenocyte 12month TG Biologic Replicate 1

value: Spleen

value: splenocyte

value: HMGA1a transgenic


title: Splenocyte 12month WT Biologic Replicate 1


title: P2 - suprabasal

description: laser capture microdissection tissue


title: P2 - basal

description: laser capture microdissection tissue


title: sdiA Mutant in LB, Replicate 4

source_name: sdiA mutant in LB, OD600=1

value: sdiA mutant

value: LB

source_name: Wild type in LB


title: Splenocyte 2month TG Biologic Replicate 1

source_name: Splenocytes 2 months transgenic biologic replicate 1


title: sdiA Mutant in LB, Replicate 3


title: Wild Type in LB + 2mM Indole, Replicate 3

source_name: Wild type in LB + 2mM indole, OD600=1


title: Wild Type in LB + 2mM Indole, Replicate 1


title: Wild Type in LB + 2mM Indole, Replicate 2


title: Res-Let (AD + Letrozole) replicate 2

city: Lyon

first: Julie

middle: A

last: Vendrell

state: Select a State or Province

address: 8 avenue Rockefeller

department: INSERM U1052

country: France

institute: ISPBL - Faculté de Pharmacie de Lyon

description: miRNA expression data from cell population of MCF-7aro displaying resistance to letrozole (Res-Let) treated in the presence of 25 nM of androstenedione and 10-6M of letrozole, cell culture replicate 2

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Scanned images of microarray chips were analyzed using Expression Console (Affymetrix) with the default settings. Raw data were processed using different algorithms. Detected Above Background algorithm (DABD) and RMA Background Adjustment algorithm were performed in order to remove the background value.

source_name: cell population of MCF-7 stably transfected with the human placental aromatase gene resistant to letrozole (Res-Let cells)

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Cells were grown in DMEM medium supplemented with 10% fetal bovine serum

extract_protocol: Total RNA from cell culture was prepared using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations and subsequently quantified on a Nanodrop ND1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). RNA integrity was checked using the BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Prior to experiment, cells were purged in Dulbecco’s Modified Eagle Medium without phenol red, supplemented with 3% steroid-depleted, dextran-coated and charcoal-treated fetal calf serum (DCC medium) for 4 days. MCF-7aro and Res-Let cells were then grown for 4 days in the presence of 25 nM of androstenedione combined or not with 10-6 M of letrozole. Media and treatment were changed every 2 days.

tag: cell line


title: Splenocyte 2month WT Biologic Replicate 1


title: FC-MT Rep 2_VmT

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files. Signals quantile normalized and log2 ratios (Cy5/Cy3) calculated.

organism: Junco hyemalis

source_name: ventromedial telencephalon

label_protocol: ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

extract_protocol:
Total RNA was extracted in TRIzol Reagent, following manufacturer's directions (Invitrogen, Carlsbad, CA, USA).
Target protocol: Total RNA primed with Oligo-dT (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with ChargeSwitch PCR Clean Up Kit (Invitrogen).
Quality assessement protocol: Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.

value: MT

tag: biological replicate

value: FC


title: P1 - reticular dermis

description: laser capture microdissection tissue

tag: cell type

value: reticular dermis cells


title: normal skin 10

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

value: healthy volunteer 10

value: normal epidermis

tag: material

value: sliced section


title: MC-MT Rep 2_VmT

value: MC


title: FT-MC Rep 2_VmT

value: FT


title: MC-FC Rep 2_VmT


title: Res-Let (AD) replicate 1

description: miRNA expression data from cell population of MCF-7aro displaying resistance to letrozole (Res-Let) treated in the presence of 25 nM of androstenedione, cell culture replicate 1


title: Res-Let (AD) replicate 2

description: miRNA expression data from cell population of MCF-7aro displaying resistance to letrozole (Res-Let) treated in the presence of 25 nM of androstenedione, cell culture replicate 2


title: Res-Let (AD + Letrozole) replicate 1

description: miRNA expression data from cell population of MCF-7aro displaying resistance to letrozole (Res-Let) treated in the presence of 25 nM of androstenedione and 10-6M of letrozole, cell culture replicate 1


title: MCF-7aro (AD + Letrozole) replicate 2

description: miRNA expression data from cell population of MCF-7aro treated in the presence of 25 nM of androstenedione and 10-6M of letrozole, cell culture replicate 2

source_name: cell population of MCF-7 stably transfected with the human placental aromatase gene sensitive to letrozole (MCF-7aro cells)


title: P1 - basal

description: laser capture microdissection tissue

value: basal cells


title: P1 - suprabasal

description: laser capture microdissection tissue

value: suprabasal cells


title: P2 - reticular dermis

description: laser capture microdissection tissue


title: FC-FT Rep 1_VmT


title: sdiA Mutant in LB, Replicate 2

tag: genotype/variation


title: sdiA Mutant in LB, Replicate 1


title: FT-MT Rep 1_VmT


title: FT-FC Rep 2_VmT


title: MCF-7aro (AD + Letrozole) replicate 1

description: miRNA expression data from cell population of MCF-7aro treated in the presence of 25 nM of androstenedione and 10-6M of letrozole, cell culture replicate 1


title: Wild Type in LB, Replicate 4

source_name: Wild type in LB, OD600=1


title: HP1876 beta cells card A

description: Test

source_name: Beta cells from human pancreatic islets

value: pancreas

value: Beta cells

tag: sample type

value: Test


title: Wild Type in LB, Replicate 3

value: wild type


title: normal skin 9

source_name: normal skin epidermal cells

value: healthy volunteer 9


title: normal skin 8

value: healthy volunteer 8


title: HP1915 beta cells card A

description: Test


title: MCF-7aro (AD) replicate 2

description: miRNA expression data from cell population of MCF-7aro treated in the presence of 25 nM of androstenedione, cell culture replicate 2


title: normal skin 7

value: healthy volunteer 7


title: PA070810 beta cells card A

description: Test


title: normal skin 6

value: healthy volunteer 6


title: Wild Type in LB, Replicate 2

value: LB


title: HP1914 beta cells card A

description: Test


title: MCF-7aro (AD) replicate 1

description: miRNA expression data from cell population of MCF-7aro treated in the presence of 25 nM of androstenedione, cell culture replicate 1


title: normal skin 5

value: healthy volunteer 5


title: MT-FT Rep 1_VmT

tag: treatment

value: MT


title: normal skin 4

tag: patient

value: healthy volunteer 4

value: normal epidermis


title: MycF/F,ERT2-Cre + Wy Replicate 4

city: Bethesda

first: Aijuan

last: Qu

state: Maryland

address: 9000 Rockville Pike

institute: NIH

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G26000 scanner. Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1).

