GEO DataSets

(Submitter supplied) Although the well-known importance of pig in agriculture, as well as a model for human biology, the miRNA catalog of pig has been largely undefined. Identification and preliminary characterization of adipose- and muscle-specific miRNAs would be a prerequisite for a thorough understanding of their roles in regulating adipose deposition and muscle growth. In the present study, we get insight into the miRNA transcriptome in eight adipose tissues, two skeletal muscles and cardiac muscle of pig using deep sequencing technology, and to elucidate their characteristic tissue-specific profiles and genomic context.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10945

11 Samples

Download data

(Submitter supplied) It is evident that epigenetic factors, especially DNA methylation, play essential roles in obesity development. To learn systematic association of DNA methylation to obesity, we used pig as a model, and sampled eight diverse adipose tissues and two distinct skeletal muscle tissues from three pig breeds with distinguished fat levels: the lean Landrace, the fatty Rongchang, and the feral Tibetan pig. We sequenced 180 methylated DNA immunoprecipitation (MeDIP) libraries, generated 1,381 Gbp sequence data, and provided a genome-wide DNA methylation map for pig adipose and muscle studies. The analysis showed global similarities and differences between breeds, genders and tissues, and identified the differentially methylated regions (DMRs) that are preferentially located in intermediate CpG promoters and CpG island shores. The DMRs in promoters are highly associated to obesity development. We also analyzed methylation and regulation of the known obesity-related genes and predicted novel candidate genes. The comprehensive map here provides a solid base for exploring epigenetic mechanisms of adipose deposition and muscle growth.

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11429

180 Samples

Download data: WIG

(Submitter supplied) Obese and lean-type pig breeds show obvious differences in adipose deposition and muscle growth; however, the molecular mechanisms underlying this phenotypic variation remains unclear. Landrace (a leaner, Western breed), Rongchang (a fatty, Chinese breed) and Tibetan (a feral, indigenous Chinese breed that has not undergone artificial selection) pig breeds were used in this study. We collected eight diverse adipose tissues and two phenotypically distinct skeletal muscle tissues from three well-defined pig models with distinct fat rates, and studied mRNA expression differences among breeds, males and females, and tissues. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL10162

180 Samples

Download data: TXT

(Submitter supplied) MicroRNAs are a class of molecular regulators found to participate in numerous biological processes, including adipogenesis. However, whether dietary changes impact on microRNA (miRNA) in ruminants has not been reported. Therefore, this study aimed to evaluate the dietary effect on miRNA expression in subcutaneous (backfat) and visceral fat depots (perirenal fat) from beef steers fed with different diets containing high or low fat levels. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by array

Platform:

GPL15110

32 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of this study is to explore the role of miRNAs in dairy cow response to E. coli and S. aureus, mastitis causing pathogens, is not well understood. Results: The global expression of miRNAs in bovine mammary epithelial cells (MAC-T cells) challenged with heat-inactivated Staphylococcus aureus (S. aureus) or Escherichia coli (E. coli) bacteria (treatments: 6, 12, 24 and 48 hr) and without challenge (control: 0, 6, 12, 24 and 48 hr) was profiled using next-generation-sequencing. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17875

13 Samples

Download data: TXT

(Submitter supplied) Using Next Generation Sequencing (NGS) we profiled miRNA expression in the retina and choroid during degenerative and NV phases of oxygen-induced retinopathy (OIR).

Organism:

Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20084

12 Samples

Download data: XLSX

(Submitter supplied) DNA methylation is a key epigenetic modification in mammals, have essential and important roles in muscle development. Here, using cattle as a model, we investigate the systematic association between DNA methylation and muscle development. We sample longissimus thoracis tissues from a famous elite native breed of Chinese Qinchuan cattle living within comparable environments under fetal and adult stages. more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL15749

2 Samples

Download data: WIG

(Submitter supplied) Purpose: MicroRNAs (miRNAs) are non-coding small miRNA ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and theses difference are programmed during prenatal muscle development.To shed directly light on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: XLS

(Submitter supplied) MicroRNAs (miRNAs) are small non-coding RNAs found to regulate several biological processes including adipogenesis. Understanding adipose tissue regulation is critical for beef cattle as fat is an important determinant of beef quality and nutrient value . This study analyzed the association between genomic context characteristics of miRNAs with their expression and function in bovine adipose tissue. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by array

Platform:

GPL15110

24 Samples

Download data: TXT

(Submitter supplied) miRNA profiles were investigated in severely obese individuals before and after a weight loss induced by diet and moderate exercise.

