Selection of cashmere fineness functional genes by translatomics
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ABSTRACT:
PROVIDER: PRJNA776890 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16683232_1.fastq.gz | Fastqsanger.gz | |||
| SRR16683232_2.fastq.gz | Fastqsanger.gz | |||
| SRR16683233_1.fastq.gz | Fastqsanger.gz | |||
| SRR16683233_2.fastq.gz | Fastqsanger.gz | |||
| SRR16683234_1.fastq.gz | Fastqsanger.gz |
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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: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:Secondary hair follicles (SHFs) produce the cashmere of goats. In the present study, SHF clusters were isolated under the microscope by cutting out the epidermis and removing the connective tissues. RNA sequencing was performed on the collected SHFs. Through genome-wide transcriptomic analysis, we discovered and characterized differentially expressed molecular signatures across the annual growth cycle of cashmere and demonstrated their differential expression features and importance in cashmere growth.
2023-01-31 | GSE221472 | 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.
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Project description:The aim of this study was to elucidate the molecular mechanisms underlying the differences of fineness and coarse type cashmere produced by Tibetan cashmere goats.
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Project description:Cashmere is regarded as a specialty and luxury fiber due to its scarcity and high economic value. For fiber quality assessment, it is technically very challenging to distinguish and quantify the cashmere fiber from yak or wool fibers because of their highly similar physical appearance and substantial protein sequence homology. To address this issue, we propose a workflow combining untargeted and targeted proteomics strategies for selecting, verifying and quantifying biomarkers for cashmere textile authentication. Untargeted proteomic surveys were first applied to identify 174, 157, and 156 proteins from cashmere, wool and yak fibers respectively. After marker selection at different levels, peptides turned out to afford much higher selectivity than proteins for fiber species discrimination. Collective use of these peptide makers allowed us to discriminate and quantify cashmere fibers in commercial finished fabrics that have undergone heavy chemical treatments. Cashmere proportion measurement in fabric samples using our proteomic approach was in good agreement with results from traditional light microscopy, yet our method can be more readily standardized to become an objective and robust assay for assessing authenticity of fibers and textiles.
2018-10-25 | PXD003107 | Pride
Project description:Molecular Signatures and Functional Analysis of Secondary Hair Follicles in Cashmere Goat During Annual Cashmere Growth
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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:skin tissue of LCG was taken as the research object in this study, and quantitative proteomics strategy of LC-MS/MS mass spectrometry was used to identify and quantitatively analyze differential proteins. Combined with bioinformatics analysis, the formation mechanism of cashmere in LCG was discussed in depth, in order to find the internal relationship between phosphorylation modification and hair follicle development in cashmere goat, and to comprehend the regulation of protein phosphorylation modification on fiber growth in LCG.
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Project description:This study investigates regulatory molecules and machanisms of cashmere growth by profiling dermal papilla cells (DPCs) from secondary (SHF) and primary hair follicles (PHF) during the early and mid-anagen phases in both male and female cashmere goats. A comprehensive genome-wide transcriptomic analysis was then performed to characterize the differentially expressed molecular signatures associated with follicle types (SHF vs. PHF), developmental phases, and sex.
2025-11-13 | GSE307628 | GEO