Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MicroRNA profiling of different adipose tissues and muscles

ABSTRACT: Purpose: The goals of this study are to compare microRNA profiling in different adipose tissues and muscles using microRNA arrays. Methods: Tissue microRNA profiles of 2-3-month old mice were generated by using miRCURYâ¢ LNA microRNA Array. The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission. Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been calculated the median. We use Median Normalization Method to obtain âNormalized Dataâ, Normalized Data = (Foreground-Background) Â/ Âmedian, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. Results and conclusion: The miRNA expression profiling was completed on our samples. The profiling identified a subset of the total number of miRNAs analyzed by the miRCURYâ¢ array that are differentially expressed in brown adipose tissue, inguinal adipose tissue, epidydimal adipose tissue, gastrocnemius muscle, and soleus muscle. Tissue microRNA profiles of 2-3-month old mice were generated by microarray, using miRCURYâ¢ LNA Array.

ORGANISM(S): Mus musculus

SUBMITTER: Hao Ying

PROVIDER: E-GEOD-81976 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

microRNA profiling of different adipose tissues and muscles

Project description:Purpose: The goals of this study are to compare microRNA profiling in different adipose tissues and muscles using microRNA arrays. Methods: Tissue microRNA profiles of 2-3-month old mice were generated by using miRCURY™ LNA microRNA Array. The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission. Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been calculated the median. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data = (Foreground-Background) / median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. Results and conclusion: The miRNA expression profiling was completed on our samples. The profiling identified a subset of the total number of miRNAs analyzed by the miRCURY™ array that are differentially expressed in brown adipose tissue, inguinal adipose tissue, epidydimal adipose tissue, gastrocnemius muscle, and soleus muscle.

2016-05-28 | GSE81976 | GEO

Analysis of miRNA expression profiling in 3 samples(normal, cigarette smoking and lung cancer population's serum)

Project description:Using the highly sensitive miRNA array, we determined the serum miRNAs profiles of 10 non-smokers, 10 smokers and 10 lung cancer patients by miRCURY LNA™ microRNA Arrays. Differential expressed miRNAs were further validated in a larger scale samples. We found that let-7i-3p and miR-154-5p were significantly downregulation in serum of smokers and lung cancer patients. The serum level of let-7i-3p and miR-154-5p is associated with smoking and smoking-related lung cancer. In this study, we mix 10 samples with equal volume of each group(non-smoking control group,smoking group and lung cancer group ) and run RNA extractions. And then miRCURYTM LNA Array (v.16.0) was applied in the studying of miRNA expression profile and its alteration to gain the miRNA expression profile to compare the variety between each two groups respectively.

2014-06-17 | E-GEOD-58540 | biostudies-arrayexpress

Impaired adipose-neuronal crosstalk in obesity

Project description:Label-free LC-MS/MS was used to characterise and quantify the secretory profiles of murine perivascular adipose tissue, canonical white adipose tissue, and brown adipose tissue.

2022-11-15 | PXD031271 | Pride

MicroRNA response to Snail overexpression in lung cancer cell lines

Project description:Analysis of four lung cancer cell lines transfected with a vector expressing the transcriptional repressor Snail versus a vector control. Aberrant Snail expression is known to induce an EMT program in lung cancers. Four lung cancer cell lines (H292, H358, H441, H1437) with stable overexpression of the human SNAI1 gene and vector expressing controls were collected at equal confluency with the miRNeasy Mini kit (Qiagen). One microgram of total RNA was labeled using miRCURY LNA™ microRNA Array Power Labeling kit by the UCLA Clinical Microarray Core. The labeled miRNAs were hybridized to Exiqon miRCURY LNA microRNA Array-6th Generation according to the manufacturer’s instructions. This array includes 927/648/351 human/mouse/rat miRNAs as well as 438 miRPlus miRNAs. The miRNA array slides were scanned using Axon GenePix 4000B scanner (Axon Instruments, Foster City, CA) and processed by using the GenePix Pro 6.0 software (Axon Instruments). The raw data were normalized by using a combination of housekeeping miRNA, spike-in miRNA and invariant endogenous miRNAs.

