SeekSpace™ Single Cell Spatial Transcriptome-seq Kit

Single-cell spatial transcriptomics kit for OCT-embedded fresh frozen tissue, combining spatial barcoding with droplet-based single-nucleus sequencing to link gene expression with tissue location.

• Resolve cell-level gene expression while retaining spatial localization from the original tissue section
• Capture mRNA with both Oligo-dT and random primers for broader transcript information
• Integrate spatial labels and transcriptome barcodes through the SeekOne™ DD droplet workflow
• Generate separate transcriptome and spatial barcode libraries compatible with Illumina and GeneMind sequencing platforms
• Support research into tumor microenvironments, developmental mapping, and disease mechanism studies 

Product Details

Single-cell spatial transcriptomics from OCT-embedded tissue sections

The SeekSpace™ Single Cell Spatial Transcriptome-seq Kit is designed for single-cell spatial transcriptomics using tissue sections derived from OCT-embedded samples. The workflow spatially labels nuclei directly in the tissue section, converts the section into a single-nucleus suspension, and then links transcriptome information to positional barcode sequences. The result is a paired single-nucleus transcriptome library and spatial barcode library for downstream spatial analysis.

Spatial chips designed to encode fine tissue-position information

The SeekSpace™ Spatial Chip contains two labeling regions, each measuring 5.5 x 15 mm. Each chip includes approximately 30 million spatial label clusters, with clusters of about 900 nm diameter and approximately 1.5 µm center-to-center spacing. Each spatial label contains an enzymatic cleavage site, TruSeq Read 2 primer sequence, 32 bp spatial barcode, and 30 bp Poly A region.

Combined Oligo-dT and random priming for transcript capture

After spatial labeling and nuclei extraction, preliminary reverse transcription uses multiplex barcodes to label both mRNA and spatial oligos in single nuclei. The primer design includes Oligo-dT primers for Poly A-containing mRNA and spatial label sequences, plus random primers to support more comprehensive mRNA capture. This approach is intended to preserve both expression and positional information before droplet-based single-cell barcoding.

Droplet-based indexing links nuclei, transcripts, and spatial labels

The kit uses the SeekOne™ Digital Droplet platform to generate water-in-oil droplets for high-throughput single-nucleus barcoding. Droplet bead barcodes are bridged with multiplex barcodes, allowing spatial and transcriptome information from the same nucleus to share a linked barcode structure. Decrosslinking, secondary reverse transcription, pre-amplification, and independent library construction then generate transcriptome and spatial barcode libraries.

Complete reagent system for ultrasonic-assisted nuclei extraction workflows

The kit includes the SeekSpace™ sc-Spatial Chip, chip accessories for ultrasonic nuclei extraction, spatial labeling reagents, SeekOne™ DD Chip S3 components, barcoded beads, reverse transcription reagents, sample multiplexing reagents, TSO reagents, barcode ligation reagents, decrosslinking reagents, library amplification reagents, and cleanup reagents. Kit versions labeled “Ultrasonic Nuclei Extraction” are specifically intended for workflows using ultrasonic-assisted nuclei extraction. The user manual states that the kit version should be verified according to the selected workflow.

Research-use workflow for spatial biology, not direct clinical use

The kit is intended for research applications, including tumor microenvironment cell interaction studies, cell development mapping, and investigation of disease occurrence and progression mechanisms. The manufacturer states that results should not be used directly for clinical diagnosis or treatment. Users should also account for potential workflow-related sources of error, including sample and operating conditions, when interpreting data.

Step-by-Step Overview of SeekSpace

True single-nucleus spatial transcriptomics combining spatial localization and gene expression from the same tissue slice.

From Sample to Insight in Seven Steps

What Stories Does the Data Tell?

Turning Spatial Data into Biological Insights

Figure 3: Compatible with Single-Cell Algorithm for advanced visualizationand deeper exploration  of spatial data.

Figure 4: Interactive Spatial Selection & Annotation for cellular distributions and targeted downstream analysis.

More performance data can be found in SeekGene's SeekSpace scRNA-seq Brochure.

SeekOne DD Series Products

Explore the SeekOne™ Digital Droplet System and related products within the SeekOne DD Series Portfolio. For detailed information about the complete range of SeekGene's Multi-Omics Single-Cell Kits please refer to the SeekOne DD Comparison Guide.