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and LOWESS normalization.

source_name: whole mouse liver

label_protocol:
labeling for Cy3 and Cy5
NHS ester containing dyes coupling reaction
1. Resuspend cDNA pellet in 5  l of 2Xcoupling buffer
2. The first time a tube of dye is used, resuspend in 45 l DMSO.
3. Add 5  l of the resuspend monofunctional reactive dye to cDNA solution. (Cy3, Cy5)
4. Mix gently by pipetting
5. Incubate for 30 to 90 minutes at room temp in the dark and flicking the tubes occasionally .
6. Add 10  l of 3M Sodium acetate( PH 5.2) to the reaction and mix well
7. Purification of Dye-coupled cDNA
Cy5 mono-Reactive Dye Pack from GE Healthcare, Life Sciences: PA25001
Cy3 mono-Reactive Dye Pack from GE Healthcare, Life Sciences: PA23001

extract_protocol: Total RNAs were extracted using miRNeasy Mini Kit following the manufacturer's instruction, and antisense RNAs were amplified with Amino Allyl MessageAmp™ II aRNA Kit and labelled with MonoReactive Dye Pack

treatment_protocol: MycF/F or MycF/F,ERT2-Cre mice were treated with control or 0.1% Wy-14643 diet for 2 days and whole liver were exercised.

value: ko

tag: agent

tag: tissue

value: whole liver

source_name: pooled whole mouse liver [reference RNA]

value: pooled whole liver

value: reference


title: MC-FT Rep 1_VmT

value: FT

value: MC


title: HP1908 beta cells card A

description: Test

value: pancreas

value: Beta cells

value: Test


title: normal skin 3

value: healthy volunteer 3

value: sliced section


title: Wild Type in LB, Replicate 1

value: wild type


title: FC-MT Rep 2_hypothalamus

source_name: hypothalamus tissue

value: FC


title: MycF/F,ERT2-Cre + Wy Replicate 3


title: HP1901 beta cells card A

description: Test


title: PA070810 alpha cells card A

description: Control

source_name: Alpha cells from human pancreatic islets

value: Alpha cells

value: Control


title: normal skin 2

value: healthy volunteer 2


title: normal skin 1

value: healthy volunteer 1

value: normal epidermis


title: MT-FC Rep 1_VmT

value: MT


title: MycF/F,ERT2-Cre + Wy Replicate 2

value: ko

value: whole liver

value: pooled whole liver


title: HP1876 alpha cells card A

description: Control


title: HP1915 alpha cells card A

description: Control


title: FC-MC Rep 1_VmT

value: MC


title: MycF/F,ERT2-Cre + Wy Replicate 1

value: reference


title: Porcine colon_with fiber_160d_10

city: Chengdu

first: Lianqiang

last: Che

address: Huiming Road 211,Wenjiang

institute: Sichuan Agricultural University

hyb_protocol: Agilent (Palo Alto, CA, USA) G2519F porcine gene expression microarray slides containing more than 40,000 probes were used.  Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ng 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. Microarrays were hybridized at 65℃ for 17 h and washed with a Gene Expression Washing Buffer Kit (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) 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: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Sus scrofa

source_name: Colon_with fiber_160d

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.

growth_protocol: The weaned pigs were individually fed in pig experimental pens (0.6×0.8m) and then transferred to growing-finishing pig pen (2.0×3.0m) when pig body weight was app. 20 kg. The pigs were fed in the atmosphere-controlled environment (22～24℃).

extract_protocol: Total RNA was extracted from frozen colonic tissues using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) 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).

treatment_protocol: All pigs were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of  pea fiber from weaning age until d 160 post-weaning.

tag: diet

value: fibrous diet

value: Colon


title: HP1914 alpha cells card A

description: Control

value: pancreas


title: Porcine colon_without fiber_160d_9

source_name: Colon_without fiber_160d

value: control


title: HP1908 alpha cells card A

description: Control


title: MT-MC Rep 1_VmT


title: MC-MT Rep 2_hypothalamus


title: FT-MC Rep 2_hypothalamus

value: FT


title: HP1901 alpha cells card A

description: Control


title: MC-FC Rep 2_hypothalamus

value: FC


title: Porcine colon_with fiber_160d_8


title: MycF/F,ERT2-Cre + Con Replicate 2


title: FT-FC Rep 2_hypothalamus


title: MycF/F,ERT2-Cre + Con Replicate 3


title: MycF/F,ERT2-Cre + Con Replicate 1


title: FC-FT Rep 1_hypothalamus


title: FT-MT Rep 1_hypothalamus


title: Porcine colon_without fiber_160d_7


title: Porcine colon_without fiber_160d_5


title: Porcine colon_with fiber_160d_4


title: Porcine colon_without fiber_160d_3


title: MT-FT Rep 1_hypothalamus


title: AMC-ARC-1

status: Public on Jan 29 2013

city: London

first: Laura

last: Roca-Alonso

address: Du Cane Rd

department: Surgery and Cancer

institute: Imperial College London

description: miRTags for 423 rat miRNAs (miRbase 17) in solution. 6 positive and 8 negative assay controls included. Also, 4 mRNA of houskeeping genes and 5 non-mammalian miRNA sequences included for further normalization

hyb_protocol: standard Nanostring flow cell protocol

scan_protocol: nCounter Digital Analyser using nCounter Analysis System to count miRNA-specific reporter probes

data_processing: Raw data was normalized to three different types of controls included in the microarray platform: background was removed in relation to negative controls, signal intensity variation was normalized to positive controls and changes in sample contents were normalized according to housekeeping gene intensities (mRNA controls)

label: specific miRTag sequence

source_name: Pure adult rat cardiomyocytes isolated from healthy age-matched controls, undergoing the same time in culture (panning of apoptotic cells) prior to RNA extraction

label_protocol: standard Nanostring protocol

growth_protocol: Adult rat cardiomyocytes (ARC) maintained in M199 when in culture

extract_protocol: TRIzol reagent

treatment_protocol: Following in vitro treatment or isolation from hearts of in vivo models, ARC were plated in laminin-coated dishes for 1h to discard apoptotic cells prior to RNA extraction of attached viable cells.

