NGS Services:
NGS Data Analysis:
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Plant RNA Sequencing
Short-read RNA sequencing (RNA-Seq) is a meaningful tool for plant transcriptomics which is generally applied in fields like plant research, crop sciences, and agricultural biology (AgBio). Different types of plant tissues or cultivation methods pose diverse and complex challenges for RNA-Seq, like efficient RNA isolation, negative effects caused by plant metabolites, high abundance of plant ribosomal RNA, or co-existence with bacteria, yeast, viruses etc.
Lexogen’s Plant RNA-Seq service provides excellent, cost-efficient transcriptome profiling from any plant material, including lowly concentrated and degraded RNA samples. Our success in processing these complex samples comes from years of hands-on experience and well-established and optimized workflows for expression profiling, small RNA profiling and discovery, whole transcriptome and whole genome sequencing.
Benefits
- Compatible with low-quality plant material
- Ideal for low input plant RNA samples
- Effective isolation of RNA from any plant material, including roots, seedlings, leaves, flowers, etc.
- Transcriptomic co-analysis of plant and other organisms (microbiome studies)
- Multi-omics approach in combination with DNA-Seq applications
Applications
- Cost-efficient plant gene expression profiling
- Whole Transcriptome Sequencing of plant material, e.g., for detection of fusion genes, isoforms, SNPs etc.
- Microbiome studies in hosts, soil, and environmental samples
- Analysis of non-coding transcripts, including lncRNA, snRNA, snoRNA, circRNA, etc.
- Plant-Microbe dual RNA-Seq
- Alternative polyadenylation (APA) studies
- Small RNA Sequencing
- Analysis of plant extracellular vesicles
- High-throughput gene expression sequencing
- Targeted RNA sequencing
- Whole Genome Sequencing, including Low-Pass Sequencing
Deliverables
- Demultiplexed files (FASTQ)
- Trimmed files (FASTQ)
- Aligned files (BAM)
- Rseqc (.txt)
- Gene counts and counting summary (.tsv)
- Differential expression and DE summary (.tsv)
- Multiqc reports – raw, trimmed, alignment, rseqc (.html)
- PCA plot
- Deliverables summarized in a PDF report
Working with us
Consultations
- Together we will identify the best experimental design for your project.
- Shipment support (such as help with customs and export documents), or organizing the shipment under certain conditions.
Sample Extraction
- RNA extraction from any plant material, including roots, seedlings, leaves, flowers.
- Sample QC included.
Library Preparation
- Various library preparation solutions, depending on and adapted to your specific experimental objectives.
- Library QC included.
Sequencing
- Read mode and read depth most suitable for your application.
Data Analysis and Report
- Data quality control.
- Data analysis in-house.
- Standard data analysis options, on-demand, custom-design data analyses, and custom pipeline development.
