Generate high-quality gene expression insights using Illumina-based RNA-Seq analysis, advanced bioinformatics pipelines, and differential expression analysis for bacterial and eukaryotic samples.
RNA-Seq analysis is a powerful transcriptomics approach used to measure and compare gene expression levels across biological samples. By sequencing RNA molecules, researchers can determine which genes are actively expressed, quantify transcript abundance, and identify changes in gene expression under different conditions. BaseClear offers RNA-Seq analysis for both bacterial and eukaryotic samples, supporting applications such as functional genomics, strain characterization, pathway analysis, host response studies, product development, and biomarker discovery. De novo transcriptome assembly is not part of this service; analyses are performed against a reference genome provided by the customer.
This service is designed for biotechnology companies, pharmaceutical developers, academic researchers, food and feed innovators, industrial microbiology organizations, and human health researchers seeking to understand biological mechanisms at the gene expression level. Typical projects include comparing treated versus untreated samples, evaluating fermentation or culture conditions, investigating mechanisms of action, studying host-pathogen interactions, identifying differentially expressed genes, and characterizing responses to environmental, genetic, or process-related changes. Projects can start from a single sample, while differential gene expression studies typically include biological replicates to maximize statistical power.
BaseClear combines high-quality Illumina sequencing with validated library preparation workflows and a state-of-the-art bioinformatics pipeline. Following sequencing, reads are aligned to the supplied reference genome and analyzed using updated RNA-Seq workflows to generate gene expression profiles and differential expression results.
Clients receive both raw sequencing data and fully processed gene expression results. Deliverables include quality-filtered FASTQ files, aligned reads in BAM format with index files, and gene expression tables containing both raw counts and normalized TPM values for each sample. For differential expression projects, BaseClear provides statistical comparison tables together with publication-ready visualizations such as PCA plots, MA plots, and volcano plots. Every project is accompanied by a detailed methods and quality report, regular project status updates, and expert support from the BaseClear NGS team, enabling researchers to move efficiently from RNA samples to biologically meaningful insights.
Together, we review your research objectives, sample type, reference genome, and experimental design. For differential expression projects, we help ensure that sample groups and comparisons are clearly defined before the project starts.
You send either cells or purified RNA samples together with the required project information. Our team performs RNA quality control and keeps you informed about sample quality, project status, and next steps throughout the study.
Your samples are processed using stranded RNA-Seq library preparation and sequenced on the Illumina Nextseq platform. Sequencing depth is tailored to your application, ensuring sufficient data for accurate gene expression analysis.
BaseClear aligns sequencing reads to your reference genome and quantifies gene expression levels using a state-of-the-art RNA-Seq analysis pipeline. If requested, differential expression analysis is performed to identify genes that are significantly up- or downregulated between conditions.
You receive quality-filtered sequencing data, gene expression tables, alignment files, and a comprehensive analysis report. Differential expression projects also include visualizations such as PCA plots, MA plots, and volcano plots to support interpretation and publication-ready reporting.
End-to-end microbial safety assessment capabilities
Regulatory-ready data generation and interpretation
Integrated wet-lab and bioinformatics expertise
Structured support for EFSA and global submissions
An annotated reference genome is required for BaseClear’s standard RNA-Seq analysis workflow. Customers must provide the species name and either an NCBI accession number or an annotated GenBank file to enable accurate read alignment and gene quantification. Because this service is designed for gene expression profiling rather than transcript discovery, de novo transcriptome assembly is not included in the standard analysis.
BaseClear uses organism-specific library preparation workflows to maximize transcriptome coverage and data quality. Bacterial samples are processed using rRNA depletion with Illumina Stranded Total RNA Prep and Ribo-Zero Plus, while eukaryotic samples undergo stranded polyA-selected mRNA enrichment. This tailored approach ensures that sequencing capacity is focused on biologically relevant transcripts while minimizing non-informative RNA species.
The recommended sequencing depth depends on the organism and study objectives. For bacterial samples, approximately 5 million reads per sample are typically sufficient for gene expression profiling, whereas eukaryotic samples generally require 10–30 million reads per sample. Higher sequencing depths can be selected for complex transcriptomes, low-abundance transcripts, or projects requiring increased statistical power.
Differential gene expression analysis includes both quantitative results and publication-ready visualizations. Clients receive tables containing fold changes, statistical significance values, and differential expression results, together with PCA plots, MA plots, and volcano plots that facilitate interpretation of transcriptional differences between experimental groups or conditions.
All RNA samples undergo quality control assessment before library preparation to verify RNA quantity and integrity. BaseClear recommends high-quality RNA with RIN values above 7.0 for bacterial samples and above 8.0 for eukaryotic samples, together with sufficient concentration and purity. If samples fail quality control, customers are informed promptly and alternative options are discussed before proceeding with the project.
SERVICES
Phenotypic assessment of antimicrobial resistance aligned with EFSA guidelines
SERVICES
Phenotypic assessment of antimicrobial and cytotoxic production
Speak with our experts to design a WGS strategy aligned with your regulatory needs. Your first consultation is free and without obligation.
