Cattle Adipose RNA-Seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB71475 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
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2024-05-10 | PXD020518 | Pride
Project description:While genetic markers related to meat production traits have been identified in many other breeds of cattle, research on weight in Hanwoo cattle (Korean native cattle) has been relatively limited. In this study, we performed expression quantitative trait loci (eQTL) analysis and differential gene expression analysis to detect candidate genes influencing the weight characteristics of 32 castrated Hanwoo cattle across 22 tissues and identify variants that affect gene expression levels. In total, we identified a total of 2,465 differentially expressed genes, among which we discovered key genes such as UBD, RGS2, FASN, and SCD that have functions related to adipogenesis, body weight, obesity, and lipid metabolism. Gene-set enrichment analysis revealed that candidate genes in adipose tissue are involved in metabolic pathways related to Obesity-related traits, adipose metabolism, and lipid metabolism. Additionally, we found that decreased expression of TRIM31 contributes to weight gain which can be explained by the associated candidate cis-eQTL genotypes for TRIM31 and their effect on differential gene expression between the lower and higher weight groups. Our findings revealed candidate genes associated with the weight of Hanwoo cattle and perhaps can provide comprehensive insights into the association of weight with various tissues beyond adipose tissue and muscle, indicating the potential for expanding the focus of livestock trait research.
2024-03-21 | E-MTAB-13398 | biostudies-arrayexpress
Project description:The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDRM-bM-^IM-$0.001 AND |log2Ratio|M-bM-^IM-%1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds. Three Luxi and three Angus cattle that were eighteen months of age were generated by RNA-Seq
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Project description:Adipose tissue plays essential roles in adapting to harsh environmental conditions in Mongolian cattle. To dig out the cellular and molecular mechanism of adipose tissue taking part in the tolerance of rough feeding, cold temperature and disease of Mongolian cattle, here, we applied single-nucleus RNA-seq to map the landscape of cell types and profiles of transcriptome of adipose tissues at different anatomical depots at single-nucleus resolution. The entire adipogenic trajectory from preadipocyte commitment to mature adipocytes was analyzed. The results showed that the existence of different adipocyte subpopulations at subcutaneous, perirenal and greater omentum for which acting as a storage depot for body energy to protect vital organs and to insulate the body against heat loss.The interaction between macrophages and adipocytes and as an endocrine and immunologically active organ to regulate systemic energy and metabolism homeostasis and to modulate T cell activity and subsequent adipose tissue inflammation through antigen presentation of adipocytes to T cells.The data provide a powerful resource for future hypothesis-driven investigations of the mechanisms of adipocyte differentiation and adipose tissue plasticity.
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Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research. The custom aCGH chips that interrogated the whole genome CNVs were build for 90 cattles from diverse breeds, with Hereford L1 Dominette 01449 as refference sample.
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Project description:In this study, we use mRNA-Seq to characterize and compare the leukocyte transcriptomes of Holstein, Jersey, and Cholistani with respect to variations in sequence, expression, and splicing. Poly A+ RNA are extracted from leukocytes of pools of blood drawn from cows of three different breeds, Holstein, Jersey, and Cholistani. The objective of the study is to compare sequence variation and gene expression of the three cattle breeds.
2013-07-02 | E-GEOD-48487 | biostudies-arrayexpress
Project description:Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis revealed breed-specific frequency differences and reflected aspects of the known ancestry of these cattle breeds. Selected CNVs were further validated by independent methods using qPCR and FISH. Approximately 67% of the CNVRs (119/177) completely or partially span cattle genes and 61% of the CNVRs (108/177) directly overlap with segmental duplications. The CNVRs span about 400 annotated cattle genes that are significantly enriched for specific biological functions such as immunity, lactation, reproduction and rumination. Multiple gene families, including ULBP, have gone through ruminant lineage-specific gene amplification. We detected and confirmed marked differences in their CNV frequencies across diverse breeds, indicating that some cattle CNVs are likely to arise independently in breeds and contribute to breed differences. Our results provide a valuable resource beyond microsatellites and single nucleotide polymorphisms to explore the full dimension of genetic variability for future cattle genomic research.
2010-03-03 | GSE19866 | GEO
Project description:The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA-Seq to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in both Chinese Luxi and Angus beef cattle. More than 9,243,921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (FDR≤0.001 AND |log2Ratio|≥1). Among the DGEs, we determined that 147 genes were down-regulated and 85 genes were up-regulated. GO and Pathway analysis were performed to analyze the biological role of the DGEs and determine their contribution to the differences seen in muscle growth and development between local Chinese Luxi cattle and the introduced Angus cattle. This article suggests that RNA-Seq is a useful tool for predicting differences in gene expression between Luxi and Angus beef cattle; moreover, our result provides unprecedented resolution of mRNAs that are expressed across the two breeds.
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