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Triticum aestivum subsp. yunnanense cultivar:HD2985 and HD2329

ABSTRACT: Triticum aestivum subsp. yunnanense cultivar:HD2985 and HD2329 Transcriptome or Gene expression

PROVIDER: PRJNA270262 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR1714932.fastq.gz	Fastqsanger.gz
	SRR1714932_1.fastq.gz	Fastqsanger.gz
	SRR1714932_2.fastq.gz	Fastqsanger.gz
	SRR1714874_1.fastq.gz	Fastqsanger.gz
	SRR1714874_2.fastq.gz	Fastqsanger.gz

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Triticum aestivum strain:HD2985, HD2329 Transcriptome or Gene expression

Project description:The study was conducted in order to find out the differential change in the transcript of tolerant and susceptible wheat cultivar under heat stress and to decipher the mechanism of thermotolerance in wheat by identifying novel genes and transcription factors involved in the pathways. Wheat cultivar HD2985 (thermotolerant) and HD2329 (thermosusceptible) were exposed to heat stress of 42 degree for 4h at pollination stage and samples were collected from both control and heat shock treated plants for further characterization.

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Project description:Mass spectrometry-based wheat proteomics is challenging because the current interpretation of mass spectrometry data relies on public databases that are not exhaustive (UniProtKB/Swiss-Prot) or contain many redundant and poor or un-annotated entries (UniProtKB/TrEMBL). Here we report the development of a manually curated database of the metabolic proteins of Triticum aestivum (hexaploid wheat), named TriMet_DB (Triticum aestivum Metabolic Proteins DataBase). The manually curated TriMet_DB was generated in FASTA format, so that it can be read directly by programs used to interpret the mass spectrometry data. Furthermore, the complete list of entries included in the TriMet_DB is reported in a freely available resource, which includes for each protein the description, the gene code, the protein family,and the allergen name (if any). To evaluate its performance, the TriMet_DB was used to interpret the mass spectrometry data acquired on the metabolic protein fraction extracted from the MEC cultivar of Triticum aestivum.

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Transcriptome of Triticum aestivum genotypes associated with resistance against the Wheat dwarf virus

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived Triticum aestivum transcriptome (RNA-seq) profiling methods and to evaluate genotypes associated with resistance against the Wheat dwarf virus. Methods: Triticum aestivum mRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated by deep sequencing, in four replicates, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our study represents the first detailed analysis of Triticum aestivum transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA and miRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

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