Transcriptomics Large Chip Design

Stereo-seq Large Chip Designs Product Note Stereo-seq Transcriptomics Set for Large Chip Designs User Manual Stereo-seq Permeabilization Set for Large Chip Designs User Manual

Solution Overview

STOmics Stereo-seq Transcriptomics for Large Chip Designs (LCD) pioneered whole-transcriptome analysis of entire tissue sections and was first offered to the market in 1 × 2 cm, 2 × 2 cm, and 2 × 3 cm standard formats.This species-agnostic tissue-to-data solution supports large-area transcriptomics for fresh frozen samples, combining large-area spatial sequencing with in situ capture of the polyadenylated whole transcriptome at nanoscale resolution. For exceptional requirements, customized configurations up to 13 × 13 cm may support decimeter-scale spatial transcriptomics, subject to project design, laboratory equipment, and regional support agreements.Within the STOmics portfolio, LCD is STOmics’ largest spatial omics solution; customized availability must be confirmed for each project.

Product Highlight

Broad capturing area

Larger capture area with chip sizes up to 2cm by 3cm without compromising the capture efficiency

Species-agnostic

Unlimited by species and tissue types, compatible with fresh frozen samples

High-throughput and scalability

Large capture areas enhance high-throughput studies by profiling multiple co-embedded tissue sections in parallel, increasing experimental efficiency

Whole transcriptome profiling

Unbiased in situ capturing of the whole transcriptome with true nanoscale resolution

Publication

Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex

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Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex

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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

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Demo Case

Unlock Multi-Organ Insights within a Single Section with Stereo-seq Large Chip Designs

Stereo-seq Large Chip Design Solution enables the simultaneous detection of multiple organs within a single section, as well as precisely identifying different cell types within individual organ.

In a single sagittal section of an E18.5 mouse embryo on a 1 × 2 cm chip, Stereo-seq Large Chip Designs captures the spatial context of multiple organs while supporting refined cell-type analysis within individual structures. The example spans the brain, liver, kidney, inner ear, submandibular gland, lung, and gastrointestinal tract.

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High fidelity spatial profiling of stage-specific ossification across skeletal structures

Across the mandible, spine, ribs, pelvis, and long bones of the mouse embryo, spatial profiling reveals the progression of endochondral ossification. Chondrocytes proliferate, enlarge through hypertrophy, undergo apoptosis, and are subsequently replaced by bone tissue, allowing stage-specific changes to be compared across skeletal structures.

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Whole-Organ Spatial Sequencing Across Large Tissues

Review large-tissue spatial omics results with single-cell resolution across human, rat, mouse, and macaque samples. Each card reports sample-specific capture area, RNA quality, sequencing depth, saturation, and median gene-type detection and should be interpreted within that sample context.

Human renal carcinoma PT1
Capture area size: 2cm x 3cm
RIN: 7.8
Total reads: 4.1B
Sequencing saturation: 32.6%
Median gene type counts per cellbin: 188

Human prostate
Capture area size: 2cm x 3cm
RIN: /
Total reads: 4.1B
Sequencing saturation: 15.3%
Median gene type counts per cellbin: 174

Rat hemisphere 2
Capture area size: 2cm x 3cm
RIN: 8.1
Total reads: 1.5B
Sequencing saturation: 31.1%
Median gene type counts per cellbin: 145

Mouse embryo E16.5
Capture area size: 1cm x 2cm
RIN: 8.1
Total reads: 3.6B
Sequencing saturation: 63.8%
Median gene type counts per cellbin: 284

Macaque brain RM-9A
Capture area size: 1cm x 2cm
RIN: 6.3
Total reads: 2.3B
Sequencing saturation: 51.6%
Median gene type counts per cellbin: 567

Rat whole brain
Capture area size: 1cm x 2cm
RIN: 8.4
Total reads: 2.1B
Sequencing saturation: 61.3%
Median gene type counts per cellbin: 607

Human renal carcinoma LCC
Capture area size: 2cm x 2cm
RIN: 5.7
Total reads: 3.8B
Sequencing saturation: 64%
Median gene type counts per cellbin: 166

Rat hemisphere 1
Capture area size: 2cm x 2cm
RIN: 8.2
Total reads: 4.2B
Sequencing saturation: 36.8%
Median gene type counts per cellbin: 726