value: Pure isolated adult rat cardiomyocytes

tag: nature of treatment

value: in vivo CON (age-matched)

value: Sprague Dawley


title: AMC-ARC-3


title: MycF/F+wy Replicate 2

value: wt


title: Rat-4wMI-3

value: Left coronary artery ligation to induce myocardial infarction leading to failure after 4 wks

tag: cardiac toxicity models

value: MI induction

value: in vivo


title: MycF/F+wy Replicate 1

value: whole liver


title: Rat-DOX-3

source_name: Repeated DOX injections in adult rats to induce heart failure

value: DOX-induced failure


title: Rat-4wMI-1

source_name: Left coronary artery ligation to induce myocardial infarction leading to failure


title: MycF/F+wy Replicate 3

value: pooled whole liver


title: Porcine colon_with fiber_160d_6


title: Rat-4wMI-2


title: MycF/F+ Con Replicate 1

source_name: pooled whole mouse liver

value: reference


title: AMC-ARC-2


title: MC-FT Rep 1_hypothalamus

value: MC


title: MT-FC Rep 1_hypothalamus

value: MT


title: MT-MC Rep 1_hypothalamus


title: Rat-DOX-1

value: Repeated DOX injections in adult rats to induce heart failure


title: FC-MC Rep 1_hypothalamus


title: ARC-CON6h-3

source_name: Pure healthy adult rat cardiomyocytes treated with vehicle (saline)  in vitro

value: vehicle (saline)  in vitro for 6h

value: in vitro CON


title: ARC-CON6h-2


title: ARC-DOX6h-2

source_name: Pure healthy adult rat cardiomyocytes treated with DOX  in vitro

value: DOX  in vitro for 6h

value: DOX acute

value: in vitro


title: Rat-DOX-2

value: Pure isolated adult rat cardiomyocytes

value: Sprague Dawley


title: ARC-DOX6h-1


title: ARC-CON6h-1


title: ARC-DOX6h-3


title: Macrophages Uninfected 4

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

institute: bioMérieux

description: Macrophages non infected

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing: The data processing and analyses were performed using R software and BioConductor libraries. Statistical supervised analysis was performed using the significance analysis of microarrays (SAM), and the genes with an absolute fold change (FC) greater than 2.0 and a False Discovery Rate (FDR) value less than 0.01 were considered differentially modulated.

source_name: Macrophages non infected

label_protocol: The amplification of RNAs and Cy3 labeling of cDNAs were generated using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Massy, France).

growth_protocol: O. tsutsugamushi, strain Kato (CSUR R163), was propagated and titered in L929 cells. Peripheral blood mononuclear cells were isolated from leukopacks (Etablissement Français du Sang, Marseille, France) over a Ficoll gradient (MSL, Eurobio, Les Ulis, France). Monocytes were isolated by adherence in 24-well plates containing or not 12-mm glass coverslips. They were then differentiated into macrophages. Briefly, monocytes were cultivated in RPMI 1640 containing 25 mM HEPES, 2 mM L-glutamine (Invitrogen, Cergy Pontoise, France) and 10% heat-inactivated human AB sera (Lonza, Verviers, Belgium) for three days and human serum was replaced by 10% fetal bovine serum (FBS, Invitrogen) for additional periods ranging from 4 to 6 days. Cultivated cells were designed as monocyte-derived macrophages because more 90% of them did not express CD14 but expressed CD68.

extract_protocol: RNAs were extracted from infected and uninfected macrophages using an RNeasy Mini kit (Qiagen) with a DNase digestion step.

treatment_protocol: Macrophages (1.5 × 10.5 cells per assay) were incubated in RPMI 1640 containing 25 mM HEPES, 2 mM L-glutamine and 10% heat-inactivated FBS in the presence of O. tsutsugamushi at a bacterium-to-cell ratio of 10:1 for 2 hours. Macrophages were then washed to discard unbound organisms and cultivated for different periods. The uptake and the intracellular fate of bacterial pathogens were determined using confocal microscopy and quantitative real-time PCR (qPCR).

tag: infection

value: NO

value: Macrophages


title: Control

city: Deajeon

first: Heui Man

last: Kim

state: Deajeon

address: 99 Daehak ro

department: College of Veterinary Medicine

country: South Korea

institute: Chungnam national university

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Rat Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

organism: Mustela putorius

source_name: Uninfected ferrets control

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: In-vivo (ferret's lung)

extract_protocol: RNA extraction using Trizol

treatment_protocol: Influenza virus infected and uninfected

value: Lung RNA


title: CL

source_name: Infected ferrets depleted of alveolar macrophages


title: Kid_Paternal_5

city: Leicester

first: Yuri

middle: E

last: Dubrova

address: University Road

department: Genetics

institute: University of Leicester

description: Four technical replicas used to generate the data for SAMPLE 16.

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization System 4 following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using GenePix Axon 4200 AL scanner, following their standard operating protocol.

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.).

source_name: Kidney F1_irradiated male_male 5

label_protocol: Labeling was performe using the NimbleGen One-Color DNA Labeling Kit.

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).

treatment_protocol: 1 Gy of acute X-rays delivered at 0.5 Gy/min (250 kV constant potential, HLV 1.5 mm Cu, Pantak industrial X-ray machine, Connecticut, USA).

tag: strain

value: BALB/c

value: Male offspring of irradiated male, 1Gy acute X-rays

value: Kidney


title: Macrophages Infected 3

description: Macrophages infected with O. tsutsugamushi

value: YES


title: PBS

source_name: Infected ferrets non-depleted of alveolar macrophages


title: Macrophages Uninfected 3

description: Macrophages non infected


title: Kid_Maternal_5

description: Two technical replicas used to generate the data for SAMPLE 11.

source_name: Kidney F1_irradiated female_male 5

value: Male offspring of irradiated female, 1Gy acute X-rays


title: Macrophages Uninfected 2

description: Macrophages non infected


title: Kid_Paternal_6

description: These data were used to generate the data for SAMPLE 17.

source_name: Kidney F1_irradiated male_male 6


title: Kid_Paternal_3

description: Two technical replicas used to generate the data for SAMPLE 15.

source_name: Kidney F1_irradiated male_male 3


title: Kid_Paternal_1

description: Six technical replicas used to generate the data for SAMPLE 13.

source_name: Kidney F1_irradiated male_male 1


title: Kid_Paternal_2

description: Three technical replicas used to generate the data for SAMPLE 14.

source_name: Kidney F1_irradiated male_male 2


title: Kid_Maternal_1

description: Four technical replicas used to generate the data for SAMPLE 7.

source_name: Kidney F1_irradiated female_male 1


title: Macrophages Uninfected 1

description: Macrophages non infected


title: Macrophages Infected 1

source_name: Macrophages infected with O. tsutsugamushi


title: Macrophages Infected 2


title: Kid_Maternal_4

description: Four technical replicas used to generate the data for SAMPLE 10.

source_name: Kidney F1_irradiated female_male 4


title: Macrophages Infected 4


title: Kid_Maternal_6

description: Three technical replicas used to generate the data for SAMPLE 12.

