Introduction to 3’ GEX sc/snRNA-seq for gene expression
3′ Gene Expression (GEX) sequencing is a widely used approach for profiling transcriptomes at single-cell or single-nucleus resolution. By capturing and sequencing the 3′ end of polyadenylated RNA molecules, this method enables gene expression profiling across individual cells or nuclei in a single experiment.
In single-cell RNA sequencing (scRNA-seq), 3′ GEX reveals transcriptional heterogeneity among cells, supporting the identification of distinct cell types, functional states, and dynamic responses to biological stimuli. Complementarily, single-nucleus RNA sequencing (snRNA-seq) extends this capability to frozen or difficult-to-dissociate tissues by profiling nuclear RNA, enabling unbiased analysis of cell populations that are otherwise challenging to study.
Overall, 3′ GEX sc/snRNA-seq offers a powerful framework for dissecting cellular composition, uncovering rare populations, and gaining deeper insights into gene expression that drive development, disease, and therapeutic response.
At Novogene, our sc/snRNA-seq solutions are powered by the latest 10X Genomics’ Chromium iX platform and the newest GEM-X chemistry, providing researchers with hassle-free, accurate and reliable results for their research. Our standardized, efficient end-to-end workflow is complete with sample processing and QC, single-cell library preparation, sequencing on the NovaSeq X Plus and bioinformatics analysis to assist with data interpretation, including the generation of “publication-ready’’ figures for easy data visualization.
Applications of sc/snRNA-seq
sc/snRNA-seq has been assisting researchers in the following research areas, including:
- Developmental biology
- Cancer research
- Neuroscience
- Immunology
Benefits of Novogene’s sc/snRNA-seq
- End-to-end service: Includes sample processing (nuclei isolation, fresh tissue/organoid dissociation, dead cell removal, red blood cell lysis as applicable for the sample type) and QC, single-cell library preparation, sequencing on the NovaSeq X Plus and bioinformatics analysis with “publication-ready” figures.
- Extensive Experience: Novogene has extensive global experience with offering scRNA-seq for a large variety of species and tissue types.
- High-Quality Data: We offer data output guarantee and high-quality sequencing data that meets leading industry standards, for samples that pass our quality control criteria.
- Bioinformatics Support: We provide comprehensive bioinformatics support, including 10X Genomics’ Cell Ranger analysis, to help researchers gain deeper insights from their biological data. Whether you need standard pipelines utilizing latest analysis algorithms in the field or tailored solutions, we’ve got you covered.
- Latest technology: Leveraging 10x Genomics’ latest Chromium iX and the newest GEM-X chemistry, we provide state-of-the-art sc/snRNA-seq services.
- Fast Turnaround Times: Our sc/snRNA-sequencing lab is located near you, in Munich, Germany, allowing for reduced shipping times. With our large sequencing capacity, automated and streamlined workflows, we ensure that you receive your data promptly without compromising on quality.
- Customer Service System (CSS): Novogene’s Customer Self Service System (CSS) is an online portal that streamlines project management and provides direct access to all your sequencing projects in one place. You can view your sequencing project(s), track their progress, access reports, collaborate with your team members and obtain other useful information in one place.
scRNA-seq specifications: Sample requirements
| Sample type | Assay | Sample processing | Remarks |
| Fresh frozen tissues/organoids | 3’ GEX (snRNA-seq) |
Nuclei isolation | Sample amount < 50 mg requires evaluation |
| Cryopreserved cell suspensions | 3’ GEX (scRNA-seq) | Dead cell removal, if necessary | Cell count < 500K requires evaluation |
| Fresh tissues/organoids | Fresh tissue dissociation Dead cell removal, if necessary |
Novogene will ship tissue storage solution in advance. Samples must arrive in the lab within 2 days of sample retrieval. |
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| Blood/Bone marrow | Red blood cell lysis Mononuclear cell isolation |
Collected in vacutainer tubes with anticoagulants |
scRNA-seq specifications: Sequencing and analysis
| Sequencing Platform | Illumina NovaSeq X Plus Sequencing System |
| Read length | Paired-end 150 bp (Trimmed data can be delivered upon request) |
| Data Output | Recommended: 100-150 Gb per sample* *Number of reads/cell can be increased depending on the research application |
| Data Analysis Capability |
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Project workflow of Novogene scRNA-seq service
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