Automated Spatial Transcriptomics System for Precise Experiments

Sequential hybridization figures by Lubeck et al. (2014) and Shah et al. (2016)

AUTOMATED FLUIDIC CONTROL IN SPATIAL TRANSCRIPTOMICS

Simple, plug-and-play fluidic automation for merfish, seqfish, and seqfish+

Talk to an expert

Devices for spatial transcriptomics

Ideal pack for your setup of fluorescence in situ hybridization

Simple sequential injection

Switch between solutions quickly using just one flow controller

Automation and integration

Use TTL triggers and SDK to automate customized sequences and synchronize microscopes

Highlights

SPATIAL TRANSCRIPTOMICS SYSTEM

Easily execute your MERFISH/seqFISH/seqFISH+ investigations with this comprehensive, easily navigable, adaptable, and automated spatial transcriptomics package. Compared to syringe pumps, this pack is more affordable, and simple to use because it uses the state-of-the-art OB1 flow controller in conjunction with other Elveflow instruments, such as the selecting valve MUX Distributor, to precisely and automatically dispense tens of dyes, imaging, and washing solutions. The fact that this platform can instantly adjust to the solutions needed for the FISH experiment makes it incredibly adaptable and versatile as well. By drastically lowering the volume of solution used in each experiment, this pack attempts to enable you to do multiplexed fluorescence in situ hybridization at a microfluidic scale, hence reducing the cost of each experiment. It also enhances the reproducibility of outcomes and makes the system suited to automation. A few essential features of this user-friendly microfluidic spatial transcriptomics for MERFISH/seqFISH pack are its fast and simple sequential injection between various solutions, its precise and well-controlled flow rate for a precisely dispensed volume, and its adaptable software for sequence setting and automation with the integrated automation sequencer. With the help of the sequence scheduler, you can simply flow through a multitude of alternatives for your spatial transcriptomics setup. It may also be synchronized with other scientific equipment, such as a fluorescence microscope. For assistance integrating your experiment via TTL triggers or direct software integration via SDK, get in touch with our experts. By utilizing multiple microfluidic chips in parallel or a single microfluidic chip with multiple channels, spatial transcriptomics analysis can be extended even further. In conjunction with flow rate sensors that form a feedback loop with the OB1, the OB1 MK4 flow controller provides pulseless and quick reaction flow control. Our microfluidic platforms have great stability and don’t have any chance of dangerous pressure spikes, making them perfect for long-term research. Spatial transcriptomics is carried out on a microfluidic chip. The chips exhibit transparency, come in various forms and materials, have varying numbers of inlets and outlets, and work with various FISH techniques. With this pack, we can offer several chips with particular channel heights, widths, lengths, and materials. Our all-in-one kit ensures seamless integration between the many instruments, lets you get started with your experiment straight immediately, is controlled by a single piece of software, and has other uses. We also offer complete and ongoing customer assistance to help you achieve the objectives of your trial.

Setup

SPATIAL TRANSCRIPTOMICS SYSTEM SETUP

FLUIDIC SETUP

The pack contains:

OB1 flow controller
Microfluidic flow sensor
One or two 12:1 MUX distribution valves depending of the number of dyes you want to inject
Tubings and luers
Several Eppendorfs or Falcon reservoirs
Microfluidic chips
Microfluidic Software
A user guide

upcoming Microscope Setup

Applications

SPATIAL TRANSCRIPTOMICS SYSTEM Principle

To improve our understanding of complex multicellular biological systems and their interactions, the study of spatially resolved transcriptomes has garnered attention recently [2]. Additionally, Nature Methods has selected it as the 2020 “Method of the Year” [3].

Through molecular and cellular mechanisms, cells are able to perceive their local environment as well as those of their neighbors. For this reason, it is essential to research complicated biological events in order to quantify the phenotypic and genomic states of individual cells in their different spatial placements [4].

For single-cell spatial transcriptomics, two in situ hybridization encoding techniques that involve probe detection are SeqFISH and MERFISH [5]. They are an enhanced form of the smFISH method, which is employed to investigate changes in gene expression and their implications [6]. In recent years, further techniques for obtaining spatially resolved transcriptomes have also been developed at an increasing rate [7].

