Ontology highlight
ABSTRACT:
PROVIDER: PRJNA913675 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22805342_1.fastq.gz | Fastqsanger.gz | |||
| SRR22805342_2.fastq.gz | Fastqsanger.gz | |||
| SRR22805343_1.fastq.gz | Fastqsanger.gz | |||
| SRR22805343_2.fastq.gz | Fastqsanger.gz | |||
| SRR22805344_1.fastq.gz | Fastqsanger.gz |
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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:we evaluated the Arbas Cashmere goat, a species that is especially used in this type of research. The goats were exposed to an experimentally controlled short photoperiod to study the regulation of cyclical cashmere growth. Exposure to a short photoperiod extended the anagen phase of the Cashmere goat hair follicle to increase cashmere production. Based on assessments of tissue sections, it was observed that the short photoperiod significantly induced cashmere growth. A comparison of the differences in gene expression between the short photoperiod and the natural conditions using gene chip technology supported this conclusion. Using the gene chip data, we identified genes that showed altered expression under the short photoperiod compared to natural conditions, and it was found that these genes are involved in the biological processes of hair follicle growth, structural composition of the hair follicle, and the morphogenesis of the surrounding skin appendages.
2015-11-11 | GSE74860 | GEO
Project description:Guard hair and cashmere undercoat are developed from primary and secondary hair follicle, respectively. Little is known about the gene expression differences between primary and secondary hair follicle cycling. In this study, we obtained RNA-seq data from cashmere and milk goats grown at four different seasons. We studied the differentially expressed genes (DEGs) during the yearly hair follicle cycling, and between cashmere and milk goats. WNT, NOTCH, MAPK, BMP, TGFβ and Hedgehog signaling pathways were involved in hair follicle cycling in both cashmere and milk goat. However, Milk goat DEGs between different months were significantly more than cashmere goat DEGs, with the largest difference being identified in December. Some expression dynamics were confirmed by quantitative PCR and western blot, and immunohistochemistry. This study offers new information sources related to hair follicle cycling in milk and cashmere goats, which could be applicable to improve the wool production and quality.
2019-07-19 | GSE84947 | GEO
Project description:Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber. But the fineness is not enough,improving the fineness of cashmere is an important problem.Therefore, it is important to find genes involved in cashmere fineness that can be used in future in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new development through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through a translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With this data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes(expressed,not co-expressed). From these, 343 genes were up-regulated in the fine LCG group in relation to the coarse LCG group and 186 down-regulated in the same relationship.Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of human papillomavirus infection pathway was the most. We found that COL6A5 gene may affect cashmere fineness. The characteristics and expression analysis of COL6A5 gene may play an important role in the study of LCG cashmere fineness.
2021-11-05 | GSE186959 | GEO
Project description:Secondary hair follicles (SHF) produce the thermoregulatory cashmere in goat. MiRNAs were reported playing indispensable roles in hair follicle formation and growth. However, most studies examining miRNAs related to cashmere have been performed on goat skin. It still remains obscure that which miRNAs are highly expressed in SHFs or how miRNAs affect the cashmere growth. In the present study, we isolated the SHFs under dissecting microscope and analyzed the miRNA signatures during annual cashmere growth. Small RNA sequencing followed by genome-wide expression analysis reveals that early anagen is a crucial phase for miRNA regulation on the cashmere growth, which was uncovered by two predominant groups of miRNAs. Although they exhibit opposite expression patterns, both groups demonstrated sharp changes of expression when transit from early anagen to mid-anagen. In addition, we identified 96 miRNA signatures that differentially expressed between different phases among 376 miRNAs. Functional analysis of the predicted target genes for highly expressed or differentially expressed miRNAs indicated that these miRNAs were involved in signal pathways associated with SHF development, regeneration and regression. Furthermore, miR-143-3p is preferentially expressed in SHFs and Itga6 was identified as one of targets. The dual-luciferase and in situ hybridization assay demonstrated that miR-143-3p directly repressed the expression of Itga6, suggesting a possible novel role for miR-143-3p in the cashmere growth.
2022-12-10 | GSE220211 | GEO
Project description:we evaluated the Arbas Cashmere goat, a species that is especially used in this type of research. The goats were exposed to an experimentally controlled short photoperiod to study the regulation of cyclical cashmere growth. Exposure to a short photoperiod extended the anagen phase of the Cashmere goat hair follicle to increase cashmere production. Based on assessments of tissue sections, it was observed that the short photoperiod significantly induced cashmere growth. A comparison of the differences in gene expression between the short photoperiod and the natural conditions using gene chip technology supported this conclusion. Using the gene chip data, we identified genes that showed altered expression under the short photoperiod compared to natural conditions, and it was found that these genes are involved in the biological processes of hair follicle growth, structural composition of the hair follicle, and the morphogenesis of the surrounding skin appendages. Based on their similar weights, health conditions and good reproductive performance in a group of the same strain, we chose 62-year-old female adult Arbas Cashmere goats as our research specimens and randomly divided them into a test group (T1, T2, T3) and a control group (C1, C2, C3).The goats in the test group were grazed, fed, and allowed to drink from 9:30-16:30 daily, and they were housed in a dark shed with good air conditions for the rest of the time. The temperature in the shed was 1 degree less than that outside, and the opacity was controlled at approximately 0.1 lux. The control group was grazed in natural conditions. We used regular management to care for all of the goats.
2015-11-11 | E-GEOD-74860 | 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. 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:we used single-cell RNA sequencing (scRNA-seq) and computational models to identify 13 skin cell types in Liaoning Cashmere Goats. We also analyzed the molecular changes by Cell Trajectory Analysis in the development process and revealed the maturation process in gene expression profile in Liaoning Cashmere Goats. Weighted gene co-expression network analysis (WGCNA) explored hub genes in cell clusters related to cashmere formation. Secondary hair follicle dermal papilla cells (SDPCs) play an important role in the growth and density of cashmere. ACTA2, a marker gene of SDPCs, was selected for immunofluorescence (IF) and western blot (WB) verification. Our results indicate that ACTA2 is mainly expressed in SDPCs, and WB results showed different expression levels. COL1A1 is a highly expressed gene in SDPCs, which was verified by IF and WB. We then selected CXCL8 of SDPCs to verify, and prove the differential expression in the coarse type and the fine type of Liaoning Cashmere Goats. Therefore, CXCL8 gene may regulate cashmere fineness. These genes may be involved in regulating the fineness of cashmere in goat secondary hair follicle dermal papilla cells, our research will provide new insights into the mechanism of cashmere growth and cashmere fineness regulation by cells.
2021-08-25 | GSE182474 | 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