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Research Services

5′ GEX (scRNA-seq for gene expression and immune profiling)

Introduction to 5’ GEX scRNA-seq for gene expression and immune profiling 

5′ Gene Expression (GEX) sequencing enables transcriptome profiling at single-cell resolution while preserving information from the 5′ end of transcripts. This approach not only supports robust gene expression analysis across individual cells, but also allows direct integration with immune repertoire profiling, making it particularly valuable for immunology-focused studies. 

5′ GEX captures transcriptional heterogeneity among intact immune and non-immune cells, facilitating the identification of cell types, activation states, and functional programs. When combined with T cell receptor (TCR) and B cell receptor (BCR) sequencing, this platform enables simultaneous analysis of gene expression and immune clonality, providing insights into clonal expansion and immune cell phenotypes. 

Overall, 5′ GEX with immune profiling offers a platform for linking transcriptional states with adaptive immune receptor information, supporting studies of immune development, disease mechanisms, immuno-oncology, autoimmunity, and therapeutic response.  

At Novogene, our 5′ GEX and immune profiling solutions are powered by the latest 10x Genomics Chromium iX platform and GEM-X chemistry based Universal 5’ Gene Expression assay, delivering high sensitivity, reproducibility, and reliable performance. Our streamlined, end-to-end workflow includes sample processing and quality control, single-cell library preparation, high-throughput sequencing on the NovaSeq X Plus, and comprehensive bioinformatics analysis. We also provide clear, publication-ready visualizations to support intuitive data interpretation and accelerate biological discovery. 

Applications of 5’ GEX with immune profiling: 

5’GEX with immune profiling has been assisting researchers in the following research areas, including: 

  • Cancer research
  • Immunology 
  • Infectious disease research 

Benefits of Novogene’s 5’ GEX with immune profiling

 

  • End-to-end service: Includes sample processing (fresh tissue/organoid dissociation, dead cell removal, red blood cell lysis as appliable for the sample type) and QC, single-cell library preparation, sequencing on the NovaSeq X Plus and bioinformatics analysis with “publication-ready” figures.
  • 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 standards.
  • Bioinformatics Support: We provide comprehensive bioinformatics support, 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.
  • 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 scRNA-seq services with immune profiling. 
  • Fast Turnaround Times: Our scRNA-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.

5’ GEX and immune profiling specifications: Sample requirements

Sample type  
(Mouse and human only for TCR/BCR)  		Assay  Sample processing  Remarks 
Cryopreserved cell suspensions  5’ GEX + TCR/BCR  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. 
Blood/Bone marrow  Red blood cell lysis 
Mononuclear cell isolation  		Collected in vacutainer tubes with anticoagulants 

5’ GEX and immune profiling 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
  • Data Quality Control
  • “Cell Ranger only’’ analysis
    • Demultiplex BCL files from a sequencer into FASTQs
    • Alignment of reads to the genome
    • Gene expression quantification (Matrix files)
  • Standard analysis
    • “Cell Ranger only’’ analysis (Details above)
    • Identification of highly variable genes (HVGs)
    • Cell Subpopulation Identification
    • Marker gene detection (Differentially expression analysis between clusters)
    • Enrichment Analysis
    • Functional Annotation of Transcription Factor
    • Protein-Protein Interaction Network Analysis

Project workflow of Novogene scRNA-seq service

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