A initial in situ hybridization using a single pair of fluorescent FISH probes and a labeled dye is required for seqFISH. After then, the fluorophores are eliminated using DNase. The mRNA is labeled with a different dye and hybridized with the same FISH probes. Many genes can be barcoded in a single cell using multiple colors and rounds of hybridization [8].

By combining seqFISH with a confocal microscope, seqFISH has been enhanced to seqFISH+, which may be used for cell spatial and biological process research. 10,000 genes in a single cell were multiplexed and super-resolution imaging was carried out using this [9].

Error Multiplexed By massively parallelizing and simultaneously identifying hundreds to thousands of RNA species with spatial information, Robust Fluorescence In Situ Hybridization (MERFISH) improves upon the single-molecule Fluorescence In Situ Hybridization (smFISH) approach.
Because unassigned binary barcodes can identify problems that can be fixed, this approach is also error-robust. This is the primary distinction between this technique and color-coded seqFISH [10].

There are numerous advantages to using microfluidic platforms and lab-on-a-chip technologies over seqFISH and MERFISH. primarily to shorten the experimentation period, cut down on costs, which can be somewhat significant for these methods, and automate the procedure [11].

References

Shah, Sheel & Lubeck, Eric & Zhou, Wen & Cai, Long. (2016). In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. Neuron. 92. 342-357.
Asp M., Bergenstrahle J., Lundeberg J., Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration, BioEssays, 2020, 42 (10)
Marx, V. Method of the Year: spatially resolved transcriptomics. Nat Methods 18, 9–14 (2021).
Mayr U., Serra D., Liberali P. Exploring single cells in space and time during tissue development, homeostasis and regeneration. Development, 2019, 146(12),
Zhou Y, Jia E, Pan M, Zhao X, Ge Q. Encoding Method of Single-cell Spatial Transcriptomics Sequencing. Int J Biol Sci 2020; 16(14):2663-2674.
Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell. 2008;135:216–226.
Asp, M., Bergenstråhle, J., Lundeberg, J., Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration. BioEssays 2020, 42, 1900221.
Lubeck, E., Coskun, A., Zhiyentayev, T. et al. Single-cell in situ RNA profiling by sequential hybridization. Nat Methods 11, 360–361 (2014).
Eng, CH.L., Lawson, M., Zhu, Q. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature 568, 235–239 (2019).
Moffitt, J R, and X Zhuang. “RNA Imaging with Multiplexed Error-Robust Fluorescence In Situ Hybridization (MERFISH).” Methods in enzymology vol. 572 (2016): 1-49.
Rodriguez-Mateos, P., Azevedo, N.F., Almeida, C. et al. FISH and chips: a review of microfluidic platforms for FISH analysis. Med Microbiol Immunol 209, 373–391 (2020).

Why use it?

uses of microfluidics for fluorecence in situ hybridization

Microfluidics is the most effective way to observe multiple genes and their spatial configuration through MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization) or seqFISH (sequential Fluorescence In Situ Hybridization), as it allows for experimentation with a significantly smaller amount of costly dye and buffer solutions and is compatible with biological applications and microscope observations.

As was already explained, the solutions can be injected into the cell using an automated process. Additionally, the system can be configured to link many chips, making it simple to view multiple samples simultaneously.

Before setting up a fluorescence in situ hybridization system, this pack can also be used in conjunction with other microfluidic procedures; for instance, microfluidic single-cell encapsulation can be used for single-cell isolation [1].

Microfluidics can also be applied to barcoding (DBiT-seq) or the oscillatory flows of diluted probe solutions used in the MA-FISH approach.

Over the course of more than a decade, the Microfluidics Innovation Center acquired competence in microfluidics. It can offer its cutting-edge biological and engineering skills, making it the ideal partner for you as you make the switch to microfluidics.

References

1. Mayr U., Serra D., Liberali P. Exploring single cells in space and time during tissue development, homeostasis and regeneration. Development, 2019, 146(12),

Configuration

Customize your fluidic control in spatial transcriptomics setup

You can easily modify this setup to match the specifications of your experiment and the spatial transcriptomics techniques (MERFISH, seqFISH, etc.). Speak with one of our professionals if you’re unclear which instrument options and settings are best for your needs! The pack can have more pumping channels added for the flow rate sensors and OB1 flow controller. To further enhance flow management, the MFS can be swapped out for Coriolis flow sensors. Cells may have trouble with bubbles; an effective bubble remover can be found in the instrument pack.