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.

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.

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.

Key Features

• 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
• Whole-transcriptome spatial mapping: Perform whole-transcriptome spatial mapping with validated protocols (Species compatibility: Eukaryotes)
• T-cell receptor (TCR) profiling with whole-transcriptome spatial mapping: 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. (Species compatibility: Human and mouse)

Applications

• Whole-transcriptome spatial mapping
• T-cell receptor (TCR) profiling with whole-transcriptome spatial mapping

Specifications

Documents

• Seeker 3x3 Bundle V1.1 User Manual [protocol for: Whole-transcriptome spatial mapping; protocol for: T-cell receptor (TCR) profiling with whole-transcriptome spatial mapping]
• Seeker 10x10 Bundle V1.1 User Manual [protocol for: Whole-transcriptome spatial mapping; protocol for: T-cell receptor (TCR) profiling with whole-transcriptome spatial mapping]
• Seeker TCR Library Preparation User Guide [protocol for: T-cell receptor (TCR) profiling with whole-transcriptome spatial mapping]
• Cloud Analysis of Seeker and Trekker Data User Manual [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• Seeker TCR Library Preparation User Guide [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• Secondary Data Analysis Workflow User Guide [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• Seeker 3x3 Bundle V1.1 User Manual [Seeker® 3x3 Bundle V1.1; Seeker® Dual Indexing Primer Kit V2]
• Seeker 10x10 Bundle V1.1 User Manual [Seeker® 10x10 Bundle V1.1]
• Trekker and Seeker Preserving and Sectioning Tissue Protocol-At-A-Glance [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• Bead Wash Buffer SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• cDNA Amp Buffer SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• cDNA Amp Enzyme SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• cDNA Amp Primer Mix SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• CryoCube SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• dNTP SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• Hyb Buffer SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• RNase Inhibitor SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• RT Enzyme SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• RT/SS Buffer SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• Seeker 3x3 Tile V1.1 SDS (EU English) [Seeker® 3x3 Bundle V1.1]
• SS Enzyme SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• SS Primer SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• TC Buffer SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• TC Enzyme SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]
• TE SDS (EU English) [Seeker® 3x3 Bundle V1.1; Seeker® 10x10 Bundle V1.1]

Related Products

• Trekker Single Cell Spatial Mapping Kit