2013-07-17 | E-GEOD-48922 | biostudies-arrayexpress

miRNA profile of rat vascular smooth muscle cell stimulated by 2.6 mM high-phosphate

Project description:We compared time-series miRNA expression profile in high-phosphateM-bM-^@M-^Sstimulated rat vascular smooth muscle cells at 0, 3, and 12 hr respectively. Total RNA of rat VSMCs stimulated with 2.6 mM inorganic phosphate for 0, 3 or 12 hr was harvested by the Trizol method (Invitrogen) or use of the miRNeasy mini kit (QIAGEN). The samples were labeled by use of the miRCURYM-bM-^DM-" Hy3M-bM-^DM-"/Hy5M-bM-^DM-" Power labeling kit and hybridized on the miRCURYM-bM-^DM-" LNA Array (v.16.0) (Exiqon, Denmark). After washing slides were scanned by use of the Axon GenePix 4000B microarray scanner. Expressed data were normalized by the Median normalization method, and then relative fold change at each time was detected by level of fluorescence in the phosphate-treated group normalized to that in the control group. Finally, hierarchical clustering was performed for miRNA expression profiling. Student t test was used to compare differences between 2 groups, and a 1.5-fold change was considered significant.

2012-07-27 | E-GEOD-39700 | biostudies-arrayexpress

miRNA expression profile in subcutaneous adipose tissue from morbid obese patients

Project description:To evaluate wether miRNA expression patterns contributes to obesity total RNA were purified from subcutaneous adipose tissue (SAT)and used in miRNA microarrays. Platform contain LNA-modified probes for all human miRNAs present in release 8.2 of the miRBase microRNA Registry. Two RNA pools from 3 non obese men (CM) and from 5 non obese women (CW) were used as controls. Expression profiling revealed that a large set of miRNAs is expressed in SAT. Forty two miRNAs changed by at least 1.5 folds in 17/20 obese subjects versus non obese control pool. Particularly, 21/42 were up-regulated and 21/42 were down-regulated. Among the differentially expressed miRNA, miR-519d, miR-498 and miR-150 were up-regulated, miR-659 and miR-371-3p_MM2 were down-regulated consistently in 20/20 obese subjects. To search for miRNAs eventually associated with obesity we used a microarray to evaluate the expression of 1458 different miRNAs in 10 obese women (OBW) and 10 obese men (OBM). Two RNA pools from 3 non obese men (CM) and from 5 non obese women (CW) were used as controls.

2010-06-25 | E-GEOD-12726 | biostudies-arrayexpress

MicroRNA Expression Profile of serum exosomes from Bortezomib-resistant and Bortezomib-response patients in multiple myeloma

Project description:MicroRNA microarray profilling analysis was performed on exosomes derived from serum in patients with myeloma in two conditions of therapeutic efficacy, Bortezomib resistance and Bortezomib response. Bortezomib is approved and widely used treating myeloma. Two kinds of sample were analyzed. MicroRNA microarray profilling analysis (using miRCURY LNA microRNA Array, 7th generation REV - hsa, mmu & rno, mirBase release 18, ProductNumber=208520,208521,208522) was performed on exosomes derived from serum in patients with myeloma in two conditions of therapeutic efficacy, Bortezomib resistance and Bortezomib response.