source_name: Kidney F1_irradiated female_male


title: Kid_Maternal_2

description: Four technical replicas used to generate the data for SAMPLE 8.

source_name: Kidney F1_irradiated female_male 2


title: Kid_Maternal_3

description: Two technical replicas used to generate the data for SAMPLE 9.

source_name: Kidney F1_irradiated female_male 3


title: Monocytes Control 7

description: Monocytes-derived transcriptome of Control patient from pair A

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours..

scan_protocol: he arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing:
Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered for probes with signals below background and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, principal component analysis (PCA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Genes were considered to be differentially expressed when the false discovery rae [23] was below 1% and absolute fold change (FC) was above 2.0 in at least one of the 18 pair combinations.
the "processed signal" from feature extractor was used, with no further background correction
the normalization was done with the "quantile" algorithm as mentioned
the dataset was filtered to remove controls, spot below BG, spot not found (Agilent FLAG), and saturated spots (Agilent FLAG). For each probe, the probe ws removed if the FLAG was set TRUE in > 75% of the samples
the dataset was then summarized for replicated (identical) probes (to keep only one)

label_protocol: In brief, 250 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: Whole blood (2.5 ml) was collected from patients using PAXgene blood RNA tube (Qiagen). After collection, the tubes were stored at –20°C for 24 hours then were transferred at -80°C. Ten ml of blood was taken in two tubes of 5 ml with ethylene diamine tetraacetic acid (EDTA). PBMCs were recovered from the Ficoll-Hypaque interface (MSL, Eurobio). Mononuclear cells were isolated from PBMCs by positive selection (Miltenyi Biotec) using magnetic beads coated with anti-CD14. Monocytes were suspended in complete medium containing RPMI 1640, 20 mM HEPES, 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen) and stored at –80°C for further RNA extraction.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.

treatment_protocol: HEV-infected patients enrolled in the study presented CHE, defined by persistence in blood of HEV RNA detection for longer than 6 months. Control patients enrolled in the study were free of every acute or chronic viral infection at the inclusion and were matched up with CHE patients for sex, age, time since kidney-transplant, and immunosuppressive treatment (presence of a calcineurin inhibitor in the treatment).

value: Monocytes

tag: patient type

value: Control

tag: chip number

tag: patient number

tag: age (y)

tag: Sex

value: M

tag: severity

tag: graft duration (months)

tag: pairing

value: A

tag: hev load

tag: disease state

value: monocyte


title: Monocytes Control 11

description: Monocytes-derived transcriptome of Control patient from pair C

tag: sample type

value: C

tag: cell type


title: Monocytes Control 6

description: Monocytes-derived transcriptome of Control patient from pair H

value: H


title: Kid_Con_8

description: Two technical replicas used to generate the data for SAMPLE 6.

source_name: Kidney Control male 8

tag: treatment

tag: tissue


title: Kid_Con_6

description: Four technical replicas used to generate the data for SAMPLE 4.

source_name: Kidney Control male 6


title: MycF/F,ERT2-Cre + Con Replicate 4

source_name: whole mouse liver

tag: genotype/variation

value: ko

tag: agent

value: control

value: whole liver

source_name: pooled whole mouse liver [reference RNA]

value: pooled whole liver

value: reference


title: Monocytes Control 14

description: Monocytes-derived transcriptome of Control patient from pair D

tag: infection

value: D


title: Kid_Con_7

description: Two technical replicas used to generate the data for SAMPLE 5.

source_name: Kidney Control male 7

tag: strain

value: BALB/c


title: Kid_Con_3

description: Two technical replicas used to generate the data for SAMPLE 3.

source_name: Kidney Control male 3

value: Kidney


title: Monocytes Infected 4

description: Monocytes-derived transcriptome of Infected patient from pair D

tag: patient type

value: Infected

tag: chip number

value: Mild

value: Mild chronic hepatitis E infection


title: Kid_Con_1

description: Four technical replicas used to generate the data for SAMPLE 1.

source_name: Kidney Control male 1

value: Control


title: Monocytes Infected 9

description: Monocytes-derived transcriptome of Infected patient from pair F

value: Monocytes

tag: patient number

tag: age (y)

value: M

value: F


title: Monocytes Control 5

description: Monocytes-derived transcriptome of Control patient from pair G

tag: Sex

tag: severity

value: G

value: monocyte


title: Monocytes Control 12

description: Monocytes-derived transcriptome of Control patient from pair F

tag: graft duration (months)

tag: pairing


title: Monocytes Control 16

description: Monocytes-derived transcriptome of Control patient from pair E

value: E

tag: hev load

tag: disease state


title: Whole Blood Infected 13

description: Whole_Blood-derived transcriptome of Infected patient from pair H

tag: sample type

value: Whole Blood

value: Moderate

value: H

value: Moderate chronic hepatitis E infection

value: whole blood


title: Monocytes Infected 8

description: Monocytes-derived transcriptome of Infected patient from pair E

tag: cell type


title: Monocytes Infected 1

description: Monocytes-derived transcriptome of Infected patient from pair A

value: A


title: Monocytes Infected 2

description: Monocytes-derived transcriptome of Infected patient from pair B

value: Severe

value: B

value: Severe chronic hepatitis E infection


title: Monocytes Infected 10

description: Monocytes-derived transcriptome of Infected patient from pair G

value: Infected


title: Monocytes Infected 3

description: Monocytes-derived transcriptome of Infected patient from pair C

value: C


title: Monocytes Infected 13

description: Monocytes-derived transcriptome of Infected patient from pair H

value: Monocytes


title: Whole Blood Control 15

description: Whole_Blood-derived transcriptome of Control patient from pair B

value: Control

tag: tissue


title: Monocytes Control 15

description: Monocytes-derived transcriptome of Control patient from pair B

value: F


title: Whole Blood Infected 9

description: Whole_Blood-derived transcriptome of Infected patient from pair F

value: M

value: Mild

value: Mild chronic hepatitis E infection


title: Kid_Con_2

description: Four technical replicas used to generate the data for SAMPLE 2.

