Introduction: The transcriptome, in a broad sense, refers to the complete set of transcribed products—both mRNA and non-coding RNAs (ncRNAs)—present in a specific cell under a given functional state. It serves as an essential link between genomic genetic information and biological function. Transcriptome sequencing in eukaryotes, based on high-throughput sequencing technologies, enables rapid identification of the full complement of transcripts expressed in a particular cell type or tissue under a specific condition, facilitating studies on gene structure and function, alternative splicing, and the discovery of novel transcripts.

Transcriptomic studies enable the investigation of gene function and gene structure at a systems‑level, and have become a priority approach for elucidating the regulatory mechanisms underlying organismal growth and development, adaptation to environmental stress, evolutionary patterns, and disease pathogenesis, as well as for identifying critical targets in the regulation of disease‑causing genes. These approaches are now widely employed in basic research, clinical diagnostics, and drug discovery. In fields such as plant and animal breeding.

Features
Capable of handling complex samples.
Extensive experience in library construction, with the incorporation of library normalization techniques.
Assist clients in conducting bioinformatics analyses quickly and accurately.
Customized information analysis can be flexibly tailored to meet the client’s specific needs.

Initial Sample Amount and Submission Recommendations

Precautions:

① Tissue samples are recommended to be stored in RNAlater, RNAHold, RNAProtect, or other suitable tissue preservation solutions, and then either frozen at −80°C or shipped on dry ice.
② After thoroughly lysing the cell samples with a lysis buffer such as TRIzol, store them at −80°C or ship them on dry ice.
③ For more detailed sample preparation guidelines, please contact online customer service.

Bioinformatics Analysis Workflow and Analytical Content

Application Scenarios and Case Studies

Use Case 1: Differential Gene Screening and Functional Analysis
Scope of Application: Any field, including clinical medicine, basic medicine, biochemistry, and research on animals, plants, and fungi.
Using eukaryotic reference‑based transcriptome sequencing, differentially expressed genes can be identified by comparing gene expression levels between experimental and control groups. These differentially expressed genes are then further characterized through GO and KEGG enrichment analyses, as well as GSEA, and their functions are annotated by integrating published literature from PubMed and previously established key molecular markers within the research group. This allows for focused analysis of functionally relevant genes. Once the experimental validation phase begins, the selected differentially expressed genes can be validated using qPCR, Northern blotting, Western blotting, FISH, and by employing gene knockout or overexpression strategies.
Application Scenario 2: Time-series analysis or concentration-gradient analysis
Scope of Application: Clinical samples, cell samples, and animal and plant samples include specimens collected at multiple time points or treated with different drug concentrations.
In transcriptomic data analysis, there is a special type of experimental design. This involves collecting samples at different time points or testing samples across a range of concentrations of drugs, reagents, and other agents. Subsequently, the expression patterns of various genes across these time points or concentration gradients are investigated. Such analyses are commonly referred to as “time-course analysis.”
Use Case 3: Identification of upstream regulatory genes, such as transcription factors, regulatory factors, and splicing factors.
Scope of Application: Any research area, including clinical medicine, basic medicine, biochemistry, and animal and plant sciences.
Conventional differential transcriptome analysis is highly likely to identify a large number of differentially expressed genes, posing challenges for target prioritization in subsequent experimental validation. In the absence of specific pathways or key molecules of interest, transcription factors represent an excellent starting point. Transcription factors can modulate chromatin accessibility, recruit RNA polymerase to initiate transcription, and assemble co‑factors to regulate distinct stages of the transcriptional process, thereby orchestrating numerous biological processes, including immune responses and developmental patterning. Consequently, analyzing the expression and regulatory activity of transcription factors is crucial for unraveling complex cellular and physiological processes. Other regulatory elements, such as alternative splicing, also contribute to upstream gene regulation.
Application Scenario 4: Large-Scale Studies
Scope of Application: Plant and animal breeding, genetic populations and the origins of species, population cohorts, and biomarker discovery
With the rapid advancement of sequencing technologies, transcriptomic studies based on small sample sizes can no longer adequately address complex biological questions. Researchers have begun leveraging large-scale transcriptomic datasets, integrating statistical methods and machine learning approaches to identify core genes that conform to specific patterns and serve research objectives. Techniques such as Mendelian randomization, correlation analysis, linear regression, LASSO regression, and Cox regression are employed to examine gene expression profiles across diverse samples and genomic variations, thereby uncovering deeper and more comprehensive biological insights.

Project Workflow

HeYuan Bio’s eukaryotic reference‑based transcriptome sequencing offers researchers a comprehensive end‑to‑end service pipeline—covering sample extraction, library construction and sequencing, and data analysis—delivering high‑quality results and providing robust evidence to support downstream research.
Meanwhile, HeYuan Bio’s reference‑based transcriptome cloud analysis has been fully upgraded, offering a wide range of analytical services to meet both standard and customized research needs.

Original article link: HeYuan Bio – Eukaryotic Transcriptome Sequencing