Dataset Information

Identification of key proteinIdentification of key proteins related to cashmere fibre diameter by integrated proteomics and bioinformatic analysiss related to cashmere fibre diameter by integrated proteomics and bioinformatic analysis

ABSTRACT: Goat (Capra hircus) has always been a source of fibre for human use and holds an important place in international high-end textiles. Fibre diameter is the most concerned economic indicator for producers. Understanding the formation mechanism of fibre diameter and related key proteins can help optimize and control the production of cashmere. Although mass spectrometry (MS)-based workflows have made great progress in achieving near-genome-wide coverage, the equivalent complete map of cashmere proteome is still elusive. Here, we performed label-free liquid chromatography coupled with tandem MS to profile the cashmere proteome. Firstly, by measuring the fibre diameter, it was found that the average fibre diameter of Alxa cashmere was significantly smaller than that of Alpas. With the help of proteomics technology,170 proteins were detected with high confidence. A total of 68 differentially expressed proteins were identified in the two cashmere, 131 proteins were specifically expressed in Alpas, and 40 proteins were specifically expressed in Alxa. Through Gene Ontology enrichment analysis, the Kyoto Encyclopedia of Genes and Genomes, Protein-Protein Interaction network construction, and the CytoHubba plugin of the Cytoscape software were used to interpret the proteomic data. Finally, KRT10, KRT14, KRT17, and KRT82 played a key role in leading to the difference in the diameter of the two fibres. Combined with bioinformatics, the structure and function of these proteins were further studied to provide a more com-prehensive perspective for understanding the regulation mechanism of cashmere diameter. At the same time, combined with the information on genetics and gene expression, the genetic factors and epigenetic regulation mechanisms affecting cashmere fibre diameter can be further studied.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Capra Hircus (goat)

TISSUE(S): Skin

SUBMITTER: Chongyan Zhang

LAB HEAD: Chongyan Zhang

PROVIDER: PXD050828 | Pride | 2024-03-21

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	702056R_SWATH_20181121_gas12_2ul_01.wiff	Wiff
	702056R_SWATH_20181121_gas12_2ul_01.wiff.scan	Wiff
	702056R_SWATH_20181121_gas12_2ul_02.wiff	Wiff
	702056R_SWATH_20181121_gas12_2ul_02.wiff.scan	Wiff
	702056R_SWATH_20181121_gas12_2ul_03.wiff	Wiff

Items per page:

1 - 5 of 50

Similar Datasets

Project description:Comparative analysis of transcriptome profiles of G. arboreum L. cv. and its fuzzy-lintless mutant (ANOI 1960) at 0 and 10 dpa. Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The fuzzy-lintless ovules of cotton mutants are ideal source for identifying genes involved in fibre development by comparing with fibre bearing ovules of wild-type. To decipher molecular mechanisms involved in fibre cell development, transcriptome analysis has been carried out by comparing G. arboreum cv. (wild-type) with its fuzzy-lintless mutant (ANOI 1960). Fuzzed-lintless mutant line was generated by back cross breeding between FL and Fl (recurrent parent) lines (personal communication by Dr. I. S. Katageri). Basically Fibre less type was a RIL, first recovered from cross between G.arboreum (linted) and G. anomalum (lint less). This RIL was used as donor parent and crossed with normal arboreum (as recurrent parent) to develop G. arboreum FL and G. arboreum Fl isogenic lines. This G. arboreum Fl line is named as ANOI 1960. Cotton bolls were collected at fibre initiation (0 dpa/days post anthesis) and elongation (10 dpa) and gene expression profiles were analyzed in wild-type and ANOI 1960 mutant using Affymetrix cotton GeneChip Genome array. Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during fibre development stages. Total RNA was isolated from fibre bearing ovules of wild-type (WT) and fuzzy-lintless ovules of mutant (ANOI 1960) collected at various (0 and 10 dpa) fibre development stages using SpectrumTM Plant Total RNA kit (Sigma, USA) according to the manufacturerM-bM-^@M-^Ys protocol. Affymetrix cotton GeneChip Genome array (Affymetrix, USA) having 23,977 probe sets representing 21,854 cotton transcripts was used for transcriptome analysis. Three biological replicates were maintained to test the reproducibility and quality of the chip hybridization. cDNA labeling, array hybridization, staining and washing procedures were carried out as described in the Affymetrix protocols. CEL files having estimated probe intensity values were analyzed with GeneSpring GX-11.5 software (Agilent Technologies, USA) to get differentially expressed transcripts. The Robust Multiarray Average (RMA) algorithm was used for the back ground correction, quantile normalization and median polished probe set summarization to generate single expression value for each probe set. Normalized expression values were log2-transformed and differential expression analysis was performed using unpaired t-test. The p-values were corrected by applying the false discovery rate (FDR) correction (Benjamini and Hochberg, 2000).

Project description:Methods for studying mitochondrial adaptations in skeletal muscle have mostly used whole-muscle samples, where results may be confounded by the presence of a mixture of type I and II skeletal muscle fibres. In this project, we utilised the latest Mass spectrometry (MS) techniques to provide new insights into mitochondrial adaptations in type I and II fibres in response to two different types of training – moderate-intensity-continuous training (MICT) and sprint-interval training (SIT). An 8-week training intervention was undertaken by 23 men who performed either MICT or SIT. Single muscle fibres from skeletal muscle biopsies were collected at rest, before and after the 8 weeks of training, and pooled for subsequent MS analysis. A proteomic workflow was applied that permitted a three-tiered comparison and quantification of mitochondrial proteins in different fibre types. Our protocol includes tandem mass tag labelling for increased identification of low-abundant proteins. We quantified more than 45% of known mitochondrial proteins in skeletal muscle. When comparing type I to type II fibres,24 mitochondrial proteins were differentially expressed following MICT and 10 following SIT. These altered proteins were associated with known cellular pathways within the mitochondria, including oxidative phosphorylation, the TCA cycle and fatty acid oxidation. There were distinct trends for fibre-type-specific protein responses to different types of exercise training. Following MICT proteins mostly increased in abundance in type I fibres, without analogous changes observed following SIT. This greater upregulation of mitochondrial proteins observed following MICT, suggests exercise volume is a powerful stimulus for mitochondrial adaptations. This upregulation mostly seen in type I fibres is consistent with the predominate recruitment of this fibre type with MICT. When normalised to mitochondrial content further evidence to fibre-specific non-stoichiometrically induced increases in the expression of fatty acid mitochondrial proteins is presented, highlighting mitochondria as a pivotal subcellular site in facilitating substrate utilisation to increase ATP production in type I fibres. Conversely, the research suggests very high-intensity exercise training altered the systematic biogenesis of oxidative phosphorylation (OXPHOS) components, in particular complex IV subunits of the OXPHOS pathway. These results question the existing knowledge of fibre-type-specific changes to mitochondrial proteins in response to exercise training and provide a valuable contribution to understanding the mechanisms by which exercise helps to improve health and prevent disease.

Dataset Information

Identification of key proteinIdentification of key proteins related to cashmere fibre diameter by integrated proteomics and bioinformatic analysiss related to cashmere fibre diameter by integrated proteomics and bioinformatic analysis

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets