Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing Analysis of adipose in six month calf Chinese swamp buffalo

ABSTRACT: Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Three small RNA libraries were constructed. A total of 32762032 raw reads were obtained from adipose groups, respectively. After filtering the adaptor and low quality reads, 32054381 clean reads were retained. In total, 623 miRNAs were identified.

ORGANISM(S): Bubalus bubalis

PROVIDER: GSE171146 | GEO | 2021/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Small RNA sequencing Analysis of muscle and adipose in Chinese swamp buffalo

Project description:Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Six small RNA libraries were constructed. A total of 66,128,645 and 70,974,347 raw reads were obtained from muscle and adipose groups, respectively. After filtering the adaptor and low quality reads, 60,765,257 and 67,327,095 clean reads were retained. In total, 721 miRNAs were identified.

2021-08-27 | GSE119064 | GEO

Comparative transcriptome analysis in adipose and muscle between Chinese buffalo and cattle.

Project description:Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. To identify transcripts with potential regulatory role in lipid accumulated in muscle tissue, RNA sequencing was performed to compare the mRNAs, lncRNAs, and circRNAs expression patterns in the longissimus dorsi muscle and back fat between Chinese buffalo and cattle. Results: A total of 12 cDNA libraries were constructed. A total of 925,441,106 and 512,507,068 raw reads were obtained from buffalo and cattle, respectively. After filtering the adaptor and low quality reads, 909,040,352 and 491,967,820 clean reads were retained. In total, 19,917 mRNAs, 43,975 lncRNAs, and 10,701 circRNAs were identified in buffalo and 19,383 mRNAs, 8,265 lncRNAs, and 18,535 circRNAs were identified in cattle.

2020-10-20 | GSE139102 | GEO

Activation of skeletal ChREBP increases IMFlevel in mice and Broiler Chickens

Project description:Intramuscular fat (IMF) content is one of the key factors affecting meat quality. Carbohydrate response element binding protein (ChREBP) can promote glucose metabolism and fat synthesis by activating the expression of glycolysis and lipogenesis-related genes, but its function and regulatory mechanism in IMF are still unclear. This study evaluated the correlation between TG content and ChREBP expression level in muscles of different species to reveal the relationship between ChREBP and IMF. RNA-seq analysis showed that overexpressing ChREBP in C2C12 cells can significantly up-regulate fatty acid synthesis pathways, while significantly down-regulate the expression levels of muscle development pathways and related genes. In vivo, we found that overexpression of ChREBP or activation by fructose significantly increased the triglyceride content of the tibialis anterior muscle (TA) and the IMF content of yellow feather chicken leg and breast muscle in mice. And lipidomics data also found that feeding fructose can change the lipid composition of yellow feather broiler breast muscle and improve the flavor substances. This study demonstrated that ChREBP is a key gene regulating IMF deposition, providing a new target for genetic selection and nutritional regulation of IMF content.

2024-08-08 | GSE228899 | GEO

miRNA expression data from bulls with high and low intramusclar fat (IMF) content

Project description:Intramuscular fat content is a known trait that attributes to meat quality, taste and juiciness. MicroRNAs have been reported to play key role in lipid metabolism, hence in fat deposition. There is little understanding of miRNA regulation of IMF content and identification of these non-coding factors is important for further understanding of pathways involved in intramuscular fat deposition Differentially expressed miRNAs were identified and their gene targets predicted.

2020-03-28 | GSE147622 | GEO

Transcriptome Profiling of Longissimus Dorsi Muscle of Donkeys with High and Low Intramuscular Fat Content

Project description:The content of intramuscular fat (IMF) is closely related to meat quality traits. In this study, in order to explore the candidate genes related to IMF content, the longissimus dorsi muscle of Guangling donkey was measured for intramuscular fat content. According to its intramuscular fat content, it was divided into two groups, the low fat group (L , N=3) and high-fat group (H, n=3), using RNA-seq to identify differentially expressed genes (DGEs) on the longissimus dorsi muscle tissue of Guangling donkey with high and low intramuscular fat content to reveal the possibility Gene network and metabolic pathways that help increase intramuscular fat content. A total of 167 DEGs (|log2Fold Change|>=1 and FDR<0.05) were detected in the high (H) and low (L) groups of Guangling donkeys, of which 64 were up-regulated genes and 103 were down-regulated genes. The GO enrichment and KEGG pathway analysis showed that these differential genes were enriched in several biological processes and pathways related to adipocyte differentiation, lipid biosynthesis, and neutral lipid metabolism. These results will help to further explore the molecular mechanism of IMF deposition in donkeys and provide a theoretical basis for the molecular breeding of Guangling donkeys.

