Capra hircus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA273650 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1772681.fastq.gz | Fastqsanger.gz | |||
| SRR1772682.fastq.gz | Fastqsanger.gz | |||
| SRR1772683.fastq.gz | Fastqsanger.gz | |||
| SRR1772684.fastq.gz | Fastqsanger.gz | |||
| SRR1772685.fastq.gz | Fastqsanger.gz |
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Project description:Discovery of novel and differentially expressed microRNAs between fetal and six month old skeletal muscle in goat
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Project description:Enzootic nasal adenocarcinoma (ENA), an epithelial tumor induced in goats and sheep by enzootic nasal tumor virus (ENTV), is a chronic, progressive, contact sexually transmitted disease. This study aimed to identify novel and differentially expressed miRNAs in the tumor and para-carcinoma nasal tissues of Nanjiang yellow goats with ENA. Small RNA Illumina high-throughput sequencing was used to construct a goat nasal miRNA library; 406 known miRNAs and 29 novel miRNAs were identified. A total of 116 miRNAs were significantly differentially expressed in para-carcinoma nasal tissues and ENA (54 downregulated; 60 upregulated; 2 only expressed in control group); Target gene prediction and functional analysis revealed that 6176 non-redundancy target genes, 1792 significant GO and 97 significant KEGG pathway for 121 miRNAs (116 significant expression miRNAs and 5 star sequence) were predicted. GO and KEGG pathway analysis revealed the majority of target genes in ENA are involved in cell proliferation, signal transduction and other processes associated with cancer. This is the first large-scale identification of miRNAs in Capra hircus ENA and provides a theoretical basis for investigating the complicated miRNA-mediated regulatory networks involved in the pathogenesis and progression of ENA.
2016-01-25 | GSE65305 | GEO
Project description:The domestic goat, Capra hircus (2n=60), is one of the most important domestic livestock species in the world. Here we report its high quality reference genome generated by combining Illumina short reads sequencing and a new automated and high throughput whole genome mapping system based on the optical mapping technology which was used to generate extremely long super-scaffolds. The N50 size of contigs, scaffolds, and super-scaffolds for the sequence assembly reported herein are 18.7 kb, 3.06 Mb, and 18.2 Mb, respectively. Almost 95% of the supper-scaffolds are anchored on chromosomes based on conserved syntenic information with cattle. The assembly is strongly supported by the RH map of goat chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Rapidly evolving genes and gene families are enriched in metabolism and immune systems, consistent with the fact that the goat is one of the most adaptable and geographically widespread livestock species. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study not only provides a high quality reference genome for an important livestock species, but also shows that the new automated optical mapping technology can be used in a de novo assembly of large genomes. We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues(Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DEG analysis. Corresponding whole genome sequencing is available in NCBI BioProject PRJNA158393.
2012-12-23 | GSE37456 | GEO
Project description:The domestic goat, Capra hircus (2n=60), is one of the most important domestic livestock species in the world. Here we report its high quality reference genome generated by combining Illumina short reads sequencing and a new automated and high throughput whole genome mapping system based on the optical mapping technology which was used to generate extremely long super-scaffolds. The N50 size of contigs, scaffolds, and super-scaffolds for the sequence assembly reported herein are 18.7 kb, 3.06 Mb, and 18.2 Mb, respectively. Almost 95% of the supper-scaffolds are anchored on chromosomes based on conserved syntenic information with cattle. The assembly is strongly supported by the RH map of goat chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Rapidly evolving genes and gene families are enriched in metabolism and immune systems, consistent with the fact that the goat is one of the most adaptable and geographically widespread livestock species. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study not only provides a high quality reference genome for an important livestock species, but also shows that the new automated optical mapping technology can be used in a de novo assembly of large genomes. Corresponding whole genome sequencing is available in NCBI BioProject PRJNA158393. We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues (Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DGE analysis. This submission represents RNA-Seq component of study.
