Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1022840 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26246232.fastq.gz | Fastqsanger.gz | |||
| SRR26246233.fastq.gz | Fastqsanger.gz | |||
| SRR26246234.fastq.gz | Fastqsanger.gz | |||
| SRR26246235.fastq.gz | Fastqsanger.gz | |||
| SRR26246236.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this microarray experiment was to validate the Del-Mar 14K Chicken Integrated Systems Microarray for different chicken tissues and to determine the utility of this chicken cDNA microarray for other closely related and more distant avian species. The Del-Mar 14 K array was constructed from cDNAs amplified from EST clones sequenced from five normalized chicken cDNA libraries derived from neuroendocrine (5,929), abdominal fat (4,800), liver (2,635), skeletal muscle (2,398), reproductive tract (2,008), 387 long (70mer) oligonucleotides and 72 quality control spots. The array contains 17,770 cDNA clones, where protein matches were found by BlastX analysis for 68% of chicken contigs and 46% of singleton sequences represented on the array. A reference RNA design was used for the hybridization of total RNA from four chicken tissues (liver, abdominal fat, breast muscle and hypothalamus) and the cross-species hybridization (CSH) of total RNA from tissue from birds representing four orders of the Class Aves [Galliformes (chicken, Coturnix quail and domestic turkey), Anseriformes (Peking duck), Falconiformes (American kestrel) and Passeriformes (American tree sparrow)]. A reference RNA pool was made from an equal amount of high-quality total RNA extracted from chicken liver, abdominal fat, breast muscle and hypothalamus. Each of the 43 microarrays was co-hybridized with Cy3-labeled cDNA targets from one of the avian tissue samples and Cy5-labled cDNA targets from the reference chicken RNA pool. Loess-normalized data were used to determine the number of cDNAs expressed in chicken tissues and the number of genes (cDNAs) detectable by cross-hybridization with various avian tissue samples. The Cy5-labeled reference samples were used to determine the coefficient of variation across the 43 microarrays. This study shows a remarkably high level of cross hybridization of Cy3-labeled cDNA targets from a wide range of avian species to the Del-Mar 14K microarray, where 38 to 62% of the cDNA probes on the chicken array (genes) were detectable. Keywords: Transcriptional profiling, Del-Mar 14K Chicken Integrated Systems Microarray validation, multi-tissues, cross-species hybridization, class Aves
2007-11-12 | GSE9500 | GEO
Project description:Gut microbiome - Chicken Abdominal Fat Deposition
| PRJNA704780 | ENA
Project description:Background: Yellow catfish (Pelteobagrus fulvidraco) is one of the important aquaculture species in China. In recent years, due to the high breeding density, the increasing frequency of feeding, and the excessive addition of feed fat, the excessive deposition of body fat in cultured yellow catfish has become more frequent. MicroRNAs (miRNAs) are an important gene expression regulatory signal molecule that regulates liver fat synthesis and transport and play an important role in fat deposition. However, there is a little research on the mechanism of fatty liver caused by excessive deposition of liver fat. Results: After 60 days of high-fat stress, the growth and feed conversion rate of hybrid yellow catfish (Pelteobagrus fuIvidraco♀×P. vachelli♂) were significantly inhibited, and hepatosomatic index, viscerosomatic index, hepatic triglyceride and cholesterol, and red lipid droplets in liver tissues were increased. Through high-throughput sequencing, we constructed miRNA libraries of high-fat stress at 60d, identified 346 conserved miRNAs and 410 novel miRNAs, among which 13 differentially expressed miRNAs were screened between high-fat diet group and normal-fat diet group. Also, we constructed mRNA transcriptome libraries after high-fat stress. Potential target genes for differentially expressed miRNAs were identified by bioinformatics analysis. Seven miRNA-mRNA pairs were screened. The expression of differential miRNA and mRNA and potential binding sites were analyzed by qRT-PCR and dual luciferase assay. Hybrid yellow catfish could promote the oxidative degradation of liver glucose, reduce fatty acid peroxidation, regulate antioxidant enzyme activity and response of immune and inflammatory to relieve fat deposition and liver stress. Conclusions: The disorders of fat metabolism in liver not only result in feed wastage, increase metabolic burden of yellow catfish, but also cause immune function damage, resulting in a variety of nutritional diseases. The development of this study is to understand the molecular mechanism of hepatic fat deposition in yellow catfish. It has important biological significance for improving protection of liver against stress and healthy culture.
2020-07-17 | GSE117401 | GEO
Project description:we collected tissues of subcutaneous fat and longissimus dorsi (LD) muscle from individuals that have divergent of backfat thickness and intramuscular fat content, and have similar age and body weight. The transcriptomic and proteomic data were gained using RNA-Seq and TMT to identify the key genes and pathways that specifically regulate the subcutaneous fat and intramuscular fat deposition in Dingyuan pig.
2022-04-04 | PXD027061 | Pride
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression. Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 7-week-old chicken leg muscle tissues, and the other group consisted of dwarf recessive White Rock 7-week-old chicken leg muscle tissues. The control samples were labeled as A1b, A2b, A3b, and the dwarf chicken samples were labeled as B1b, B2b, and B3b. 9 total chickens per breed, 3 chickens used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system. REPLACE This submission represents the miRNA profiling component of the study.
2012-04-17 | E-GEOD-37367 | biostudies-arrayexpress
Project description:The prevalence of obesity and overweight is steadily rising, posing a significant global challenge for humanity. The fundamental cause of obesity and overweight lies in the abnormal accumulation of adipose tissue. While numerous regulatory factors related to fat deposition have been identified in previous studies, a considerable number of regulatory mechanisms remain unknown. tRNA-derived small RNAs (tsRNAs), a novel class of non-coding RNAs, have emerged as significant regulators in various biological processes. In this study, we obtained small RNA sequencing data from subcutaneous white adipose tissue and omental white adipose tissue of lean and obese pigs. In addition, we similarly obtained tsRNAs profiles from scapular brown adipose tissue (BAT), inguinal white adipose tissue (iWAT) and epididymal white adipose tissue (eWAT) of normal mice. Finally, we successfully identified a large number of expressed tsRNAs in each tissue type and identified tsRNAs conserved in different adipose tissues of pigs and mice. These datasets will be a valuable resource for elucidating the epigenetic mechanisms of fat deposition.
2023-06-20 | GSE235087 | GEO