Organism:

Mus musculus cytomegalovirus 2; Betapolyomavirus macacae; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus hominis; Mus musculus; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Merkel cell polyomavirus; Human alphaherpesvirus 2; Murid gammaherpesvirus 4

Type:

Non-coding RNA profiling by array

Platform:

GPL11434

24 Samples

Download data: PDF, TXT

(Submitter supplied) Purpose: Porcine alveolar macrophage was infected by T. gondii including Rh strain and Me49 strain. We want to explore the change of miRNAs after infected with T. gondii in porcine alveolar macrophages. Results: Our study generated six mi RNA expression profiles from macrophages which infect with Rh strain and Me49 and control group in different time. Compare with T. gondii-infected and uninfected with T. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19176

6 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) play an important role in the regulation of gene expression and are often dysregulated in disease. The recent development of the CRISPR-Cas9 gene-editing system, composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA), allows researchers to direct DNA cleavage at a predetermined site and to conduct genome-scale knockout screens. To determine the functional role of miRNAs in cancer, we designed and constructed a library of 7,382 sgRNAs to target 85% of the 1,881 annotated human miRNA stem-loops. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

5 Samples

Download data: CSV

(Submitter supplied) Twenty-four triple-negative breast cancer and 14 adjacent normal tissues were collected from breast cancer patients during surgeries at National Taiwan University Hospital (NTUH, Taipei, Taiwan). All triple-negative breast cancer samples were invasive ductal carcinomas (IDC) and were negative in immunohistochemical statuses of ER, PR, and HER2 receptors, as confirmed by professional pathologists. Treatment procedure of all patients followed the National Comprehensive Cancer Network (NCCN) guideline. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13393

38 Samples

Download data: TXT

(Submitter supplied) To identify miRNAs involved in muscle development, three independent small RNA libraries from porcine skeletal muscle at the age of 63d、98d and 161d were constructed. A total of 4105184， 4606375 and 5113984 mappable small RNA sequences were generated in the three small RNA libraries, respectively, and 887 known and 472 new candidate miRNAs were obtained.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11429

3 Samples

Download data: TXT

(Submitter supplied) Gene expression data of micro RNA of pig, in the first part of this study, they were analysed for correlation of transcripts levels with body weight and meat quality grade traits

Organism:

synthetic construct; Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

209 Samples

Download data: CEL

(Submitter supplied) We report the application of Illumina short RNA sequencing for characterization and discovery of miRNAs and moRNAs in two Italian Large White pig backfat tissue.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10945

2 Samples

Download data: TSV, TXT

(Submitter supplied) Whole genome microRNA microarray expression profiling was employed as a discovery platform to identify microRNAs dysregulated in end-stage idiopathic pulmonary arterial hypertension (IPAH) patients. Lung tissue from seven IPAH patients and eight failed donor controls were subjected to microarray screening. Twenty-one miRNAs were identified dyeregulated in IPAH patients compared to controls. In miRNA real-time PCR validation, 22 IPAH patients and 22 control subjects were enrolled, including the 7 IPAH and 8 controls in microarray screening. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL18402

15 Samples

Download data: TXT

(Submitter supplied) To investigate the role of miRNA in the placental development, we analyzed miRNA expression profiles in the first and third trimester human placentas. Total RNA was isolated from 12 placentas (6 from first trimester and 6 from third trimester). miRNA expression profiles were determined by Affymetrix GeneChip 2.0 miRNA Microarray.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL14613

12 Samples

Download data: CEL, CHP

(Submitter supplied) Objective: Potential regulators of adipogenesis include microRNAs (miRNAs), small non-coding RNAs that have been recently shown related to adiposity and differentially expressed in fat depots. However, to date no study is available regarding the relationship of miRNAs expression profile, biological pathway and cellular phenotype during human adipogenesis. Thereby, the aim of this study was to investigate whether miRNA expression profile in human adipocytes is related to adipogenesis and to test whether miRNA profile in human subcutaneous adipose tissue is associated to human obesity and co-morbidities. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL7731

28 Samples

Download data: TXT

(Submitter supplied) Objective: Potential regulators of adipogenesis include microRNAs (miRNAs), small non-coding RNAs that have been recently shown related to adiposity and differentially expressed in fat depots. However, to date no study is available regarding the relationship of miRNAs expression profile, biological pathway and cellular phenotype during human adipogenesis. Thereby, the aim of this study was to investigate whether miRNA expression profile in human adipocytes is related to adipogenesis and to test whether miRNA profile in human subcutaneous adipose tissue is associated to human obesity and co-morbidities. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL7731

18 Samples

Download data: TXT