2021-09-01 | GSE156840 | GEO

Transcriptome profiling of the intramuscular fat content in Longissimus dorsi between Angus and Chinese Simmental cattle

Project description:The intramuscular fat (IMF) content of different beef cattle breeds varies greatly, which plays an important role in taste and nutritional value. However, the molecular mechanism of fat metabolism and deposition in beef cattle is still not very clear. In this study, the meat quality traits of Angus cattle and Chinese Simmental cattle were compared, the transcriptome of the longissimus dorsi muscle (LD) between Angus cattle and Chinese Simmental cattle was then analyzed to identify key genes related to fat metabolism and adipogenesis by high-throughput RNA-seq technology. In the current study conducted a comprehensive analysis on the transcriptome of the longissimus dorsi muscle (LD) of Angus and Simmental cattle, and identified differentially expressed genes related to lipid metabolism，which may have a great impact on on the formation of IMF.

2022-04-30 | GSE171876 | GEO

Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects

Project description:Intramuscular fat (IMF) storage is a biological process with strong impact on nutritional and technological properties of meat, and also with relevant consequences on human health. The genetic architecture of IMF content and composition phenotypes has been thoroughly studied in pigs through the identification of quantitative trait loci (QTL) and the estimation of genetic parameters. A question that has not been elucidated yet is if the genetic determinants of IMF-related phenotypes are muscle specific or, conversely, they have broad effects on the whole skeletal muscle compartment. We have addressed this question by generating lipid QTL maps for two muscles with a high commercial value, gluteus medius (GM) and longissimus thoracis et lumborum (LTL), in a Duroc commercial population (N=350). As a complementary approach, we have analysed the mRNA expression pattern of both muscles at a whole genome scale. The lack of concordance between the GM and LTL QTL maps evidenced that the effects of polymorphisms influencing IMF, cholesterol and fatty acids contents are modulated to some extent by complex spatial factors related with muscle location, metabolism and function. This interpretation was supported by our finding that genes influencing cell differentiation, muscle development and function and lipid metabolism are differentially expressed between muscles. These results have important implications on the implementation of genomic selection schemes aimed to improve the lipid profile of swine meat. Moreover, they confirm pigs as a valuable model to dissect the genetic basis of muscle lipid phenotypes of clinical interest in human. Longissimus thoracis et lumborum muscle tissue from 10 high and 9 low fattening Duroc pigs were compared in this study.

2010-12-01 | E-GEOD-25708 | biostudies-arrayexpress

Gene expression profiling in a Duroc/Landrace pig population differing in intramuscular fat content

Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays

2013-01-01 | E-GEOD-12927 | biostudies-arrayexpress

RNA sequencing data from pigs with high and low intramuscular fat content.

Project description:Intramuscular fat (IMF) content in pork is an important element of consumer preference, and is positively correlated with meat quality, including tenderness and juiciness. With advances in RNA sequencing technologies, transcriptome-related differences can be associated with specific traits in animals. The objective of this study was to investigate the differentially expressed genes (DEG) closely related with IMF content in porcine longissimus muscle using RNA sequencing. A total of 107 Berkshire pigs were used for IMF content measurements and significant difference between extremely high (H, n=3) and low (L, n=3) IMF content groups was found (P < 0.0001). From multi-dimensional scaling analyses, it was observed that the relationships between H and L groups were similar to each other. Here, we identified a total of 134 genes that were differentially expressed between the groups (FDR < 0.05, and FC ≥ 2). Functional analyses with DEGs revealed that the lipid metabolism (SCD and FASN) was one of the significant biological processes related with IMF content determination. In addition, we also found that DEGs related with muscle regeneration (MYOG and VEGFA) and extracellular matrix (COL1A1, COL1A2, COL5A1, COL14A1, and COL15A1) were changed between individuals with the extreme IMF contents, interestingly. These results will aid in understanding the regulation of IMF contents in pigs.

2017-06-15 | GSE86086 | GEO

Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA-sequencing

Project description:Intramuscular fat (IMF) content is an important trait closely correlated with meat quality, which is highly variable among swine breeds from diverse genetic backgrounds. In order to elucidate the molecular mechanism underlying porcine meat quality, we adopted RNA-sequencing to detect transcriptome in the longissimus dorsi muscle of Wei pigs (a Chinese indigenous breed) and Yorkshire pigs (a Western lean-type breed) with different IMF content. A total of 717 differentially expressed genes (DEGs) were identified in our study, with 323 up-regulated and 394 down-regulated genes in Wei pigs compared with Yorkshire pigs. GO analysis showed that DEGs significantly related to muscle proliferation and development, lipid storage and catabolic, extracellular matrix structural constituent, and neutral amino acid transmembrane transporter activity. Pathway analysis revealed that DEGs associated with fatty acid metabolism, steroid biosynthesis, glycerophospholipid metabolism, protein digestion and absorption, and amino acid metabolism. Quantitative real time PCR confirmed the differential expression of 11 selected DEGs from both pig breeds. The results provide useful information to investigate the transcriptional profiling in skeletal muscle of different pig breeds with divergent phenotypes, and several DEGs can be taken as functional candidate genes for affecting pork quality.

2017-05-20 | GSE99092 | GEO

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