Sequences to Differences in Gene Expression: Analysis of RNA-Seq Data

Pavlovich, Polina V.; Cauchy, Pierre

doi:10.1007/978-1-0716-2376-3_20

Cited by 3 publications

(2 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Transcriptome sequencing is an accurate and efficient sequencing method that has grown to be one of the most popular histological assays. Because it allows unbiased quantification of the entire genome and identification of differentially expressed genes, it has been used to reveal the mechanisms of plant response to various biotic and abiotic stresses at the molecular level [ 29 , 30 , 31 , 32 ]. Therefore, in this study, transcriptome sequencing was used to analyze the differential gene expression transcription profiles of S. tenuifolia under different MeJA levels, to identify gene clusters in response to MeJA in S. tenuifolia , and to screen genes and transcription factors involved in JA signal transduction and monoterpenoid biosynthesis.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomics Reveals the Molecular Basis for Methyl Jasmonate to Promote the Synthesis of Monoterpenoids in Schizonepeta tenuifolia Briq.

Shi

Cui

Zhang

et al. 2023

CIMB

View full text Add to dashboard Cite

Background: Methyl jasmonate has an important effect on the synthesis of plant secondary metabolites. Schizonepeta tenuifolia Briq. has a wide range of pharmacological effects and the secondary metabolites are dominated by monoterpenes (pulegone, menthone). Objective: It is essential to determine the changes in secondary metabolites in S. tenuifolia under methyl jasmonate treatment and to probe the molecular mechanism. This can improve the accumulation of secondary metabolites in the medicinal plant S. tenuifolia and enrich the information gene expression at different MeJA levels, which can help to elucidate the molecular mechanism of monoterpenoid synthesis in S. tenuifolia. Methods: In this study, we determined the changes in the content of monoterpenoids in S. tenuifolia under methyl jasmonate treatment. Meanwhile, we established a transcriptome database of S. tenuifolia under methyl jasmonate level using high-throughput sequencing. Results: A certain concentration of MeJA promoted the accumulation of monoterpenoids in S. tenuifolia. The transcriptome database of S. tenuifolia leaves under 0, 50, 100 and 250 μM MeJA treatment was established. We generated 88,373 unigenes with an N50 length of 2678 bp, of which 50,843 (57.53%) can be annotated in at least one database. Compared with the CK (0 μM) group, 12,557 (50 μM), 15,409 (100 μM) and 13,286 (250 μM) differentially expressed genes were identified. GO and KEGG enrichment analysis revealed that JA signal transduction and monoterpenoid synthesis were the two most significant enrichment pathways. The expression levels of related DEGs involved in JA signaling and monoterpenoid synthesis were significantly up-regulated by MeJA. In addition, our phenotypic and differentially expressed gene association analysis revealed that monoterpenoid biosynthesis in S. tenuifolia was more associated with genes involved in plant trichome branching, phytohormone signaling and transcriptional regulation. Conclusions: This study confirmed that methyl jasmonate significantly promoted monoterpenoid biosynthesis in S. tenuifolia. A large number of genes responding to methyl jasmonate were associated with JA signaling and monoterpenoid biosynthesis.

show abstract

Section: Introductionmentioning

confidence: 99%

Transcriptomics Reveals the Molecular Basis for Methyl Jasmonate to Promote the Synthesis of Monoterpenoids in Schizonepeta tenuifolia Briq.

Shi

Cui

Zhang

et al. 2023

CIMB

View full text Add to dashboard Cite

show abstract

“…mRNA-Seq measures gene expression, while ATAC-Seq measures chromatin accessibility, both without the need to optimize the assay for a specific set of molecules or genomic regions. Many pipelines exist to analyze mRNA-Seq and ATAC-Seq data, but most of them only go as far as peak calling for ATAC-Seq [10][11][12] or differential gene expression analysis for mRNA-Seq [13,14], leaving many researchers in need of deeper biological insights. Particularly, combining omics results from different methods and performing enrichment analyses is often done in a lowthroughput, time-consuming, and hard-to-reproduce manner, creating a strong need for pipelines that offer easy automation of these steps.…”

Section: Introductionmentioning

confidence: 99%

Cactus: a user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis

Salignon

Millán-Ariño

Garcia

et al. 2023

Preprint

View full text Add to dashboard Cite

Summary: With the recent rapid advancements in sequencing technology, the analysis of omics data has become increasingly important for biomedical research. However, many laboratories lack the time or expertise to thoroughly analyze such data. Among omics assays, ATAC-Seq (Assay for transposase-accessible chromatin using sequencing) and mRNA-Seq (messenger RNA sequencing) are easy and cost-effective methods that are commonly used to define chromatin accessibility and gene expression levels, respectively. Here we introduce Cactus (Chromatin accessibility and transcriptomics unifying software), a pipeline that streamlines the individual or integrated analysis of ATAC-Seq and mRNA-Seq data. The pipeline is written in Nextflow for efficient scaling, caching, and parallelization, and all tools are packaged in Singularity/Docker containers or conda/Mamba virtual environments for simple installation and high reproducibility. Cactus conducts preprocessing on raw sequencing reads, followed by differential analysis between conditions. Results are split into Differential Analysis Subsets (DASs) based on significance threshold, direction of change, annotated genomic regions, and experiment type. Then, Cactus computes enrichments of entries from internal (i.e., DASs) and external (i.e., ontologies, pathways, DNA binding motifs, ChIP-Seq (Chromatin immunoprecipitation sequencing) binding sites, and chromatin states) databases in DASs and presents results in barplots and customizable heatmaps. The visualization of the results is simplified by the generation of merged PDFs, merged tables, and formatted Excel tables. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, easy, and reproducible manner.

show abstract

Integrative omics approach for identification of genes associated with disease

Yadav,

Singh

2024

Integrative Omics

View full text Add to dashboard Cite

Sequences to Differences in Gene Expression: Analysis of RNA-Seq Data

Cited by 3 publications

References 69 publications

Transcriptomics Reveals the Molecular Basis for Methyl Jasmonate to Promote the Synthesis of Monoterpenoids in Schizonepeta tenuifolia Briq.

Transcriptomics Reveals the Molecular Basis for Methyl Jasmonate to Promote the Synthesis of Monoterpenoids in Schizonepeta tenuifolia Briq.

Cactus: a user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis

Integrative omics approach for identification of genes associated with disease

Contact Info

Product

Resources

About