Macaque brain RM-8A
Capture area size: 2cm x 2cm
RIN: 7.5
Total reads: 3.6B
Sequencing saturation: 16.4%
Median gene type counts per cellbin: 382

Demo Data

Mouse Embryo

Chip size: 1 cm x 2 cm
Analyze Software Version : SAW V8.1, StereoMap V4.1
Bin200 Median MID : 82,562
Bin200 Median Gene Type : 10,952
Bin20 Median MID : 832
Bin20 Median Gene Type : 593
Cell Bin Gene Type : 433
Cell Bin MID : 569
Sequencing Saturation : 13.20%
Fraction MID in Spots Under Tissue : 88.23%

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Rat Brain

Chip size: 2 cm x 3 cm
Analyze Software Version : SAW V7.0, StereoMap V3.0
Bin200 Median MID : 68,103
Bin200 Median Gene Type : 8,217
Cell Bin Gene Type : 514
Cell Bin MID : 1,031
Sequencing Saturation : 93.60%
Fraction MID in Spots Under Tissue : 84.60%

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Workflow

Sample Preparation

Stain and image

mRNA capture & cDNA synthesis

Library Construction

Sequencing

Data analysis & visualization

Sample Preparation

Embed, section, and mount fresh frozen tissue sections on the Stereo-seq Chips (1cm x 2cm, 2cm x 2cm and 2cm x 3cm)

Stereo-seq Sample Preparation Guide for Fresh Frozen Samples on Stereo-seq Chip Slides

Stain and image

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

mRNA capture & cDNA synthesis

To extract mRNA from fresh frozen tissue, the tissue undergoes permeabilization. This process enables mRNA to bind to DNB-patterned array chips (Stereo-seq Chip T) that are preloaded with spatially-barcoded probes designed to capture and prime poly-adenylated mRNA from the tissue. 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 Large Chip T Experiment Operational Guide

Library Construction

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

Stereo-seq Transcriptomics FF 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.

Ordering Information

Catalog Number	Catalog Number (US use only)	Set Name	Specifications	Version	Description
111SP11124	111SP11124-CG	Stereo-seq Permeabilization Set (1cm * 2cm)	4 RXN	V1.1	For determining permeabilization parameters to optimize mRNA capture
111ST13122	111ST13122-CG	Stereo-seq Transcriptomics Set (1cm * 2cm)	2 RXN	V1.3	For generating a spatially-resolved 3' mRNA library from biological tissue sections
111SP11224	111SP11224-CG	Stereo-seq Permeabilization Set (2cm * 2cm)	4 RXN	V1.1	For determining permeabilization parameters to optimize mRNA capture
111ST13221	111ST13221-CG	Stereo-seq Transcriptomics Set (2cm * 2cm)	1 RXN	V1.3	For generating a spatially-resolved 3' mRNA library from biological tissue sections
111SP11234	111SP11234-CG	Stereo-seq Permeabilization Set (2cm * 3cm)	4 RXN	V1.1	For determining permeabilization parameters to optimize mRNA capture
111ST13231	111ST13231-CG	Stereo-seq Transcriptomics Set (2cm * 3cm)	1 RXN	V1.3	For generating a spatially-resolved 3' mRNA library from biological tissue sections
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.

FAQ

Q Is the large design (LCD) chips only available for fresh frozen samples and not for Formalin-Fixed Paraffin-Embedded (FFPE) samples?

A

Yes, currently only FF V1.3 solution has the LCD format. LCD format for FFPE samples are still in the R&D pipeline and will be released with the next major upgrade of OMNI solution.

Q Why the RIN Value Requirements for Large Design is higher (≥6) than the standard size(≥4)?

A

The recommended RIN value is derived from R&D tested results. Handling large tissue sections can pose challenges during various experimental steps, such as sample embedding and sectioning. To achieve optimal results, a higher RNA transcript quality standard was recommended for large tissue sections on LCD.

Q Can we pool LCD libraries (1cm x 2cm, 2cm x 2cm, 2cm x 3cm) with regular Stereo-seq V1.3 libraries for sequencing?

A

Yes, the DNB libraries of V1.3 different sized chips can be pooled on the same FC for sequencing. (View More Stereo-seq FAQs)