Eukaryotic mRNA-Seq
Eukaryotic mRNA-Seq
Technology Introduction
Applications of Eukaryotic mRNA-Seq
- Research on growth and developmental mechanisms of animals and plants
- Research on stress resistance in flora and fauna and potential applications
- Research on gene expression patterns in different organs
Case Study
Journal: Journal of Agricultural and Food Chemistry
IF: 5.279
Time: 2021.09
Research conclusions：
To our knowledge, this is the first study to examine the changes in GABA content, GABA-related metabolite content and enzyme activities of six quinoa varieties at different germination stages (seed, G24, G48 and G72). The molecular mechanism of GABA accumulation during germination in quinoa was explored by transcriptome sequencing. The findings enhance our understanding of the changes in bioactive compounds, particularly GABA, during quinoa germination. Moreover, it provides a solid basis for the development of novel functional foods enriched with GABA.
References：
Zhang Derui,Wei Xiaonan,Liu Ze et al. Chenopodium quinoaTranscriptome Analysis Reveals the Molecular Mechanism of GABA Accumulation during Quinoa ( Willd.) Germination.[J] .J Agric Food Chem, 2021, 69: 12171-12186.
Project Workflow of Eukaryotic mRNA-Seq
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Reference-based transcriptome |
Transcriptome with no reference |
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Expression analysis
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Overall gene expression distribution in samples |
Overall gene expression distribution in samples |
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Inter-sample correlation analysis |
Inter-sample correlation analysis |
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Differential gene expression analysis |
Differential gene expression analysis |
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Functional enrichment analysis of differentially expressed genes |
Functional enrichment analysis of differentially expressed genes |
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GESA enrichment analysis |
Weighted correlation network analysis (WGCNA) |
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Enrichment analysis (for human, rat, and mouse) based on the DO, DisGeNET, and Reactome databases |
Weighted correlation network analysis (WGCNA) |
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Protein interaction network analysis |
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Weighted correlation network analysis (WGCNA) |
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Structural analysis
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Comparison with the reference genome |
Transcriptome data splicing |
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Novel transcript prediction |
Gene functional annotation (using 7 major databases) |
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Alternative splicing analysis |
CDS prediction |
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Transcription factor annotation |
SSR analysis |
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Analysis of SNP and InDel variation |
Transcription factor annotation |
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Gene fusion analysis (human, rat, and mouse |
Technical parameters of Eukaryotic mRNA-Seq
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Eukaryotic mRNA-Seq |
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Amount |
Plant:≥500mg; Animals; ≥300mg; Cells; ≥5X106; Fungus:≥300mg or5X106 |
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Total RNA |
Amount:≥1ug; Volume:≥50ng/ul; RIN:≥6.5 |
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RNA Library |
polyA enrichment |
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Read Length |
Paired-end 150 bp |
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Data Output |
6G bases |
