Capra hircus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA207763 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR891531.fastq.gz | Fastqsanger.gz | |||
| SRR891532.fastq.gz | Fastqsanger.gz | |||
| SRR891533.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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.
2012-12-23 | E-GEOD-37456 | biostudies-arrayexpress
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 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:Identification of Conserved and Novel MicroRNAs in Cashmere Goat (Capra hircus) by Deep Sequencing
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Project description:Capra hircus breed:Tibetan cashmere goat Transcriptome or Gene expression
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Project description:Capra hircus (goat) Transcriptome or Gene expression
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Project description:Capra hircus breed:Shaanbei White Cashmere Goat Raw sequence reads
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Project description:Capra hircus breed:Shaanbei White Cashmere Goat Raw sequence reads
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Project description:Cashmere, also known as soft gold, is produced from secondary hair follicles in Cashmere goats and it’s therefore of significance to investigate the molecular profiles during Cashmere goat hair follicle development. However, our current understanding of the machinery underlying Cashmere goat hair follicle remains largely unexplored and researches regarding hair follicle development mainly used the mouse as a research model. To provides comprehensively understanding on the cellular heterogeneity and cell lineage cell fate decisions, we performed single-cell RNA sequencing on 19,705 single cells from induction (embryonic day 60), organogenesis (embryonic day 90) and cytodifferentiation (embryonic day 120) stage fetus Cashmere goat dorsal skin. Unsupervised clustering analysis identified 16 cell clusters and their corresponding cell types were also successfully characterized. Based on cell lineage inference, we revealed detailed transcriptional gene expression profiles during dermal and epidermal lineage cell fate decisions. These works together delineate unparalleled molecular profiles of different cell populations during Cashmere goat hair follicle morphogenesis and provide a valuable resource for identifying biomarkers during Cashmere goat hair follicle development.
2020-10-18 | GSE144351 | GEO
Project description:Capra hircus Hair follicle stem cells Raw sequence reads
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