source_name: Kidney Control male 2

value: BALB/c

tag: treatment

value: Kidney


title: Whole Blood Control 14

description: Whole_Blood-derived transcriptome of Control patient from pair D

value: Whole Blood

value: D


title: Whole Blood Control 12

description: Whole_Blood-derived transcriptome of Control patient from pair F

value: whole blood


title: Whole Blood Infected 10

description: Whole_Blood-derived transcriptome of Infected patient from pair G

value: Moderate

value: G

value: Moderate chronic hepatitis E infection


title: Whole Blood Control 16

description: Whole_Blood-derived transcriptome of Control patient from pair E

value: E


title: Whole Blood Infected 8

description: Whole_Blood-derived transcriptome of Infected patient from pair E

value: Infected


title: Whole Blood Control 7

description: Whole_Blood-derived transcriptome of Control patient from pair A

value: A


title: Whole Blood Control 11

description: Whole_Blood-derived transcriptome of Control patient from pair C

value: C


title: Whole Blood Control 6

description: Whole_Blood-derived transcriptome of Control patient from pair H

value: Control

value: H


title: Reference AF versus Reference AF-regular_batch 14 (aCGH)

city: Birmingham

first: Theresa

middle: V

last: Strong

state: AL

address: 1530 3rd Avenue South

department: Medicine

institute: University of Alabama at Birmingham

hyb_protocol: The 32K slides were prehybridized in 5x SCC, 0.1% SDS at 45 ºC for at least one hour, washed with ddH20 and dried using compressed dust-free air. The dried pellets from the labeling steps were re-suspended in 50 µl of hybridization solution (50% Formamide, 4% SDS, 10 %, Dextran Sulfate, M.W. 500 000, 2 X SSC) and denatured for 5 min at 95°C, followed by incubation at 45°C for 2 h to block repetitive sequences. Subsequently, the probe mixture was applied to the slide surface, covered with a lifterslip (22x60mm, Erie Scientific, Portsmouth, NH) and hybridized at 45°C for 48 hours in a slide chamber (Corning Inc. Life Sciences, Big Flats, NY). After hybridization the lifterslip was rinsed off using 1xPBS. Washing was performed in 25 % formamide, 2 X SSC, 0.1% SDS, at 45ºC, for 15 min, followed by 10 min in 1 X PBS at room temperature, and brief rinse in 0.2 X SSC. The array was immersed in deionized H2O and immediately dried using pressurized dust-free air.

scan_protocol: Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc, Union City, CA), and image analysis was carried out using the GenePixPro v6 software (Axon Instruments).

data_processing: We uploaded the GPR files from GenePix Pro into a pearl script called colloactor. This script links the information about clones to the array position. It also uploads the raw data to the BASE platform. Filtering and normalization was done using the LCB Data-WareHouse (dw.lcb.uu.se). The filters applied on the raw data removed spots containing more than 5% oversaturated pixels, spots with low Signal-to-Noise Ratio (SNR<3) and spots automatically and manually flagged as bad, absent or not found in GenePixPro program. Normalization was done using a print-tip loess method.  In the 44 tumor versus DNA samples, the value of missing values was estimated using the mean of the 2 adjacent clones.  Following estimation, clones with missing values in greater than 70% of the samples were filtered out.

source_name: Genomic DNA isolated from blood of subject AF

label_protocol: Labeling was done using 2 mcg DNA according to the BioPrime® Array CGH Genomic Labeling System protocol supplied by the manufacturer (Invitrogen, Carlsbad, CA). We used Cy3-dCTP and Cy5-dCTP (PA53021 and PA55021,  respectively; GE Healthcare, Piscataway, NJ). The labeled DNA probes were mixed together and combined with 200 µg human Cot-1 DNA (Invitrogen, Carlsbad, CA), and dried using a vacufuge concentrator (Eppendorf, Westbury, NY).

extract_protocol: Genomic DNA was isolated with phenol extraction according to the standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).

tag: gender

value: female

tag: age

value: blood

tag: race

value: African-American


title: Reference AF versus Reference F1-regular (aCGH)

source_name: Genomic DNA isolated from blood of subject F1

value: unknown

value: Caucasian


title: Reference AF versus Reference F1-dye swap (aCGH)


title: Expression data of Rad93

city: Bunkyo-ku

first: Toshiaki

last: Watanabe

state: Tokyo

department: Department of Surgical Oncology

institute: University of Tokyo

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Soute 5.0 (Scaling target 500), PerChip & PerGene normalized

source_name: Patient Rad93

label_protocol: Approximately 8 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Rectal cancers were immediately frozen in liquid nitrogen. Tissues were lysed and total RNA was isolated using RNeasy Mini Kit (QIAGEN, Chatswort,CA) according to the manufacturer's instructions.

value: Rectal Cancer

tag: response to preoperative chemoradiotherapy

value: Responder


title: Whole Blood Infected 4

description: Whole_Blood-derived transcriptome of Infected patient from pair D

value: Whole Blood

tag: infection

tag: patient type

tag: chip number

value: M

value: Mild

value: D

value: Mild chronic hepatitis E infection

value: whole blood


title: Whole Blood Infected 3

description: Whole_Blood-derived transcriptome of Infected patient from pair C

value: Infected

tag: patient number

tag: age (y)

tag: Sex

value: Severe

value: Severe chronic hepatitis E infection


title: Reference AF versus Reference AF-dye swap_batch 11 (aCGH)


title: Whole Blood Control 5

description: Whole_Blood-derived transcriptome of Control patient from pair G

value: Control

tag: severity

tag: graft duration (months)

tag: pairing

value: G


title: Expression data of Rad91

source_name: Patient Rad91


title: Reference AF versus Reference AF-regular_batch 11 (aCGH)

value: female

value: blood


title: Whole Blood Infected 2

description: Whole_Blood-derived transcriptome of Infected patient from pair B

tag: sample type

value: F

value: B

tag: hev load

tag: disease state


title: Expression data of Rad86

source_name: Patient Rad86

tag: tissue

value: Rectal Cancer

value: Non-responder


title: Whole Blood Infected 1

description: Whole_Blood-derived transcriptome of Infected patient from pair A

value: Whole Blood

value: Moderate

value: A

value: Moderate chronic hepatitis E infection


title: Tumor sample 202 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 202

tag: gender

value: breast (tumor)

tag: tumor grade

value: European-American

tag: diagnosis

value: invasive ductal carcinoma

tag: subtype

value: basal

tag: estrogen receptor

value: negative

tag: progesterone receptor

value: equivocal

value: African-American

value: reference


title: Tumor sample 201 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 201

value: female

tag: age

tag: race

value: luminal A

value: positive

value: blood


title: Expression data of Rad89

source_name: Patient Rad89

value: Rectal Cancer

tag: response to preoperative chemoradiotherapy

value: Non-responder


title: Expression data of Rad 97

source_name: Patient Rad 97

value: Responder


title: Tumor sample 197 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 197


title: Tumor sample 200 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 200


title: Expression data of B_179

source_name: Patient B_179


title: Tumor sample 199 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 199


title: Expression data of B_181

source_name: Patient B_181


title: Expression data of B_183

source_name: Patient B_183


title: Tumor sample 196 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 196

value: metastatic ductal carcinoma


title: Tumor sample 195 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 195


title: Expression data of B_173

source_name: Patient B_173


title: Expression data of B_170

source_name: Patient B_170


title: Tumor sample 194 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 194

source_name: Genomic DNA isolated from blood of subject AF


title: Expression data of B_168

source_name: Patient B_168


title: Expression data of B_175

source_name: Patient B_175


title: Tumor sample 190 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 190

value: luminal B


title: Expression data of B_166

source_name: Patient B_166


title: Tumor sample 142, rep2 (SNP)

hyb_protocol: Samples were hybridized for 16-18 hr and washed and stained on the GeneChip fluidics station 450 using the appropriate fluidics protocol.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 7G.

