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Single Cell DNA Sequencing

Service Overview
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singlecell-dna-seqAdvances in whole-genome amplification and Novogene’s expertise have made single cell sequencing easily accessible to researchers. Novogene is one of the few NGS providers with extensive experience in single cell sequencing technology, including single-cell DNA sequencing. We offer the highest quality services in amplification, library construction, sequencing, and bioinformatics analysis to our customers, and our results have been published in leading scientific journals.

With single-cell DNA sequencing, the genomic heterogeneity of cell populations can be explored at the level of the individual cell. Genetic changes, such as point mutations and copy number variation occurring during disease and normal development processes, are profiled using the minute amounts of DNA from single cells. Applications include analysis of genetic heterogeneity within unicellular and multicellular organisms, detection of chromosomal anomalies in germ line cells, preimplantation genomic screening of embryos, and defining the genetic composition of tumors for developing more targeted therapies.

The Novogene Advantage

Project Workflow

single cell dna sequencing project workflow

Sequencing Strategy

  • 350 bp insert DNA library
  • HiSeq platform, paired-end 150 bp

Data Quality Guarantee

  • Q30 ≥ 80%

Sample Requirements

  • We accept fresh single cells and laser captured single cells.
  • Sorted single cells should be stored in 1 x PBS buffer (excluding calcium and magnesium) in a total volume of ≤ 2 µL. The stored cells should be freezed in liquid nitrogen and shipped out with dry ice.

Turnaround Time

  • Amplification: within 10 working days from verification of sample quality
  • Library preparation and sequencing: within 22 working days
  • Data analysis: 8 working days

Recommended Sequencing Depth

  • For normal sample: effective sequencing depth of 30X
  • For tumor sample: effective sequencing depth of 50X

Analysis Pipeline

single cell dna sequencing analysis pipeline

Table. Representative data quality results of single cell DNA sequencing from Novogene.
Sample NameRaw readsRaw data (G)Effective (%)Error (%)Q 20 (%)Q 30(%)GC (%)

Project Example

The following studies utilized Novogene's expertise in single-cell DNA sequencing.

Single-cell exome sequencing identifies mutations in KCP, LOC440040, and LOC440563 as drivers in renal cell carcinoma stem cells
Cell Research 1-4 (2016)

Renal cell carcinoma (RCC), the most common form of adult kidney cancer, has a low mutation rate. In this study, three novel renal cancer stem cell driver mutations were discovered using Novogene’s advanced single-cell exome sequencing technology. With over 140X coverage, 297 somatic SNVs were found, with 141 of these located in coding regions. Three missense mutations in the loci KCP, LOC440563, and LOC440040 were unique to CD133+ RCC cells and have not been reported in RCC before. This study suggests that these three novel mutations could play significant roles in RCC diagnostics and therapeutic treatment.


WES Project Example Fig 1

Figure. Identification of driver genes in renal cell carcinoma stem cells via single-cell exome sequencing

Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing
Science, 338:1627-1630 (2012)

In this study, Novogene’s single-cell DNA sequencing technology was used to analyze the genomes of individual human sperm following amplification by MALBAC. The results revealed variation in the distribution of recombination events along the genome and provided new insights into meiotic mechanisms.

Lu S, Zong C, Fan W, et al. Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science, 338:1627-1630 (2012).

Figure. Identifying crossover positions in individual sperm cells.

Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution
Cell Stem Cell, 20: 1-12 (2017)

5-formylcytosine (5fC), as an oxidized derivative of 5mC (5-methylcytosine), plays important role in active DNA demethylation, yet remains unexplored at the single-cell level. Here Novogene’s HiSeq platform was adopted in a novel “CLEVER-seq” (chemical-labeling-enabled C-to-T conversion sequencing) approach, to map the 5fc dynamics at single-cell, single-base resolution. CLEVER-seq identifies the intrinsic 5fC heterogeneity in mouse gametes and early embryos, provides evidence of active DNA methylation in parental and maternal genomes, and indicates that the emergence of promoter 5fC production precedes the up-regulation of gene expression. This new CLEVER-seq displays an important resource for further epigenetic reprogramming in single cells at single base resolution.

Figure. The landscape of DNA formylation in mouse pluripotent stem cells and early embryos.

  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
  Whole Exome Sequencing
  LncRNA Sequencing
  Small RNA Sequencing
  Whole Genome Bisulfite Sequencing
  Animal & Plant Re-Sequencing
  Genotyping by Sequencing
  de novo Sequencing
  Pan-genome Sequencing
  Metagenomic Sequencing
  Single-cell DNA Sequencing
  Single-cell RNA Sequencing
  16S/18S/ITS Amplicon
  Others- please specify