Grid-Based Sample Compartmentalization for Spatial Transcriptomics
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Solution Overview
Problem
Current methods for analyzing biological samples, particularly tissues, face challenges in preserving spatial information while achieving single-cell resolution, especially in samples with limited availability and complex cellular compositions, leading to difficulties in accurately mapping cells and understanding cellular processes.
Innovation Solution
A method involving compartmentalization of biological samples using a grid system, where cells are labeled with compartment-specific labels in situ, allowing for high-resolution analysis of molecules while maintaining spatial information, and enabling the reconstruction of cellular organization in 2- and 3-dimensional spaces.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If dissociation of tissue sample is performed to achieve single-cell analysis, then single-cell resolution is improved, but spatial information of cells in the original sample is lost
Solution Approach 1:
The patent applies preliminary compartmentalization of the tissue sample into defined spatial regions before single-cell dissociation and analysis. By pre-defining spatial compartments and assigning unique identifiers to each compartment, the method preserves spatial information throughout the subsequent dissociation and sequencing processes, eliminating the information loss that normally occurs with tissue dissociation.
2Loss of information
If direct labeling of molecules in tissue is performed to preserve spatial information, then spatial information is preserved, but the number of detectable transcripts is limited
Solution Approach 1:
The patent introduces compartment-specific barcodes as an intermediary element that bridges spatial information and transcript detection. Instead of directly labeling molecules in situ with limited detection capacity, the method uses compartment barcodes to tag all transcripts from specific spatial regions, enabling comprehensive transcript detection while preserving spatial information through the barcode associations.
3Loss of information
If computational reconstruction of cellular organization is performed, then spatial information can be recovered, but highly reproducible spatial information from model organisms is required
Solution Approach 1:
The patent performs preliminary assignment of unique spatial identifiers to tissue compartments before any computational reconstruction is needed. This pre-tagging approach eliminates the need for computationally intensive reconstruction algorithms and reference spatial maps from model organisms, making the method directly applicable to human and other non-model tissues without requiring highly reproducible reference spatial information.
4Measurement precision
If compartmentalization with grid and in situ labeling is performed, then spatial information is preserved with single-cell resolution, but sample dissociation and additional processing steps are required
Solution Approach 1:
The patent merges the compartmentalization step with the labeling step by integrating barcode assignment and transcript tagging into a unified workflow. The grid-based compartmentalization is combined with in situ reverse transcription and barcode incorporation, so that spatial region definition and molecular labeling occur together, reducing the number of separate processing steps while maintaining single-cell spatial resolution.
Data Source
AI summary
The present invention relates to a method for analyzing a biological sample on a single cell level by compartmentalizing said sample using a grid and performing an optimized combinatorial indexing protocol within cells of the compartmentalized tissue while deducing cell-specific information regarding the cell identity and activity in the spatial context within the sample.