data_processing:
Genotyping Console 3.02 was used for data processing and GeneChip quality control.  Data quality control and data analysis was performed using Partek GS 6.4.  SNP calls were made using Birdseed V-2.  The following criteria were applied for quality control parameters:  Contrast QC>0.4, QC call rate >86%, SNP call rate >97% and MAPD<0.4.  Copy number calls of SNP 6.0 data were determined using a Hidden Markov Model and a minimum criterion of 50 markers was used to identify significant CNAs.

The CNA data are available as supplementary files of the GSE26232 record.

source_name: Genomic DNA isolated from breast of subject 142

label_protocol: Samples were end labeled using terminal deoxynucleotidyl transferase according to the Affymetrix protocol.

value: breast (tumor)


title: Tumor sample 193 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 193

value: European-American


title: Tumor sample 189 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 189

value: invasive ductal carcinoma


title: Expression data of B_164

source_name: Patient B_164


title: Tumor sample 202 (SNP)

source_name: Genomic DNA isolated from breast of subject 202

value: basal


title: Expression data of B_158

source_name: Patient B_158


title: Tumor sample 183 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 183

value: negative


title: Tumor sample 185 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 185

value: invasive mammary carcinoma with ductal and lobular features


title: Tumor sample 182 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 182

value: African-American


title: Expression data of B_153

source_name: Patient B_153


title: Tumor sample 129, rep2 (SNP)

source_name: Genomic DNA isolated from breast of subject 129

value: metastatic ductal carcinoma to the lymph nodes


title: Tumor sample 201 (SNP)

source_name: Genomic DNA isolated from breast of subject 201

value: female

value: equivocal


title: Oncostatin M replicate 3

city: Vienna

first: Martin

last: Bilban

institute: Medical University of Vienna

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol using a 7G scanner

data_processing: RMA normalization using Affymetrix Expression Console version 1.1

source_name: IMR90 cells

label_protocol: standard Affymetrix protocol with the Ambion WT Expression Kit

extract_protocol: RNeasy mini kit (Qiagen)

treatment_protocol: IMR90 cells stimulated with rh Oncostatin M (10 ng/mL)

tag: cell line

value: IMR90 primary lung fibroblast cells

tag: treatment


title: Expression data of B_149

source_name: Patient B_149


title: Tumor sample 199 (SNP)

source_name: Genomic DNA isolated from breast of subject 199


title: Tumor sample 200 (SNP)

source_name: Genomic DNA isolated from breast of subject 200


title: Tumor sample 116, rep2 (SNP)

label: bioitin

source_name: Genomic DNA isolated from breast of subject 116

value: invasive ductal carcinoma with focal mucinous features

value: positive


title: Tumor sample 195 (SNP)

source_name: Genomic DNA isolated from breast of subject 195


title: Expression data of 143Rad

source_name: Patient 143Rad

value: Rectal Cancer

value: Non-responder


title: Oncostatin M replicate 2

value: stimulated with rh Oncostatin M (10 ng/mL)


title: Tumor sample 120, rep2 (SNP)

source_name: Genomic DNA isolated from breast of subject 120

value: 30% ductal carcinoma in situ/20% Invasive ductal carcinoma/20% fibrocystic

value: luminal A


title: Tumor sample 181 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 181

value: breast (tumor)

source_name: Genomic DNA isolated from blood of subject AF

value: blood

value: reference


title: Tumor sample 196 (SNP)

source_name: Genomic DNA isolated from breast of subject 196

value: European-American

value: metastatic ductal carcinoma

value: basal

value: negative


title: Oncostatin M replicate 1


title: Tumor sample 180 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 180

value: female

value: African-American

value: metastatic lobular carcinoma


title: Control replicate 3

treatment_protocol: Untreated (Control)

value: IMR90 primary lung fibroblast cells

value: Untreated (Control)


title: Tumor sample 177 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 177

value: metastatic adenocarcinoma

value: positive


title: Tumor sample 189 (SNP)

source_name: Genomic DNA isolated from breast of subject 189

value: invasive ductal carcinoma

value: equivocal


title: Expression data of 137Rad

source_name: Patient 137Rad

value: Rectal Cancer

value: Responder


title: Tumor sample 172 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 172

value: breast (tumor)

value: blood


title: Tumor sample 197 (SNP)

source_name: Genomic DNA isolated from breast of subject 197

value: European-American

value: luminal A


title: Expression data of 135Rad

source_name: Patient 135Rad


title: Tumor sample 190 (SNP)

source_name: Genomic DNA isolated from breast of subject 190

value: luminal B


title: Tumor sample 185 (SNP)

source_name: Genomic DNA isolated from breast of subject 185

value: invasive mammary carcinoma with ductal and lobular features

value: basal

value: negative


title: Expression data of 136Rad

source_name: Patient 136Rad

value: Non-responder


title: Tumor sample 180 (SNP)

value: female

value: African-American

value: metastatic lobular carcinoma


title: Tumor sample 183 (SNP)

source_name: Genomic DNA isolated from breast of subject 183

value: positive


title: Tumor sample 168 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 168

value: invasive ductal carcinoma (ductal carcinoma in situ <10/0)

value: reference


title: Tumor sample 193 (SNP)

source_name: Genomic DNA isolated from breast of subject 193

value: invasive ductal carcinoma

value: equivocal


title: Control replicate 2

source_name: IMR90 cells

value: IMR90 primary lung fibroblast cells

value: Untreated (Control)


title: Tumor sample 170 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 170

value: breast (tumor)

value: blood


title: Tumor sample 177 (SNP)

value: metastatic adenocarcinoma

value: luminal A


title: Tumor sample 194 (SNP)

source_name: Genomic DNA isolated from breast of subject 194

value: European-American

value: basal


title: Expression data of 130Rad

source_name: Patient 130Rad

value: Rectal Cancer

value: Non-responder


title: Expression data of 131Rad

source_name: Patient 131Rad

value: Responder


title: Tumor sample 164 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 164

