Stereo-seq OMNI for FFPE solution

Stereo-seq OMNI Library Preparation User Manual Stereo-seq OMNI Transcriptomics Set User Manual Sample preparation Guide for Stereo-seq OMNI Stereo-seq OMNI Experiment Checklist Stereo-seq OMNI Product Flyer

Solution Overview

Stereo-seq OMNI, a revolutionary sequencing-based spatial transcriptomics solution to study your FFPE samples.
Stereo-seq OMNI provides true spatial single-cell total RNA information with accuracy and precision with the innovative 'Random Probe' design. Covering a continuous tissue area of 10mm by 10mm, Stereo-seq OMNI delivers best-in-class data and bioinformatics workflow for analyzing spatial total RNA information.

Product Highlight

Compatible with low-quality samples (DV200 > 30%)

Random probe design for efficient total RNA capturing

Species agnostic, enabling the study of host-microorganism interactions with spatial context

True single-cell level gene expression profiling combined with histology study

Workflow

Sample Preparation

Stain and image

RNA capture & cDNA synthesis

Library construction

Sequencing

Data analysis & visualization

Sample Preparation

Embed, section, and mount FFPE tissue sections on the Stereo-Chip Slide.

Stereo-seq Sample Preparation, Sectioning and Mounting Guide for Formalin-fixed and Paraffinembedded (FFPE) Samples on Stereo-seq Chip Slides

Guidance on FFPE Sample Sectioning and Mounting

Stain and image

Carry out tissue fixation and stain the tissue using ssDNA dye (nuclei staining, fluorescence), or hematoxylin and eosin (H&E staining, bright field) to visualize the tissue under epi-fluorescence microscopes. An upright microscope is recommended for optimal image generation.

RNA capture & cDNA synthesis

To extract the total RNA from FFPE tissues, the tissue is permeabilized to release RNA from cells, allowing it to bind with random probes and generate cDNA in situ (Stereo-seq Chip N). Each cDNA synthesized at a specific spot (500nm resolution) is attached to its spatially barcoded probe, enabling the subsequent mapping of gene expression within a tissue section after sequencing.

Stereo-seq Transcriptomics Set for FFPE User Manual

Library construction

Construct a whole-transcriptome library by amplifying and purifying the cDNA products obtained from the Stereo-seq OMNI Transcriptomics workflow.

Stereo-seq OMNI FFPE Library Preparation User Manual

Sequencing

Stereo-seq libraries can be sequenced on either DNBSEQ-T7RS or DNBSEQ-G400RS platforms using PE75 Stereo-seq Visualization Reagent set.

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Data analysis & visualization

Run your sequencing data on the Stereo-seq Analysis Workflow (SAW), which involves Linux command line-based pipelines, to map the sequenced reads back to their spatial locations on the tissue section, and then interactively display the results on StereoMap visualization software, a Windows/MacOS compatible desktop application.

Demo Results

Exploring true spatial single-cell total RNA information

with Stereo-seq OMNI

Mouse brain Bin200 clustering
Capture Area size: 1 cm x 1cm
Staining Method: H&E staining

Mouse brain Bin50 gene expression heatmap
Capture Area size: 1 cm x 1cm
Staining Method: H&E staining

Mouse brain H&E Image
Capture Area size: 1 cm x 1cm

Mouse brain single-cell clustering (cellbin)
Capture Area size: 1 cm x 1cm
Staining Method: Nucleus staining

Mouse brain nucleus staining Image
Capture Area size: 1 cm x 1cm

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