BMKMANU S1000 spatial omics chip

Product Overview

BMKMANU S1000 is a subcellular-resolution spatial transcriptomics chip developed by BMKMANU. Based on spatial barcodes on microwell-loaded beads, it captures mRNA molecules from tissue sections. BMKMANU S1000 can be widely applied in life science research including organ development, neuroscience, immune infection, stress response and genetic evolution.

BMKMANU S1000 Advantages

Multi-level Resolution Adjustment

The BMKMANU S1000 spatial transcriptomics chip supports dynamically adjustable resolution from 100 um to 4.8 um.

HE Staining Preserved

The BMKMANU S1000 chip preserves on-slide HE staining; combined with high-resolution spot clustering, it delivers more accurate results.

Flexible Capture Area Customization

The BMKMANU S1000 chip supports flexible customization of 1 to 8 capture areas.

Subcellular Resolution

The average diameter of a mammalian somatic cell is 10 um, whereas the BMKMANU S1000 chip achieves a resolution of 4.8 um, reaching the subcellular level.

Better Compatibility with Nanopore Long-Read Data

Both the correlation of UMI/Gene counts per spot between short-read and long-read data and the t-SNE/UMAP dimensionality reduction clustering show very high consistency. This demonstrates that the BMKMANU S1000-Nanopore full-length transcriptome product can independently perform data demultiplexing and mining analysis without relying on NGS data correction.
Nanopore effectively assigned nearly 50%

Nmuber of Reads	Number of Base	Reads with Valid Barcode	Bases with Valid Barcodes	N50	Bases Mapped to Transcriptome And with Valid Barcode
105,553,898	70,516,281,320	73.85%	73.42%	740	49.55%

UMI counts per spot

Gene counts per spot

Technical Principle

Within a 6.8 mm x 6.8 mm capture area there are about 2.2 million microwells of 2.5 um diameter. Microbeads of 2.5 um diameter coated with oligos (R1 + Spatial Barcode + UMI + poly(dT)VN) are randomly loaded into the microwells to form an array, with a centre-to-centre distance of 4.8 um between adjacent beads. There are 56 million distinct spatial barcodes. The spatial barcode is about 70 bp long, which improves compatibility with long-read sequencing and substantially raises barcode (BC) identification efficiency for Nanopore data.

Workflow

Selected Benchmark Data of BMKMANU S1000

Example 1: Rat Embryo Tissue

BMKMANU S1000 achieves a maximum resolution of 4.8 um, nearly 400 times higher than current mainstream spatial transcriptomics chips. At high resolution, HE-stained tissue morphology aligns more closely with the spot clustering map, enabling more accurate identification of spatial gene expression heterogeneity and region-specific features.

The BMKMANU S1000 spot diameter is 2.5 um, allowing tissue subpopulations to be re-clustered at multiple resolution levels; higher resolution yields more distinct tissue region clusters.

Example 2: BMKMANU S1000-Nanopore Long-Read

Alternative Splicing Analysis

Fusion Gene Analysis

Example 3: BMKMANU S1000 Benchmark Results Across Different Samples

Through continuous R&D and testing, BMKMANU S1000 has completed many sample tests, and the benchmark data show good performance across a wide range of samples.