Seeker Spatial Transcriptomics Kit
Seeker Spatial Transcriptomics Kits enable whole transcriptome, spatial mapping of fresh frozen tissues at industry-leading resolution. The assay is compatible with your favorite eukaryotic organism and requires no new specialized instrumentation or novel probe sets.
Seeker Spatial Transcriptomics Kits enable whole transcriptome, spatial mapping of fresh frozen tissues at industry-leading resolution. The assay is compatible with your favorite eukaryotic organism and requires no new specialized instrumentation or novel probe sets.
The workflow starts by placing a tissue section on the Seeker tile—a monolayer of tightly-packed, spatially-indexed beads that preserves spatial information. Polyadenylated mRNA is captured and hybridized on the spatially-indexed beads before reverse transcription. The indexed beads are then dissociated from the tile and the tissue digested, followed by second strand synthesis and cDNA amplification. Purified cDNA undergoes NGS library preparation and is sequenced. The Seeker bioinformatics pipeline processes FASTQ files generated from Seeker sequencing libraries into spatial gene expression maps in a single, efficient package.
The pipeline also provides quality control and preliminary cluster and spatial variable gene analyses in a simple .html report for initial data interpretation of the Seeker experiment. Gene-by-bead matrices and spatial coordinates from the pipeline are provided in data formats (.rds, .h5ad, and .mtx) that are compatible with many spatial transcriptomic and single-cell analysis packages published in R and python.
Overview
- Achieve single-cell resolution—A tightly-packed monolayer of beads delivers a continuous view of your region of interest at 10 μm resolution
- Enjoy true unbiased discovery—Analysis is not limited by predetermined targets
- Leverage standard molecular biology techniques—No new specialized instrumentation or microscopy expertise needed
- Enable flexibility across organisms and tissues—Analyze any polyadenylated RNA across a wide array of organisms and tissue types
- Utilize just the size you need—Conveniently offered in 3 mm x 3 mm or 10 mm x 10 mm tile sizes without sacrificing resolution
- Get fast time to results—Multiple tissue samples can be prepared for sequencing in just one day
- Streamline your bioinformatics pipeline workflow—Single, efficient package for generation of spatial gene expression maps
More Information
| Features | Seeker 3x3 kit | Seeker 10x10 kit |
| Plex | Whole transcriptome | |
| Resolution | 10 μm | |
| Special capital equipment | None required | |
| Sample type | Fresh frozen | |
| Analysis software included | Seeker bioinformatics pipeline | |
| Tile size | 3 mm x 3 mm | 10 mm x 10 mm |
| Duration/hands-on time | 8 hr/2.5 hr | 8 hr/2.5 hr |
| Recommended sequencing depth | 400 M | 2 B |
| Required components | Seeker 3x3 Bundle V1.1 Seeker Dual Index Primer Kit v2 |
Seeker 10x10 Bundle Seeker Dual Index Primer Kit v2 Thermal Cycler Adaptor |
| Seeker protocols by application |
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| Application | Protocol | Description | Species compatibility |
| Whole-transcriptome spatial mapping | Seeker 3x3 Bundle V1.1 User Manual | Perform whole-transcriptome spatial mapping with validated protocols | Eukaryotes |
| Seeker 10x10 Bundle V1.1 User Manual | |||
| T-cell receptor (TCR) profiling with whole-transcriptome spatial mapping | Seeker TCR Library Preparation User Guide | Perform whole-transcriptome spatial mapping and TCR profiling with a user-demonstrated protocol. Follow the Seeker TCR Library Preparation User Guide in addition to the appropriate Seeker bundle user manual. | Human and mouse |
| Seeker 3x3 Bundle V1.1 User Manual | |||
| Seeker 10x10 Bundle V1.1 User Manual | |||
Applications
- Cancer biology
- Neuroscience
- Developmental biology
- Immunology
- Study of non-mammalian organisms
Additional product information
Please see the product's Certificate of Analysis for information about storage conditions, product components, and technical specifications. Please see the Kit Components List to determine kit components. Certificates of Analysis and Kit Components Lists are located under the Documents tab.
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Delivering true single-cell spatial omics
Transform standard single-cell genomics data by incorporating a simple spatial transcriptomics kit upstream of your sequencing workflow.
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