Expression profiles of circRNAs in goat skeletal muscle development
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ABSTRACT:
PROVIDER: PRJNA827782 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18791614_1.fastq.gz | Fastqsanger.gz | |||
| SRR18791614_2.fastq.gz | Fastqsanger.gz | |||
| SRR18791615_1.fastq.gz | Fastqsanger.gz | |||
| SRR18791615_2.fastq.gz | Fastqsanger.gz | |||
| SRR18791616_1.fastq.gz | Fastqsanger.gz |
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Project description:To explore functional circRNAs during goat muscle development, we systematically investigated the circRNAs profiles using high throughput transcriptome sequencing technology (RNA-seq) at key developmental stages of fetus and Kid in Haimen goat.
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Project description:The goal of this study was to compare the transcriptome profiles (RNA-seq) of fetal and six month old goat in skeletal muscle. Total RNAs from the Chinese Xuhuai goat longissimus thoracis at fetal and six month old stages were used to construct cDNA libraries for Solexa SBS technology sequencing. After remove reads with adapters, reads in which unknown bases were more than 5% and low quality reads, we obtained 27,512,850 clean reads from the fetal caprine (FC) library and 27,582,908 clean reads from the six month old caprine (SMC) library. The total basepairs were 2,476,156,500 for FC and 2,482,461,720 for SMC. The ratio of clean reads mapped to reference genome was 45.43% for FC and 33.73% for SMC. The ratio of reads mapped to reference gene was 47.77% for FC and 34.03% for SMC. To reveal the molecular events during different development stages, genes that differentially expressed between the two libraries were identified. Clean reads that matched reference genes in each library were used to evaluate the expression level of transcripts. In total, 11663 genes were differentially expressed between the two development stages. There were 5134 genes with at least a two-fold difference in expression between FC and SMC libraries (FDR, 0.001), of which 1070 genes were up-regulated, 4064 were down-regulated in the six month old caprine compared to the fetal caprine muscle tissue, and 4911 were expressed in both library. Genes with less than one fold changes between FC and SMC libraries were excluded from further analysis. The results indicated that there were significant difference between the two development phase in gene-expression. In addition, some muscle related genes such as MyoD, Myf5, Myogenin, Mrf4, myosin heavy chain 3 (MYH3), Myoglobin and DLK1 were differentially expressed.
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Project description:This study was to identify circRNAs responsible for muscle atrophy. Skeletal muscle wasting is a common clinical feature of many chronic diseases and also occurs in response to acute events. Circular RNAs are covalently closed RNA transcripts that are involved in various physiological and pathological processes. However, the underlying mechanisms of circRNAs implicated in muscle atrophy remains unknown. Global circRNA expression profiling indicated that many circRNAs are involved in the pathophysiological processes of muscle atrophy.
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Project description:In the present study, RNA-seq technique was used to compare the expression profiles of circRNAs from goat endometrium samples at gestational day 5 (pre-receptive endometrium, PE) and day 15 (receptive endometrium, RE). A total of 21,813 circRNAs were identified in goat endometrium, of which only 31.22% (6,810) circRNAs were co-expressed at both stages, and 5,925 circRNAs were identified specifically in RE and 9,078 in PE, suggesting high stage specificity in the circRNAs in dairy goats. Further analysis found that there were 334 DECs (differentially expressed circRNAs) in RE compared to PE (P< 0.05), and circRNA8077 was up-regulated with the highest FPKM value in RE. It was noteworthy that half of the up-regulated circRNAs with top 10 highest FPKM value in RE were come from CRIM1. Moreover, GO and KEGG analysis of the hgDEGs (hosting genes of DECs) revealed some circRNAs, genes and pathways that may involve in the formation of the receptive endometrium in dairy goats. In a word, our data provided an endometrium circRNA expression atlas related to the biology of the goat receptive endometrium during embryo implantation, and the results suggested that a subset of circRNAs might involve in the processes of the formation and development of endometrial receptivity.
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