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Stereo-seq OMNI Transcriptomics for FFPE Solution V1.1
Unlock the full spatial architecture of your FFPE samples with our enhanced OMNI V1.1 solution.
Stereo-seq Solutions Stereo-seq OMNI Solution Stereo-seq Large Chip Designs Stereo-CITE Solution
Stereo-seq OMNI Transcriptomics FFPE Set V1.1 banner icon for PC
Stereo-seq OMNI Transcriptomics for FFPE Solution V1.1
Unlock the full spatial architecture of your FFPE samples with our enhanced OMNI V1.1 solution.
Stereo-seq Solutions Stereo-seq OMNI Solution Stereo-seq Large Chip Designs Stereo-CITE Solution
Stereo-seq OMNI Transcriptomics FFPE Set V1.1 banner icon for pad
Stereo-seq OMNI Transcriptomics for FFPE Solution V1.1
Unlock the full spatial architecture of your FFPE samples with our enhanced OMNI V1.1 solution.
Stereo-seq Solutions Stereo-seq OMNI Solution Stereo-seq Large Chip Designs Stereo-CITE Solution
Stereo-seq OMNI Transcriptomics FFPE Set V1.1 banner icon for app
STOmics> Products>STOmics Solutions
Solution Overview Product Highlight Demo Data Workflow Demo Result Ordering Information FAQ
Stereo-seq OMNI Transcriptomics FFPE Set V1.1 User Guidance Stereo-seq OMNI Transcriptomics FFPE Set V1.1 Flyer
Solution Overview
Stereo-seq OMNI V1.1 is a revolutionary sequencing-based spatial multi-omics solution specifically designed for Formalin-fixed and Paraffin-embedded (FFPE) samples.
It enables true single-cell level gene expression profiling combined with histology study, providing unparalleled insights for groundbreaking discoveries in biology and clinical translational research. Stereo-seq OMNI delivers best-in-class data and bioinformatics workflow for analyzing spatial whole-transcriptome information.
Solution Overview
Product Highlight
Deeper Insights Per Run
Achieve 1X–3X Higher capture efficiency for richer RNA profiling and deeper biological insights from every run
Preserved Spatial Fidelity
Enhanced tissue diffusion control retains true single-cell resolution while allowing for sample multiplexing
Improved Data Usability
Enhanced data usability of over 100% to efficiently transform data into information within clinical samples.
True Single-Cell Profiling at Scale
Achieve precise spatial single-cell analysis for well-defined tissue annotation and stratification
Demo Data
STOmics Mouse Small Intestine demo data

Mouse Small Intestine

  • Analyze Software Version : SAW V8.2, StereoMap V4.2
  • Bin200 Median MID : 42,496
  • Bin200 Median Gene Type : 7,665
  • Bin20 Median MID : 413
  • Bin20 Median Gene Type : 302
  • Cell Bin Gene Type : 243
  • Cell Bin MID : 312
  • Sequencing Saturation : 72.5%
  • Fraction MID in Spots Under Tissue : 87.88%
Operational Instructions Explore Now

Rat Embryo

  • Analyze Software Version : SAW V8.2, StereoMap V4.2
  • Bin200 Median MID : 22,340
  • Bin200 Median Gene Type : 7,164
  • Bin20 Median MID : 228
  • Bin20 Median Gene Type : 192
  • Cell Bin Gene Type : 173
  • Cell Bin MID : 207
  • Sequencing Saturation : 78.0%

  • Fraction MID in Spots Under Tissue : 87.90%

  • This demo dataset is based on standard SAW results with manual tissue correction and manual Cellbin annotation.

Operational Instructions Explore Now

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.


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.


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


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


Expand All Retract
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.


Ordering Information
Catalog Number 

Catalog Number

 (US use only)

Set Name
Specifications
Version
Description
iShot_2025-12-31_15.06.37


211SN11004
211SN11004-CG
Stereo-seq OMNI Transcriptomics FFPE Set for Chip-on-a-slide (0.5cm*0.5cm) V1.1
4 RXN
V1.1
For generating a spatially-resolved RNA library, available for Formalin-fixed and Paraffin-embedded (FFPE) biological tissue sections.
211SN11114
211SN11114-CG
Stereo-seq OMNI Transcriptomics FFPE Set for Chip-on-a-slide (1cm*1cm) V1.1
4 RXN
V1.1
111KL11160
111KL11160-CG
Stereo-seq 16 Barcode Library Preparation Kit
16 RXN
V1.1
Designed for library preparation of samples using Stereo-seq technology, enables the addition of sample barcodes and library construction.
image-202601051416
301AUX001
301AUX001-CG
Stereo-seq PCR Adaptor
2 EA
/
Compatible with PCR thermal cycler as a heating unit.



FAQ
Q Can we pool Stereo-seq OMNI FFPE V1.1 libraries with Stereo-seq FF V1.3 libraries for sequencing?
A

Yes, the DNB libraries with Stereo-seq OMNI FFPE V1.1 libraries and Stereo-seq FF V1.3 libraries can be pooled on the same FC for sequencing, and the Stereo-seq FF V1.3 libraries are not limited by the chip sizes.

Q Can we use Stereo-seq OMNI Transcriptomics FFPE Set V1.1 along with Stereo-seq 16 Barcode Library Preparation Kit V1.0?
A

No, Stereo-seq 16 Barcode Library Preparation Kit V1.0 is not compatible with OMNI V1.1 solution. Please use OMNI V1.1 with the Stereo-seq 16 Barcode Library Preparation Kit V1.1.

Q Can we mount multiplex samples on one Stereo-seq Chip N Slide for transcriptomics workflow?
A

Yes, multiplex samples mounting on one Stereo-seq Chip N Slide has been tested  internally at STOmics, which can significantly streamline the experiment time and minimize the batch effects. Should you have more concerns, please contact your local FAS.

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