Transcriptomics Large Chip Design

Stereo-seq Large Chip Designs Product Note Stereo-seq Transcritpomics 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) pioneers the whole transcriptome study for entire tissue sections. Stereo-seq for Large Chip Designs is firstly offered to the market - 1cm x 2cm, 2cm x 2cm, 2cm x 3cm. Compatible for all species (FF samples), it enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view.

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

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

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

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.

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

The mandible, spine, ribs, pelvis, and long bones in the mouse embryo primarily undergo endochondral ossification, which is also the fundamental process underlying fracture healing. In this process, chondrocytes first proliferate, enlarge (hypertrophy), and eventually undergo apoptosis, after which they are replaced by bone tissue.

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More Results

Robust whole-organ and large tissue profiling with single cell resolution

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

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
111KL160	111KL160-CG	Stereo-seq 16 Barcode Library Preparation Kit	16 RXN	V1.0	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?

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)?

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?

Yes, the DNB libraries of V1.3 different sized chips can be pooled on the same FC for sequencing.

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