Single cell omics

A scalable platform for plate-based single-cell omics workflows

Emerging methods

Recent advances in instrumentation, biochemistry and computational tools for single-cell analysis have resulted in a rapid adoption of single-cell methods across different biological disciplines, such as cancer research and immunology. While single-cell RNA-sequencing is the most widely used technique to date, several promising methods for single-cell proteomics and single-cell multi-omics are emerging.

Automated platform for plate-based single-cell analysis workflows

Performing high-throughput single-cell analysis on a routine basis requires robust instrumentation. At the same time, this highly dynamic field demands the use of flexible platforms that can accommodate a wide range of different assays. Therefore, we provide an open, robust and automated platform for plate-based single-cell analysis workflows, including single-cell RNA-seq, single-cell genome sequencing, single-cell proteomics, as well as the latest assays for single-cell multi-omics.

Image-based cell isolation

Our single-cell dispensing technology enables label-free cell isolation based on imaging. In addition, cells can be sorted based on fluorescent markers to exclude dead cells or target sub-populations. The cell isolation process is documented by a series of images. These images provide evidence that a single cell was in fact isolated but also document aspects of cell morphology, such as size, roundness or fluorescent intensity. These parameters can then be linked to the library size or the sequencing data.

Cell lysis in sub-microliter liquid volumes

Prerequisites for accurate single-cell analyses and preparation of next generation sequencing (NGS) libraries are the efficient isolation of cells from the bulk sample and their precise depositing into PCR plates. Our single-cell dispensing instruments can be equipped with an automated offset correction (AOC) module to ensure that cells are deposited into the center of each well, allowing for cell lysis in sub-microliter volumes (e.g., 350 nL).

Assay miniaturization

Leverage the I-DOT non-contact liquid handler to miniaturize assays and reduce costs

Automated liquid handling is key for routine single-cell library preparation as it reduces hands-on time and operator bias. The use of non-contact liquid-handling instruments lowers the risk for cross-contamination and saves thousands on pipette tips. Because of expensive reagents and the increasing number of single cells to be analyzed, sub-microliter reagent dispensing is being adopted by more labs. Learn more about performing smart-seq2 and NGS library preparation at 1/10th the volume of a standard reaction using the I-DOT low-volume dispensing technology.

Quantitation and Normalization of NGS libraries

Typically, cDNA amplification from single cells results in uneven concentrations, which may require normalization to ensure an even read distribution for all cells. Hundreds of libraries can be quantitated and normalized within minutes using the I-DOT, which allows for highly multiplexed dispensing of up to 96 reagents in parallel.

Library indexing and early barcoding

The ability to index NGS libraries with unique DNA barcodes provides the basis for high-throughput single-cell sequencing. For single-cell full-length transcript sequencing or whole exome sequencing, individual libraries are usually indexed after amplification and fragmentation. Other RNA-seq protocols, such as CEL-Seq2, make use of early barcoding and pooling of single cells, requiring the addition of hundreds of barcoded primers before reverse transcription. Any cross-contamination between barcode primers has to be avoided, since it would make proper de-multiplexing impossible.

Performing complex tasks at unrivaled speeds

The I-DOT non-contact dispensing technology was developed to perform even the most complex liquid-handling tasks at unrivaled speeds. Up to 2304 libraries can be uniquely barcoded with a single I-DOT source plate. Dispensing 96 unique barcodes takes less than 60 seconds.

Full-length transcriptome sequencing

To date, smart-seq2 and its variations are the most sensitive and popular protocols for single-cell RNA-sequencing. Unlike other methods, smart-seq2 is a plate-based assay that provides full-length transcript coverage, giving access to isoforms, alternative splicing events and mutations.

From single-cell RNA-seq to single-cell proteomics and multi-omics

Our platform for plate-based single-cell workflows is open, versatile and, therefore, compatible with all common single-cell analysis workflows. Our team of experienced application scientists are happy to support you in setting up and optimizing high-throughput single-cell RNA-seq protocols as well as emerging single-cell proteomics and multi-omics assays.

Related application note

Miniaturization and Automation of a Full-length Single-cell RNA-seq Workflow

An introduction to a miniaturized, highthroughput workflow in which single HEK293FT cells were sorted by the f.sight™ into 384-well PCR plates, then libraries were prepared with the I-DOT.

Featured workflow

Sample preparation

Single cell isolation

Library preparation

Sequencing & analysis

Improve efficiency throughout your workflow

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f.sight™

Enables high-throughput single-cell isolation of bacteria, yeast and other small fungi, saving you times and resources.

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b.sight™

Isolate prokaryotic cells in 96 or 384 well plates. Bright field nozzle imaging with 20x magnification. Sort single bacteria for culture, genomics or mass spec.

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I-DOT

A premier solution for noncontact liquid handling tasks. Optimizing your workflow to bring intuitive automation, precision and speed.