High throughput transcriptomics of flow sorted cells with unique molecular identifiers

Minimizing the cost but not the sensitivity of single cell RNA-seq using a miniaturized CEL-Seq2 protocol.

A novel CEL-Seq2 protocol for higher-throughput scRNA-seq

Combining index-sorting with single cell RNA-seq offers the possibility to pre-select subpopulations of interest, and to link transcriptome data with cell surface marker expression. A reliable scRNA-seq workflow requires a cDNA synthesis method that is optimized for both high sensitivity and accuracy. The CEL-Seq2 protocol of Hashimshony et al. (Genome Biol. 2016) ticks these boxes, however reagent cost becomes a limiting factor when scaling up the numbers of cells to be analyzed.

The next generation CEL-Seq2 protocol, developed at the Max Planck Institute of Immunobiology and Epigenetics, relies on automated nanolitre-scale liquid handling to achieve a step-change in throughput (Herman et al., Nature Methods 2018 & Sagar et al., Methods in Molecular Biology, 2018). This group named their mCEL-Seq2 protocol after the mosquito® LV genomics nL liquid handling robot that made it feasible to process thousands of cells per day.

Continue reading to learn more, or click here to watch the full webinar presentation from a senior scientist at the Max Planck Institute discussing mCEL-Seq2.

Miniaturized mCEL-Seq2 protocol for 384-well single cell RNA-seq using a mosquito liquid handler

Lab automation facilitates processing of FACS-sorted single cells

The new mCEL-Seq2 protocol is described in full here. Essentially, 384-well microplates are pre-prepared with lysis buffer using the mosquito liquid handler. Based on surface marker expression, individual cells are then sorted into the plates, followed by the addition of cDNA synthesis reagents with mosquito.

With this approach, one operator can process eight 384-well plates or 3072 cells per day. Subsequent in vitro-transcription and library preparation are carried out in bulk.

Click here for an enlarged version of the workflow graphic.

Miniaturized high-throughput version of CEL-Seq2 maintains high sensitivity

 mCEL-Seq2 is a cost-effective and highly sensitive scRNA-seq method

The nanolitre pipetting range of mosquito allows up to tenfold volume reduction vs. the original CEL-Seq2 protocol. Sensitivity and accuracy of miniaturized mCEL-Seq2 were extensively benchmarked against the full-volume protocol (the figure on the right is an excerpt from (Herman et al., Nature Methods 2018).

Following extensive validation, it was concluded that a five-fold volume reduction provides the optimal combination of sensitivity versus cost.

mCEL-seq2 has already proven to be a powerful tool for discovery in cell biology and immunology (Herrtwich et al., Cell, 2016 & Tsai-Hsiu Lu et al., Cell Metabolism 2018).

mCEL-Seq2 protocol with fivefold volume reduction for 384-well single cell RNA-seq using a mosquito liquid handler

Low-volume cDNA synthesis from single cells

The routine mCEL-seq2 process relies on cost-effective miniaturization of protocol steps pre-pooling to just a few hundred nanoliters using mosquito (figure, left).

This protocol combines:

  • index sorting for simultaneous measurement of cell-surface marker expression and single-cell transcriptomes
  • unique molecular identifiers to reduce amplification noise
  • cell barcoding to permit sample pooling ahead of library preparation

Please contact us for further information from our Genomics specialists.

View our related resources

Lab image

Interested? Get in touch to start the journey

Ask an expert
Subscribe to updates

Interested? Get in touch to start the journey

Find help through our cross-domain support package