GEO DataSets

(Submitter supplied) The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL18437

6 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Sus scrofa

Type:

Expression profiling by array; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL10945 GPL11429 GPL18437

14 Samples

Download data: TXT

(Submitter supplied) The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: XLSX

(Submitter supplied) The physiological, biochemical and functional difference of oxidative and glycolytic muscles play important roles in human metabolic health as well as in meat quality of animal. To explore this aspect, we firstly provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptome for PMM (psoas major muscle; oxidative) and LDM (longissimus dorsi muscle; glycotic) in this study. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10945

2 Samples

Download data: XLS

(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) The biochemical and functional differences between oxidative and glycolytic muscles affect human muscle health and animal meat quality, but the epigenetic regulation with respect to lncRNAs and circRNAs remains largely unknown. Here, we employed porcine oxidative and glycolytic skeletal muscles, at growth curve inflection point, to survey variant global lncRNAs and circRNAs expression using RNA-seq. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22475

6 Samples

Download data: XLSX

(Submitter supplied) Gene expression data of micro RNA from skeletal muscle sample of pig breed Duroc and Pietrain at adult stage.

Organism:

Sus scrofa; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL16384

20 Samples

Download data: CEL

(Submitter supplied) We performed a comparative genome-wide methylation analysis of longissimus dorsi muscles between the Japanese Black (Wagyu) and Chinese Red Steppes cattle, which exhibit significant differences in meat quality traits. This will allow us to better understand the correlation between DNA methylation variants and meat quality traits.

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

6 Samples

Download data: BW

(Submitter supplied) MicroRNAs (miRNAs) are small non-coding RNAs that can regulate the expression of their target genes at post-transcriptional level. Skeletal muscle comprises different fiber types that can be broadly classified as red, intermediate and white fiber types. Recently, a set of miRNAs were identified to be expressed on a fiber type-specific manner between red and white fiber types. Nonetheless, an integral explanation of the miRNA transcriptome differences in all three fiber types is long overdue. more...

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10945

3 Samples

Download data: XLS

(Submitter supplied) Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. more...

Organism:

Gallus gallus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL9385

2 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL14602 GPL17021

21 Samples

Download data: WIG

(Submitter supplied) Purpose: The goal of this study was to compare the genome-wide promoter methylation alterations in macrophages and endothelial cells during hindlimb ischemia among normal, hyperlipidemic and type-2 diabetic mice. Methods: Unilateral hindlimb ischemia was induced by ligating femoral artery proximal to the bifurcation of superficial and deep femoral artery in mice deficient of LDL receptor and expressing only apolipoprotein B100 (LDLR-/-ApoB100/100, C57BL/6J background) (The Jackson Laboratory, Bar Harbor,USA) and mice with β-cell specific over-expression of insulin-like growth factor-2 in atherosclerotic background (IGF-II/LDLR-/-ApoB100/100, C57BL/6J background) with type 2 diabetic features on high-fat diet (TD 88173, Harlan Teklad: 42% of calories from fat and 0.15% from cholesterol, no sodium cholate) 8 weeks prior to surgery and continued throughout the study 1. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TXT

(Submitter supplied) Objective: To define the role of epigenetics, particularly DNA methylation in adaptive vascular growth in hyperlipidemic and type 2 diabetic mouse models of hind limb ischemia Methods: Unilateral hindlimb ischemia was induced by ligating femoral artery proximal to the bifurcation of superficial and deep femoral artery. DNA was isolated from ischemic muscles collected at day 7 after ischemia induction using DNeasy Tissue kit (Qiagen). more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL14602

3 Samples

Download data: WIG

(Submitter supplied) Background: Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach. more...

Organism:

Sus scrofa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: BED

(Submitter supplied) Background Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach. more...

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL10162

6 Samples

Download data: TXT

(Submitter supplied) Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, the landscape of lncRNAs is largely unclear in Sus scrofa. Here we performed stranded RNA-seq on total RNA libraries from over 100 samples of Sus scrofa tissues. We identified 10,813 lncRNAs in Sus scrofa, of which 9,075 are novel. 57% of these lncRNAs were conserved in both human and mouse. These conserved lncRNAs tend to be more tissue-specific than pig-specific lncRNAs, and enriched in reproducible organs (i.e. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10945 GPL11429

13 Samples

Download data: FA, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

111 Samples

Download data: BED

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

42 Samples

Download data: BED

(Submitter supplied) Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

52 Samples

Download data: TXT

(Submitter supplied) Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. Utilizing RNA Sequencing, this study characterized the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Gluteobiceps (GB), Gluteus medius (GM), Rectus femoris (RF), Supraspinatus (SS), Longissimus lumborum (LL), Adductor (AD) and Psoas major (PS).

Organism:

Ovis aries

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15670

36 Samples

Download data: TXT