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Customizing single cell research - Dolomite Bio

Customizing single cell research with the Nadia Innovate

Empowering researchers with unrivaled versatility for rapid protocol optimization & application development

The Nadia Innovate unlocks a solution for all cell types by handing researchers the key to rapid development of new applications, with customizable protocols and reagents, so research can be tailored to your needs.

Why is customizing single cell research important?

Most commercially available instruments and protocols focus on commonly used cell types with predefined reagents and protocols.

However, to take full advantage of high-throughput single cell research capabilities, versatile and flexible technology is required. Cells obtained from plant or other non-model
organisms may require protocol adjustments due to cell size, buffer compositions or other variations.

In the rapidly changing field of single cell research, now more than ever, scientists are looking to increasingly customize existing protocols or develop new protocols
and applications to fit with their specific experimental needs.

A. Cribbs quote_ Innovate

Unrivaled versatility

Easy software-controlled adjustments of critical parameters on the Nadia Innovate

For an in-depth guide to customizing single cell research protocols- Read the Nadia Innovate get started guide

                            Customizing single cell research - Temperature   Customizing single cell research - Time   Customizing single cell research - Stirrers    Customizing single cell research - Pressure

What else can you achieve with the Nadia Innovate?

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How have our customers used Nadia Innovate to develop and optimize their applications, enabling them to customize their  single cell research needs?

Application

Why use the Nadia Innovate?

Which parameters were changed

Optimization process 

Important Links

scRNA-Seq with Plant leaf protoplasts

Plant leaf cells are large (>30 µm across) and
need to be stored in high viscosity osmotic-ally
balanced buffers to prevent premature lysis.
Pressure changes need to be made to reliably
generate droplets and efficiently sequence these
cells.
  • Pressure levels were increased for all buffers.
  • The speed of on-chip stirring was also slightly increased
Two different established buffers for protoplast isolation were flowed into droplets alongside oligo coated beads to be assayed using single cell RNA-Sequencing.

Read the Plant protoplast application note

Read about Dr.Aki Minoda’s plant research using Nadia Innovate 

Agarose encapsulation for cell growth

3D cell culture has distinct advantages over 2D culture for diverse cell and tissue types.

Encapsulating single cells in hydrogel droplets is the first step in many downstream workflows such as high throughput single cell screening, cell-cell or cell-pathogen interaction studies or even FACS of single cell microenvironments.

  • Increase in bead pressure.
  • Increase in stirrer speed.
  • On-chip temperature set to 4°C
Both oil and agarose flow pressure was increased to account for the high viscosity of agarose. Once droplets are produced, they can be cooled and separated from the oil phase to produce hydrogel spheres containing single cells in high throughput. This can also be achieved with collagenase gels such as Matrigel™ by cooling the Innovate chip rather than heating it.   Read the Cell Encapsulation in Agarose droplets Application note

Encapsulating deformable beads

Encapsulating deformable, rather than hard beads, means that the bead concentrations can be increased and a higher proportion of droplets will contain a bead. This can improve the cell capture rate in sequencing applications to over 70%.
  • Pressure levels were changed in all of the oil, cell and bead lines.
  • The speed of on-chip stirring was also decreased to stack beads more efficiently.
With precise pressure modifications, beads can be stacked together at the microfluidic junction and distributed into a higher proportion of droplets. Using the Nadia Innovate, pressure levels were adjusted to load beads into over 70% of droplets.  Read the Deformable Beads On Nadia Innovate Application Note

Improved mRNA capture for small cells/organelles

Less transcription-ally active cell types are difficult to access with more limited instruments. By shrinking the droplet size using the Nadia Innovate, the limited genomic material from these cells is concentrated to improve library capture. This enables sequencing and detection of material from single objects much smaller than cells, from nuclei to exosomes and other individual organelles. 
  • Oil pressure was increased, causing the aqueous flow to be cut into droplets faster. This makes the droplets smaller.
Increasing the oil pressure results in smaller droplets. With droplet size reduced from 85 µm to 65 µm, reaction volume is halved. This increases the local mRNA concentration to improve library capture of small cells.  View Dr. Chris Sibley’s sNuc-Seq poster

Read our sNuc-seq datasheet

Optimized lysis strength

Some cells, organelles and nuclei can be harder to crack than others. The genomic data obtained from single cell studies can be incomplete if the cells arent fully lysed by commercially available lysis buffers. The versatile Nadia Innovate allows users to customise the strength of thir lysis buffer to better suit their cell type
  • Increase in on-chip temperature for lysis step.
  • Increase in bead line pressure. Increased lysis time
Pressure levels can be altered to account for increased lysis buffer viscosity. A heated lysis step can improve lysis efficiency and in the case of single nucleus RNA-Sequencing, increasing the length of the lysis step improves library yield.  Read our sNuc-seq datasheet

 

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