value: female

value: luminal B

value: negative

source_name: Genomic DNA isolated from blood of subject AF

value: African-American


title: Expression data of 128Rad

source_name: Patient 128Rad


title: Control replicate 1


title: gp130FF tumour tissue, rep 7

city: Singapore

first: Zhengdeng

last: Lei

address: 8 College Road

country: Singapore

institute: Duke-NUS graduate medical school

description: replicate 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina Genome Studio (QUANTILE_NORMALIZED_SUBSTRACT_BKG)

source_name: mouse tumour tissue

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

extract_protocol: Total RNA was extracted from the frozen tissues using the RNeasy Plus Mini Kit (Qiagen) and cDNA was prepared from 2 ug RNA using the High Fidelity cDNA synthesis kit (Applied Biosystems/Roche) according to the manufacturer's instructions

tag: strain

value: MIXED background (129/sv)

tag: genotype/variation

value: tumour tissue


title: Tumor sample 182 (SNP)

source_name: Genomic DNA isolated from breast of subject 182

value: invasive ductal carcinoma

value: positive


title: gp130FF tumour tissue, rep 8

description: replicate 8


title: Tumor sample 181 (SNP)

source_name: Genomic DNA isolated from breast of subject 181

value: breast (tumor)

value: equivocal


title: Tumor sample 172 (SNP)

source_name: Genomic DNA isolated from breast of subject 172


title: Expression data of 129Rad

source_name: Patient 129Rad


title: Tumor sample 163 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 163

value: ductal carcinoma

value: blood

tag: sample type

value: reference


title: Tumor sample 159 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 159

value: European-American


title: gp130FF tumour tissue, rep 5

description: replicate 5


title: Tumor sample 160 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 160

value: basal


title: gp130FF tumour tissue, rep 6

description: replicate 6


title: Expression data of 126 Rad

source_name: Patient 126 Rad

value: Rectal Cancer


title: Expression data of 124 Rad

source_name: Patient 124 Rad

value: Responder


title: Expression data of 122 Rad

source_name: Patient 122 Rad

value: Non-responder


title: gp130FF tumour tissue, rep 4

description: replicate 4


title: Tumor sample 168 (SNP)

source_name: Genomic DNA isolated from breast of subject 168

value: female

value: invasive ductal carcinoma (ductal carcinoma in situ <10/0)

value: luminal B


title: Tumor sample 150 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 150

value: negative

value: African-American


title: Tumor sample 156 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 156

value: invasive lobular carcinoma


title: Expression data of 121 Rad

source_name: Patient 121 Rad


title: gp130FF tumour tissue, rep 3

description: replicate 3

value: MIXED background (129/sv)

value: tumour tissue


title: Tumor sample 147 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 147

value: breast (tumor)

value: invasive ductal carcinoma, ductal carcinoma in situ 20/10

value: positive

source_name: Genomic DNA isolated from blood of subject AF


title: gp130FF tumour tissue, rep 2

description: replicate 2

source_name: mouse tumour tissue


title: Tumor sample 148 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 148

value: invasive ductal carcinoma

value: blood

value: reference


title: Tumor sample 170 (SNP)

source_name: Genomic DNA isolated from breast of subject 170

value: basal


title: Expression data of 120 Rad

source_name: Patient 120 Rad

value: Rectal Cancer


title: Expression data of 118 RCa

source_name: Patient 118 RCa

value: Non-responder


title: Tumor sample 142 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 142

value: female

value: European-American


title: gp130FF tumour tissue, rep 1

description: replicate 1


title: gp130FF unaffected antral tissue, rep 7

description: replicate 7

source_name: mouse unaffected antral tissue

value: unaffected antral tissue


title: Expression data of 116 RCa

source_name: Patient 116 RCa

value: Responder


title: Tumor sample 163 (SNP)

source_name: Genomic DNA isolated from breast of subject 163

value: African-American

value: ductal carcinoma

value: negative

value: equivocal


title: Tumor sample 138 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 138

value: breast (tumor)

value: metastatic ductal carcinoma to the lymph nodes

value: luminal A


title: gp130FF unaffected antral tissue, rep 8

description: replicate 8

value: MIXED background (129/sv)


title: Tumor sample 141 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 141

value: invasive ductal carcinoma

value: blood


title: Expression data of 115 RCa

source_name: Patient 115 RCa


title: gp130FF unaffected antral tissue, rep 5

description: replicate 5


title: Expression data of 114 Rad

source_name: Patient 114 Rad


title: gp130FF unaffected antral tissue, rep 6

description: replicate 6


title: Tumor sample 137 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 137

value: basal

value: reference


title: Tumor sample 159 (SNP)

source_name: Genomic DNA isolated from breast of subject 159

value: luminal B

value: positive


title: Tumor sample 160 (SNP)

source_name: Genomic DNA isolated from breast of subject 160

value: female


title: Tumor sample 164 (SNP)

source_name: Genomic DNA isolated from breast of subject 164

value: European-American


title: Tumor sample 150 (SNP)

source_name: Genomic DNA isolated from breast of subject 150


title: Expression data of 112 Rad

source_name: Patient 112 Rad

value: Rectal Cancer

value: Responder


title: Tumor sample 130 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 130

value: African-American

source_name: Genomic DNA isolated from blood of subject AF


title: Tumor sample 131 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 131

value: invasive ductal carcinoma, ductal carcinoma in situ (2%)


title: gp130FF unaffected antral tissue, rep 3

description: replicate 3

value: unaffected antral tissue


title: gp130FF unaffected antral tissue, rep 4

description: replicate 4


title: Expression data of 113 Rad

source_name: Patient 113 Rad


title: Expression data of 111 Rad

source_name: Patient 111 Rad

value: Non-responder


title: gp130FF unaffected antral tissue, rep 2

description: replicate 2

source_name: mouse unaffected antral tissue


title: Tumor sample 129 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 129

value: breast (tumor)

value: metastatic ductal carcinoma to the lymph nodes

value: negative


title: Tumor sample 127 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 127


title: Expression data of 110 Rad

source_name: Patient 110 Rad


title: Tumor sample 156 (SNP)

source_name: Genomic DNA isolated from breast of subject 156

value: invasive lobular carcinoma


title: gp130FF unaffected antral tissue, rep 1

description: replicate 1

value: MIXED background (129/sv)


title: Tumor sample 138 (SNP)

source_name: Genomic DNA isolated from breast of subject 138

value: luminal A


title: Tumor sample 126 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 126

value: lobular carcinoma

value: blood

value: reference


title: Tumor sample 142, rep1 (SNP)

source_name: Genomic DNA isolated from breast of subject 142

value: female

value: invasive ductal carcinoma

value: basal


title: gp130WT antral tissue, rep 8

description: replicate 8

source_name: mouse antral tissue

value: antral tissue


title: gp130WT antral tissue, rep 6

description: replicate 6


title: Tumor sample 122 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 122