2016-07-31 | E-GEOD-71435 | biostudies-arrayexpress

miRNA and consolidation of cued fear memory

Project description:miRNA profiling was carried out using the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno) miRNA were profiled in amygdala brain tissue obtained from adult mice 30 mins after auditory fear conditioning and expression levels compared to tissue obtained from Home cage controls Adult male mice were fear conditioned using tone-shock pairings and brains were harvested 30 mins later. The brains of Home Cage controls and Fear Conditioned animals (n = 4/group) were then punched to collect amygdala tissue. miRNA were extracted using the Qiagen miRNeasy Kit, and then shipped to Exiqon. Exiqon performed labeling, hybridization and data analysis after use of the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno). https://www.exiqon.com/ls/Documents/Scientific/miRCURY-LNA-microRNA-Array-6th-gen-hsa-mmu-rno-manual.pdf

2014-09-30 | E-GEOD-59072 | biostudies-arrayexpress

miRNA microarray analysis to explore the expression profiles of miRNAs using the same liver tissues of NFD-fed mice and HFD-fed mice

Project description:The miRNA microarray analysis was performed to explore the expression profiles of miRNAs using the same liver tissues of NFD-fed mice and HFD-fed mice  Summary: An abstract of the experiment and the data analysis.  Project Description: Sample and experiment information.  Array Information: miRCURY™ LNA expression array information.  Data Analysis for miRNAs: 1. Low intensity filtering and data normalization: After low intensity miRNAs filtering, raw signal intensities are normalized in Median method. (miRNAs that intensities>=30 in all samples are chosen for calculating normalization factor) 2. Quality assessment of miRNA data after filtering: Contains box plot, Correlation Matrix and scatter plot for miRNAs after normalization. 3. Differentially expressed miRNAs screening: Contains significant differentially expressed miRNAs that pass Volcano Plot filtering. (Fold Change>=1.5, P-value<=0.05) 4. Heat map and hierarchical clustering: Hierarchical clustering on the significant differentially expressed miRNAs that passed Volcano Plots filtering.  Sample RNA Quality Control: Sample quality control data file from Nanodrop 1000 spectrophotometer and standard denaturing agarose gel electrophoresis.  Methods: A brief introduction for microarray, experiment, and data analysis.  FAQ: Frequently asked question Additional miRNA Array Analysis (charge an extra fee):  Prediction Analysis for Microarrays (PAM analysis)  miRNA Target Gene Prediction and Functional Analysis Additional files provided:  Graphs (*.jpg)  Raw Intensity File(*.xls, raw miRNAs signal intensity)  Layout File (*.gal, the files contain information on the positioning of the capture probes on the array and microRNA annotations for your species of interest)  Raw data files produced by GenePix Pro 6.0

2022-11-23 | E-MTAB-8731 | biostudies-arrayexpress

Differentially expressed miRNAs in liver among NFD, LSF and HSF groups

Project description:The miRNA microarray analysis was performed to explore the expression profiles of miRNAs using the same liver tissues of NFD, LSF and HSF groups Summary: An abstract of the experiment and the data analysis. Project Description: Sample and experiment information. Array Information: miRCURY™ LNA expression array information. Data Analysis for miRNAs: 1. Low intensity filtering and data normalization: After low intensity miRNAs filtering, raw signal intensities are normalized in Median method. (miRNAs that intensities>=30 in all samples are chosen for calculating normalization factor) 2. Quality assessment of miRNA data after filtering: Contains box plot, Correlation Matrix and scatter plot for miRNAs after normalization. 3. Differentially expressed miRNAs screening: Contains significant differentially expressed miRNAs that pass Volcano Plot filtering. (Fold Change>=1.5, P-value<=0.05) 4. Heat map and hierarchical clustering: Hierarchical clustering on the significant differentially expressed miRNAs that passed Volcano Plots filtering. Sample RNA Quality Control: Sample quality control data file from Nanodrop 1000 spectrophotometer and standard denaturing agarose gel electrophoresis. Methods: A brief introduction for microarray, experiment, and data analysis. FAQ: Frequently asked question Additional miRNA Array Analysis (charge an extra fee): Prediction Analysis for Microarrays (PAM analysis) miRNA Target Gene Prediction and Functional Analysis Additional files provided: Graphs (*.jpg) Raw Intensity File(*.xls, raw miRNAs signal intensity) Layout File (*.gal, the files contain information on the positioning of the capture probes on the array and microRNA annotations for your species of interest) Raw data files produced by GenePix Pro 6.0

2022-11-24 | E-MTAB-9168 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data