Ontology highlight
ABSTRACT:
PROVIDER: PRJNA689238 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13342275.fastq.gz | Fastqsanger.gz | |||
| SRR13342276.fastq.gz | Fastqsanger.gz | |||
| SRR13342277.fastq.gz | Fastqsanger.gz | |||
| SRR13342278.fastq.gz | Fastqsanger.gz | |||
| SRR13342279_1.fastq.gz | Fastqsanger.gz |
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Project description:Inner Mongolia Cashmere goat Genome sequencing and assembly
| PRJNA1104404 | ENA
Project description:Background: Inner Mongolia is a major raw-cashmere-producing province in China, Inner Mongolia cashmere goat harbors three types —Erlangshan, Aerbasi and Alashan. Nearly 700,000 Aerbasi cashmere goats are fed per year, and meat production is nearly 10,000 tons. However, there are no reports on the meat of this goat. To better understand the molecular variations underlying intramuscular fat (IMF) anabolism and catabolism in Inner Mongolian cashmere goat, the proteomic differences between the biceps femoris (BF) and longissimus dorsi (LD) were investigated by label-free strategy. Then, the proteins were verified by western blot analysis as being involved in IMF anabolism and catabolism. Results: The IMF content was significantly higher in the BF than in the LD, suggesting that IMF is accumulated more in the BF or metabolized more in the LD. We performed proteomic analysis of IMF anabolism and catabolism at the proteomic level, and 1209 proteins were identified in the BF (high-IMF) and LD (low-IMF) groups, with 993 and 896 proteins in each group. Among them, 110 were differentially expressed proteins (DEPs). Gene ontology (GO) classification statistics showed that the 110 DEPs were functionally classified into 100 annotation clusters. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that three pathways were related to IMF metabolism and deposition—fatty acid metabolism, fatty acid degradation and fatty acid elongation—and included 7 proteins. Conclusion: GO and KEGG analyses showed that differentially expressed HADHA, HADHB, ACSL1, ACADS, ACAT1 and ACAA2 in the mitochondrion act via fatty acid metabolism, fatty acid degradation and fatty acid elongation to influence the metabolism and synthesis of long-, short- and medium-chain fatty acids and influence IMF anabolism and catabolism. Protein-protein interaction (PPI) network analysis showed that IMF accumulation in different muscle tissues of Aerbasi cashmere goat was affected by not only 5 key enzymes or proteins involved in fatty acid synthesis and metabolism but also 5 DEPs (SUCLG1, SUCLG2, CS, DLST, ACO2) in the TCA cycle. Our results provide new insights into IMF deposition in goat and improve our understanding of the molecular mechanisms underlying IMF anabolism and catabolism.
2020-12-04 | PXD022901 |
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:Inner Mongolia Alpas cashmere fibers with different fiber diameters
2025-09-25 | PXD068818 |
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:Inner Mongolia Cashmere Goat is a local excellent breed of cashmere and meat dual-purpose, which is a typical heterogeneous indumentum. The hair follicles cycle through periods of vigorous growth (anagen), a regression caused by apoptosis (catagen), and relative rest (telogen). At present, it is not clear which genes affect the cycle transformation of hair follicles and unclear how proteins impact the creation and expansion of hair follicles. In this work, we investigated the possible pathways of transformation and apoptosis in goat hair follicles using multi-omics joint analysis methodologies. The results showed that 917 , 1187 and 716 proteins were specifically expressed in anagen, catagen and telogen. The result of gene ontology (GO) annotation showed that differentially expressed proteins（DEPs) are in different growth cycle periods, and enriched GO items are mostly related to the transformation of cells and proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment result indicated that the apoptosis process has a great impact on hair follicle's growth cycle. The results of the protein interaction network of differential proteins showed that the Ribosomal Protein family ( RPL4, RPL8, RPS16, RPS18, RPS2, RPS27A, RPS3 ) was the core protein in the network. The results of combined transcriptome and proteomics analysis showed that there were 16,34, and 26 overlapped DEGs and DEPs in the comparison of anagen VS catagen, catagen VS telogen and anagen VS telogen, of which API5 plays an important role in regulating protein and gene expression levels. We focused on API5 and Ribosomal protein and found that API5 affected the apoptosis process of hair follicles, and Ribosomal Protein was highly expressed in the resting stage of hair follicles. They are both useful as molecular marker candidate genes to study hair follicle growth and apoptosis, and they both have an essential function in the cycle transition process of hair follicles. The results of this study may provide a theoretical basis for further research on the growth and development of hair follicles in Inner Mongolian Cashmere goats.
2024-06-24 | PXD050798 | Pride