Bulk RNA sequencing

A powerful technique for uncovering the transcriptional profile of a pool of cells.

Bulk RNA sequencing

Bulk RNA sequencing is useful for the identification of transcripts in an isolated sample.

Highlights

Bulk RNA sequencing (RNA-seq) is the identification of transcripts in an isolated sample.
RNA-seq offers in depth discoveries of differentially expressed genes between two or more conditions.
The technique is applicable to both eukaryotic and bacterial samples.

When to use Bulk RNA sequencing?

To unravel various biological systems, it is essential to understand the complexity of transcriptomic changes. Bulk RNA sequencing serves to obtain a high-throughput representation of average transcriptomic changes between two or more conditions. Depending on the type of samples, you can use bulk RNA sequencing in:

Sample type: BACTERIA

Targets for drug and vaccine development(1)
Antibiotic resistance(2)
Infection diseases and virulence(3)
Synthesis of biomolecules for industrial use (exoenzymes, antioxidants, etc.)(4)
Metabolic activities of microbes that provide nutrients to crops (5)

Sample type: HUMAN BIOPSIES and ANIMAL MODELS

Identification of diferentially expressed genes, uncover underlying pathways and network analysis.
“Deconvolution” to cell type atlases to quantify the cell type composition in the sample (6).
Analysis of alternative splicing
Biomarker discovery (7)

Do you want to investigate splice variants using Bulk RNA sequencing?

When investigating splice variants, sequencing deeper is typically recommended(8). In principle, we can sequence as deep as necessary, and this will be a topic that is always discussed in the introduction consultation.

Technique

Technical specifications

Technical Application

Workflow Bulk RNA Sequencing

Consultation: Our service starts with an introductory meeting, where the customer’s requests and concerns are discussed. Here, the experimental setup is established.
Before receiving samples: We offer general recommendations for sample preparation but are open to customized setups.
Processing of your samples: Our experienced scientists process your samples in the lab using validated protocols. We center the flow upon rigorous quality control both before and after sequencing.
Data analysis: We offer a complete bioinformatics solution concerning the analysis of your data. You can read more about our bioinformatics service here.

Bioinformatics

I am a researcher: I need data analysis and interpretation for my findings.

Technique description: Amplexa Genetics will organize the new data and combine it with databases and, through statistics, will designate important parts that can be used to draw conclusions within diagnosis and research.

The Sample

RNA Harvesting Protocol

To help ensure more accurate results before sending samples to Amplexa Genetics, you should meet certain quality measures

How to do it?

References

Mariana, P. S. et al. in Next Generation Sequencing (ed K. Kulski Jerzy) Ch. 7 (IntechOpen, 2016).
Li, Z. et al. RNA-seq analyses of antibiotic resistance mechanisms in Serratia marcescens. Mol Med Rep 20, 745-754 (2019).
Westermann, A. J. et al. Dual RNA-seq of pathogen and host. Nat Rev Microbiol 10, 618-630 (2012).
Wiegand, S. et al. RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. BMC Genomics 14, 667 (2013).
Solaiyappan Mani, S. & Reinhold-Hurek, B. RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. Microorganisms 9 (2021).
Chen, B. et al. Profiling Tumor Infiltrating Immune Cells with CIBERSORT. Methods Mol Biol 1711, 243-259 (2018).
Hong, M. et al. RNA sequencing: new technologies and applications in cancer research. Journal of Hematology &Oncology 13, 166 (2020).
illumina. Considerations for RNA Seq read length and coverage, <https://knowledge.illumina.com/library-preparation/rna-library-prep/library-preparation-rna-library-prep-reference_material-list/000001243> (2024).

Bulk RNA sequencing