Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12915625_1.fastq.gz | Fastqsanger.gz | |||
| SRR12915625_2.fastq.gz | Fastqsanger.gz | |||
| SRR12915626_1.fastq.gz | Fastqsanger.gz | |||
| SRR12915626_2.fastq.gz | Fastqsanger.gz | |||
| SRR12915627_1.fastq.gz | Fastqsanger.gz |
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Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.
2019-12-20 | GSE123869 | GEO
Project description:The swamp eel or rice field eel (Monopterus albus) taxonomically belongs to the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, Vertebrata). It is not only an economically important freshwater fish in aquacultural production, but also an increasingly known model species for biological studies. Understanding molecular mechanisms underlying sex change is a major area of interest. The swamp eel thus offers a powerful system for studying sexual development and adaptive evolution in vertebrates.The whole genome sequencing provides valuable resources for sex control in fish production, species protection through manipulating sex reversal genes, and potentially enabling effective population control and promoting reproduction health in human. High throughput sequencing was employed for three samples,three kind s of sex gonad from swamp eel, testis,ovotestis and ovary, no replicates.
2016-07-03 | E-GEOD-43649 | biostudies-arrayexpress
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:Assay for Targeting Accessible-Chromatin with high-throughout sequencing of Swamp buffalo
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Project description:Small RNA sequencing Analysis of muscle and adipose in Chinese swamp buffalo
| PRJNA488005 | ENA
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:Buffalo breeding has become an important branch of beef cattle industry. It is of great significance to study buffalo meat production and meat quality. However, the important role of mRNA and lncRNA molecules in muscle stem cells (MuSCs) development in buffalo has not been explored. Then, we performed mRNA and lncRNA expression profiling analysis on the proliferation and differentiation of MuSCs in buffalo. The results showed that there were 4,820 differentially genes, 12,227 mRNAs, and 1,352 lncRNAs. These differentially expressed mRNAs are enriched in biological processes such as cell cycle, p53 signaling pathway, RNA transport, and Calcium signaling pathway and others. We also identified a number of genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the role of mRNA and lncRNA expression in the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.
2021-07-28 | GSE164808 | GEO