Plant Protoplast RNA-Seq

Single cell RNA-Seq (scRNA-Seq) is a tool that enables simple and robust access to the transcriptomes of thousands of single cells. With plant protoplast RNA-Seq (ppRNA-Seq), Dolomite Bio has now released a standardised application specific to the requirements of plant cells.

What to look out for when performing scRNA-Seq of plant cells

Large-scale transcriptomic studies of single protoplast cells from plant tissues have generally lagged behind those of animal models. Unlike many mammalian cell types, which dissociate from each other more readily, plant tissues require intense enzymatic digestion and specific buffer conditions to be accessible for conventional single cell and microfluidic techniques.

A wealth of single cell studies have been conducted on the root cells. However, large scale transcriptomic datasets of single leaf cells are remarkably absent. Where single cell leaf transcriptomes are available, isolation is typically conducted with microdissection, limiting potential throughput. This disparity is primarily due to technological challenges for microfluidic platforms, such as:

• Plant cells, especially those found in leaves can be anywhere between 10 µm and 60 µm within a single sample
• Plant protoplasts, once isolated, must be stored in buffers with high osmolarity to avoid osmolysis and stress responses
• Plant protoplast buffers are typically much thicker and more adherent than animal cell buffers, requiring variable pressure to be applied to each buffer to account for different flow rates

Plant Protoplast RNA-Seq on the Nadia Instrument

Dolomite Bio developed a custom workflow specifically tailored to the needs of single cell research on plant cells. The ppRNA-Seq method on Nadia generates high quality transcriptomic data from both large and small plant leaf protoplasts. The protocol is tailored to work with specialized leaf protoplast buffers to ensure plant protoplast integrity. Read below how our customers are using the Nadia Innovate to further their research on plants.

Here we demonstrate that the Nadia Innovate and Nadia Instruments are capable of efficient and high-throughput encapsulation of plant leaf protoplasts in multiple buffers tailored to plant protoplast integrity. Furthermore, we show that the integrated scRNA-Seq workflow for use with plant protoplasts developed by Dolomite Bio generates high quality transcriptomic data from both large and small plant leaf protoplasts. For researchers interested in plant research and novel protocol development that do not require a high throughput system, our new Nadia Go provides the capabilities of the Innovate, without purchasing the full Nadia platform.