Using the Nadia Instrument for Single Cell RNA-Seq

The Nadia Instrument allows single cell RNA-seq at affordable rates and extremely high rates of gene capture. It is designed to analyze thousands of single cells, allowing researchers to monitor or identify patterns of cell expression. When coupled with the Drop-Seq protocol, it can produce up to 50,000 single cell libraries in droplet form within 20 minutes.

Highlights

With the Nadia Instrument, the following features are offered:

  • The rate of doublet formation is extremely low
  • The process is very reproducible
  • Gene capture is performed with high efficiency
  • The PCR duplication rate is low
  • Single cell analysis is made affordable

Multiple Applications

The Nadia Instrument fits a host of applications in areas such as:

  • The study of how cancer cells work
  • Immune functions and phenomena
  • Stem cell studies
  • Neural cell functions
  • Plant cell physiology and structure
  • Data sets

Three independently generated datasets on Nadia were compared to a dataset published by Macosko et.al. 2015. High numbers of genes and UMIs were detected even at low sequencing depths across all samples indicating costeffective single cell analysis.

High Reproducibility with Nadia

The plot above correlates two data sets obtained with the Nadia Instrument, by two separate users on different days, showing the high degree of concordance between the users and the experiments.

Single Cell Squencing with Low Doublet Rate

This plot shows the results of species mixing experiments carried out in order to find the rate of doublets and the level of cross contamination. The Barnyard-plot displays how many mouse or human transcripts are associated with a single cell, and this yields the true single cell number. The values shown confirm that the samples and the single cell library prepared downstream are of excellent quality.

Advantage: Efficiency and Cost-Effectiveness

The Nadia Instrument allows genes to be captured at low sequencing depth so that cell analysis can be performed on an affordable scale. This was confirmed by making a comparison of the number of genes detected to the read depth, for all samples, which shows that the NSG analysis cost is reduced significantly by the efficiency of gene capturing at this level.

Drop-Seq Reduces PCR Duplication Rate

The Drop-Seq protocol reduces the cost of sequencing, as the following plot shows. It makes a comparison between the number of UMIs detected and the read depth for each cell, across all samples. The black line denotes the ideal ratio of 1 UMI: I read, since this corresponds to zero PCR duplicates. All the data sets in the plot are close to this line, showing that this protocol produces a low rate of duplication during PCR.

Nadia and the t-SNE Plot of a Mixed Species Dataset

The use of t-SNE in Partek Flow resulted in clustered mixed species data sets within a two-dimensional space, forming two separate groups as was expected. The marker genes Atp5a1 and RAP7A was used to color the cell groups for mouse and human cells respectively.

About Dolomite BioDolomite Bio

Dolomite Bio creates innovative products for high throughput single cell research including the Nadia Instrument and the Nadia Innovate. By encapsulating single cells in microfluidic droplets, our products enable rapid analysis of thousands or millions of individual cells and their biological products.

Key benefits of Dolomite Bio systems:

  • Flexible: The systems enable full control of pressures, flow rates and temperatures
  • Compatible with a range of applications: Not limited to a specific protocol
  • Productised: Complete off-the-shelf, easy to use systems
  • High precision with reproducible results: Monodisperse droplets with low doublet rate of cells and beads

Our products are complete systems enable scientists to generate thousands of single cell libraries in just a few minutes.

Our in-house team of biologists and worldwide network of local specialists work with you to provide advice for your application, product demonstrations, installation, training and support.


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Last updated: Nov 26, 2018 at 8:56 AM

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