value: European-American

value: mucinous carcinoma

value: positive

value: equivocal

value: African-American


title: Expression data of 109 Rad

source_name: Patient 109 Rad

value: Rectal Cancer

value: Responder


title: Tumor sample 141 (SNP)

source_name: Genomic DNA isolated from breast of subject 141

value: breast (tumor)

value: negative


title: Expression data of 108 Rad

source_name: Patient 108 Rad


title: Tumor sample 148 (SNP)

source_name: Genomic DNA isolated from breast of subject 148


title: gp130WT antral tissue, rep 7

description: replicate 7

value: MIXED background (129/sv)


title: Expression data of 107 Rad

source_name: Patient 107 Rad


title: Tumor sample 147 (SNP)

source_name: Genomic DNA isolated from breast of subject 147

value: invasive ductal carcinoma, ductal carcinoma in situ 20/10


title: gp130WT antral tissue, rep 5

description: replicate 5


title: Tumor sample 121 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 121

value: invasive mammary carcinoma with ductal features

value: luminal A

source_name: Genomic DNA isolated from blood of subject AF

value: blood


title: Tumor sample 137 (SNP)

source_name: Genomic DNA isolated from breast of subject 137

value: female

value: invasive ductal carcinoma


title: Tumor sample 120 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 120

value: 30% ductal carcinoma in situ/20% Invasive ductal carcinoma/20% fibrocystic

value: reference


title: Expression data of 106 Rad

source_name: Patient 106 Rad

value: Non-responder


title: gp130WT antral tissue, rep 3

description: replicate 3

value: antral tissue


title: Expression data of 105 Rad

source_name: Patient 105 Rad


title: Tumor sample 130 (SNP)

source_name: Genomic DNA isolated from breast of subject 130

value: metastatic ductal carcinoma to the lymph nodes

value: basal

value: equivocal


title: gp130WT antral tissue, rep 4

description: replicate 4


title: Tumor sample 116 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 116

value: African-American

value: invasive ductal carcinoma with focal mucinous features

value: luminal B

value: positive


title: Wild Type Mice fed high fat diet 2

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Wild Type Mice fed high fat diet

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained using Standard protocol.

scan_protocol: Affymetrix High-throughtput scanner standard protocol

data_processing: Data was normalized by a robust multi-chip analysis (RMA).

source_name: Liver

label_protocol: Affymetrix standard methods were applied using the high throughput protocal for PM arrays

extract_protocol: total RNA was extracted using Trizol Protocol.

tag: genotype

value: Wild Type

value: high fat diet

value: male

value: liver


title: Wild Type Mice fed high fat diet 1

description: Wild Type Mice fed high fat diet


title: Expression data of K104

source_name: Patient K104

value: Rectal Cancer


title: gp130WT antral tissue, rep 2

description: replicate 2

source_name: mouse antral tissue

value: MIXED background (129/sv)


title: PML Knockout Mice fed Low Fat Diet 3

description: PML Knockout Mice fed Low Fat Diet

value: PML Knockout

value: Low Fat Diet


title: Tumor sample 126 (SNP)

source_name: Genomic DNA isolated from breast of subject 126

value: female

value: breast (tumor)

value: European-American

value: lobular carcinoma

value: luminal A

value: negative


title: Tumor sample 127 (SNP)

source_name: Genomic DNA isolated from breast of subject 127

value: African-American

value: metastatic ductal carcinoma to the lymph nodes


title: Tumor sample 129, rep1 (SNP)

source_name: Genomic DNA isolated from breast of subject 129

value: basal


title: Expression data of K102_2

source_name: Patient K102

value: Non-responder


title: Tumor sample 115 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 115

value: invasive ductal carcinoma

value: blood

value: reference


title: Tumor sample 112 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 112

value: invasive lobular carcinoma

value: positive

value: equivocal


title: PML Knockout Mice fed Low Fat Diet 2

description: PML Knockout Mice fed Low Fat Diet

value: PML Knockout

value: Low Fat Diet

value: male

value: liver


title: Tumor sample 131 (SNP)

source_name: Genomic DNA isolated from breast of subject 131

value: female

value: breast (tumor)

value: European-American

value: invasive ductal carcinoma, ductal carcinoma in situ (2%)

value: luminal B


title: Tumor sample 120, rep1 (SNP)

value: African-American

value: 30% ductal carcinoma in situ/20% Invasive ductal carcinoma/20% fibrocystic

value: luminal A


title: gp130WT antral tissue, rep 1

description: replicate 1

value: MIXED background (129/sv)

value: antral tissue


title: Tumor sample 122 (SNP)

source_name: Genomic DNA isolated from breast of subject 122

value: mucinous carcinoma

value: negative


title: mock 2

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: replicate 2

data_processing: The data were preprocessed by Bioconductor lumi package (version 2.2.1). It was background adjusted, vst transformed and rsn normalized. Probes that did not have a detection p-value < 0.01 in all of the mock-transfected replicates were excluded from further analysis.

source_name: HEK293T cells

growth_protocol: HEK293T cells were grown in DMEM according to ATCC recommendations.

extract_protocol: Cells were harvested  24 hours post transfection, and the miRNAs and their bound targets were isolated using streptavidin myOne C1 Dynabeads. Beads were washed before RNA extraction using an RNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: 200pmols of synthetic biotin-labeled miRNA duplexes were transfected into HEK293T cells using HiPerFect Transfection Reagent (Qiagen).

tag: transfection molecule

value: mock

tag: pull-down


title: Tumor sample 104 versus AF (aCGH)

source_name: Genomic DNA isolated from breast of subject 104

tag: gender

tag: tissue

value: invasive ductal carcinoma & associated ductal carcinoma in situ

value: basal

source_name: Genomic DNA isolated from blood of subject AF

value: blood

value: reference


title: PML Knockout Mice fed Low Fat Diet 1

description: PML Knockout Mice fed Low Fat Diet

value: PML Knockout

value: Low Fat Diet

value: male

value: liver


title: mock 3

description: replicate 3


title: mock 1

description: replicate 1


title: Wild Type Mice fed high fat diet 3

description: Wild Type Mice fed high fat diet

value: Wild Type

value: high fat diet


title: Wild Type Mice fed Low fat diet 2

description: Wild Type Mice fed Low fat diet

value: Low fat diet


title: miR-182 1

description: replicate 1

value: pull-down


title: PML Knockout Mice fed High Fat Diet 1

description: PML Knockout Mice fed High Fat Diet

value: High Fat Diet


title: miR-182 2

description: replicate 2