Lexogen’s advanced plant transcriptomics solutions

Analysing a plant’s transcriptome can shed light on regulatory mechanisms, gene expression in response to stressors or expression networks during plant growth and development. However analysing the transcriptome of plants presents a number of challenges such as extraction of RNA from plant cells with robust walls, high quantities of rRNA getting in the way of sequencing, and data analysis of large and complex genomes. Lexogen provides solutions to the problems that can be encountered at each step of the plant transcriptomics workflow for both gene expression analysis and whole transcriptome sequencing.

Gene expression profiling

Lexogen’s plant gene expression workflow consists of RNA extraction, 3’ mRNA sequencing and data analysis. The table below outlines the common challenges faced by researchers at each point of the workflow and how Lexogen's solutions are designed to overcome these.

Whole transcriptome sequencing

The whole transcriptome sequencing workflow includes an extra step compared with gene expression profiling, as it requires the removal of rRNA (figure 1), which is especially abundant in plant genomes. RiboCop is an rRNA depletion kit designed to selectively remove rRNA from plant RNA samples to enrich the mRNA fraction, thereby improving the efficiency and cost-effectiveness of RNA-seq experiments. This is then followed by library generation using the CORALL Total RNA-seq kit.

Figure 1. RiboCop rRNA depletion workflow. 

RNA-seq data analysis with Kangooroo

Both the gene expression and whole transcriptome workflows require bioinformatic analysis for result interpretation. Analysing RNA-seq data can be complex, involving multiple steps from raw data processing to interpretation of gene expression levels. Plant RNA-seq data analysis can be particularly challenging due to the large and diverse plant genomes and transcriptomes.

Kangooroo is a data analysis tool designed to streamline and automate the RNA-seq data analysis pipeline. It handles tasks such as quality control, alignment, quantification, and differential expression analysis, tailored for plant data. This helps researchers efficiently interpret their results and gain insights from their RNA-seq experiments.

Benefits of using Kangooroo:

• RNA-seq data processing: automate the processing of raw RNA-seq data, from quality control to alignment and quantification
• Differential expression analysis: perform statistical analysis to identify differentially expressed genes under various conditions.
• Functional annotation: annotate and interpret transcriptomic data to understand gene functions and pathways.
• Integration of multi-omics data: combine RNA-seq data with other omics data (e.g., proteomics, metabolomics) for a holistic view of plant biology.

If you are starting your plant transcriptomics project, contact our Lexogen specialists for guidance today!

Material for download

RiboCop for plant transcriptomics