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Project description:Identification of Conserved and Novel MicroRNAs in Cashmere Goat (Capra hircus) by Deep Sequencing
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Project description:Identify differentially expressed genes between two development stages in Xuhuai goat skeletal muscle through RNA-Sequencing
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Project description:The study confirmed a batch of goat skin and hair follicles miRNA, by high-throughput sequencing methods.316 sequences miRNAs were obtained by the means of analysis and we confirmed the authenticity of 68 known miRNAs and discovered 248 novel miRNAs, as well as 22 miRNAs that haven’t been reported before. Through the miRNAs family analysis, we found the co-expressed miRNAs in goat and sheep located in the same region of chromosome, which may play an essential role in skin and follicle development. In addition, the prediction of novel target miRNAs followed by the analysis of target gene pathways indicated that MAPK pathway may have an important effect to the fast growth of skin follicle cell.
2012-02-25 | GSE36052 | GEO
Project description:The study confirmed a batch of goat skin and hair follicles miRNA, by high-throughput sequencing methods.316 sequences miRNAs were obtained by the means of analysis and we confirmed the authenticity of 68 known miRNAs and discovered 248 novel miRNAs, as well as 22 miRNAs that havenM-bM-^@M-^Yt been reported before. Through the miRNAs family analysis, we found the co-expressed miRNAs in goat and sheep located in the same region of chromosome, which may play an essential role in skin and follicle development. In addition, the prediction of novel target miRNAs followed by the analysis of target gene pathways indicated that MAPK pathway may have an important effect to the fast growth of skin follicle cell. We sequenced a mixed sample which contains three goat skin in anagen of cashmere
2012-02-25 | E-GEOD-36052 | biostudies-arrayexpress
Project description:Molecular mechanisms of follicular atresia and prolificacy of mammal remain unclear. We surveyed the single-cell transcriptomic landscape of ovaries from single and prolificacy goat and identified seven ovarian cell types with distinct gene-expression, transcriptional factor networks and reciprocal interactions signatures. In-depth dissection of gene-expression dynamics of granulosa cells (GCs) that displayed development stage-specific expression patterns and specific gene signatures were identified that may reflect developmental competency and ovarian reserve. what’s more, we revealed the origin of theca cells. Further analysis of cell-type-specific prolificacy-associated transcriptional changes uncovered apoptosis, anabolism and response to hormone stimulation as are crucial factor in dominant follicle development and ovulation. Additionally, differentially expressed genes (DEGs) of SERPINE2 can interact with CYP19A1 to promote cell proliferation, inhibit apoptosis and promoting the anabolism were observed in mouse granulosa cells. Thus, our work provides a comprehensive understanding of the cell-type-specific mechanisms underlying goat ovarian prolificacy at single-cell resolution, provides key insights into offers important clues for improving follicle recruitment in vivo and revealing new diagnostic biomarkers and potential therapeutic targets for ovulation disorder.
2024-06-29 | GSE206398 | GEO
Project description:Molecular mechanisms of follicular atresia and prolificacy of mammal remain unclear. We surveyed the single-cell transcriptomic landscape of ovaries from single and prolificacy goat and identified seven ovarian cell types with distinct gene-expression, transcriptional factor networks and reciprocal interactions signatures. In-depth dissection of gene-expression dynamics of granulosa cells (GCs) that displayed development stage-specific expression patterns and specific gene signatures were identified that may reflect developmental competency and ovarian reserve. what’s more, we revealed the origin of theca cells. Further analysis of cell-type-specific prolificacy-associated transcriptional changes uncovered apoptosis, anabolism and response to hormone stimulation as are crucial factor in dominant follicle development and ovulation. Additionally, differentially expressed genes (DEGs) of SERPINE2 can interact with CYP19A1 to promote cell proliferation, inhibit apoptosis and promoting the anabolism were observed in mouse granulosa cells. Thus, our work provides a comprehensive understanding of the cell-type-specific mechanisms underlying goat ovarian prolificacy at single-cell resolution, provides key insights into offers important clues for improving follicle recruitment in vivo and revealing new diagnostic biomarkers and potential therapeutic targets for ovulation disorder.
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