Single-Cell RNA Sequencing

Single-Cell RNA Sequencing

Service Description

BGI provides sequencing services for pre-made libraries from the 10x Genomics® Chromium™ system Single Cell 3′ Library Construction Kit v3 and Next GEM Single Cell 3’ Library Construction Kit v3.1.

Once your pre-made library arrives at our sequencing facility, library QC will be performed to ensure the downstream service quality. For high quality, low duplication and index-hopping-free [1] results, your library will be converted into DNBs (DNA Nanoball) for sequencing with BGI’s proprietary DNBseqTM NGS technology. Upon request, sequencing can be performed with Illumina HiSeq/NovaSeq platform.

We employ rigorous QC steps following each phase of the service workflow as described by the flow chart below. The qualified sequencing data will be offered for download and bioinformatics service is available upon request.

Applications for Research and Drug Development

DNBseq Sequencing Technology

DNBseq is an innovative high-throughput sequencing solution, developed by BGI’s Complete Genomics subsidiary in Silicon Valley. The system is powered by combinatorial Probe-Anchor Synthesis (cPAS), linear isothermal Rolling-Circle Replication and DNA Nanoballs (DNB™) technology, followed by high-resolution digital imaging.

BGISEQ human whole genome sequencing

The combination of linear amplification and DNB technology reduces the error rate while enhancing the signal. The size of the DNB is controlled in such a way that only one DNB is bound per active site on the flow cell. This densely patterned array technology provides optimal sequencing accuracy and increases flow cell utilization.

Project Workflow

Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

  • Library QC
  • Conversion QC
  • Sequencing QC
  • Data QC
  • Library Submission
  • DNB Conversion
  • Sequencing
  • Raw Data Output
  • Bioinformatics

How to order

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

Request a Quote

Send us a no obligation request for quote and our dedicated sales team will reply to you within 24 hours.

Create an Online myBGI Account

Create a myBGI account to view all our sample and shipping documentation and to manage your project moving forwards. It's quick, free and easy!

References

1. Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5569-5
2. Single-cell Transcriptomic Landscape of Nucleated Cells in Umbilical Cord Blood. bioRxiv 346106 (2018). doi:10.1101/346106 https://doi.org/10.1101/346106
3. Comparative analysis of sequencing technologies for single-cell transcriptomics. Genome Biology, volume 20, Article number: 70 (2019) https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1676-5
4. Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA sequencing. bioRxiv 552588 (2019). doi:10.1101/552588 https://www.biorxiv.org/content/10.1101/552588v2
5.Effects of Index Misassignment on Multiplexing and Downstream Analysis (Illumina white paper, 2017).

 

Sequencing Service Specification

BGI Single Cell sequencing services are executed with the DNBseq sequencing technology, featuring cPAS and DNA Nanoballs (DNB™) technology for superior data quality.

  • Sample preparation and services

    Sample preparation and services

    • 100bp Paired end sequencing
    • 20K read pairs/cell recommended
    • Raw data and bioinformatics analysis are available in standard file formats
    • Advanced and custom bioinformatics data analysis
    • Cloud-based data storage and delivery system
    • Standard single cell 3' RNA seq data analysis is available
    • Customized data analysis is available
  • Sequencing Quality Standard

    Sequencing Quality Standard

    • Guaranteed ≥80% of bases with quality score of ≥Q30
  • Turn Around Time

    Turn Around Time

    • 4 weeks from library QC acceptance to filtered RAW data availability
    • Rapid turnaround time of 2 weeks is available with qualified sample volume. Contact your local BGI specialist for details.

Sample Requirements

We can process libraries constructed with the 10x Genomics® Chromium™ system Single Cell 3′ Library Construction Kit v3 or with the Next GEM Single Cell 3’ Library Construction Kit v3.1, that meet the following requirements:

Library parameter Requirement Preferred QC method
Fragment size 400bp±100bp Agilent 2100
Concentration ≥2ng/ul Qubit
Total amount ≥30 ng Qubit

Data Analysis

In addition to raw data output, BGI offers a range of standard and customized bioinformatics pipelines for your single cell sequencing project.
Reports and output data files are delivered in industry standard FASTQ, BAM. Excel formats with publication-ready tables and figures.

Standard Anlysis for single cell RNA sequencing

  • Data filtering includes removing adaptors contamination – low quality reads from raw reads.

  • Assessment of sequencing

  • Gene expression and annotation (Gene coverage and coverage depth)

  • Gene expression difference analysis

  • Expression pattern analysis of DEGs

  • Gene ontology analysis of DEGs

  • Pathway enrichment analysis of DEGs

  • Refinement of gene structures

  • Identification of alternative spliced transcripts

Customized analysis

Further customization of Bioinformatics analysis to suit your unique project is available: Please contact your BGI technical representative

Single Cell DNA/RNA Sequencing Resources

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

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