An Overview of 10X Genomics Platforms
10x Genomics offers a comprehensive suite of solutions tailored for various single-cell and spatial genomics applications. Each product is designed to address specific research objectives, utilizing unique mechanisms and providing specialized features. Below is an overview of these products, detailing their goals, mechanisms, key features, and associated analysis tools.
1. Single Cell Gene Expression
Goal: Analyze transcriptomes at the single-cell level to understand gene expression patterns.
Mechanism: Utilizes microfluidic partitioning to capture individual cells and prepare barcoded cDNA libraries for next-generation sequencing.
- Key Features:
- High-throughput gene expression profiling.
Compatible with Feature Barcoding for protein and CRISPR screening.
- Analysis Tool:
cellranger count
2. Single Cell Immune Profiling
Goal: Profile immune cells by analyzing both gene expression and immune receptor (TCR/BCR) repertoires.
Mechanism: Combines gene expression analysis with V(D)J sequencing to study immune diversity.
- Key Features:
- Simultaneous gene expression and V(D)J sequencing.
Enables clonotype analysis of T and B cells.
- Analysis Tool:
cellranger multi
3. Single Cell ATAC (Assay for Transposase-Accessible Chromatin)
Goal: Identify open chromatin regions to study gene regulation and chromatin accessibility.
Mechanism: Employs transposase enzymes to tag accessible chromatin regions, followed by sequencing.
- Key Features:
- High-resolution chromatin accessibility mapping.
Suitable for studying gene regulatory mechanisms.
- Analysis Tool:
cellranger-atac
4. Single Cell Multiome ATAC + Gene Expression
Goal: Simultaneously assess chromatin accessibility and gene expression within the same cell.
Mechanism: Integrates ATAC and gene expression workflows to provide a multiomic profile.
- Key Features:
- Integrates epigenomic and transcriptomic data.
Provides insights into gene regulation dynamics.
- Analysis Tool:
cellranger-arc
5. Spatial Gene Expression
Goal: Map gene expression within the spatial context of tissue sections.
Mechanism: Combines histological imaging with spatially resolved transcriptomics.
- Key Features:
- Combines histological and transcriptomic data.
Maintains spatial information of gene expression.
- Analysis Tool:
spaceranger
6. Gene Expression with Feature Barcode Technology
Goal: Enhance single-cell RNA sequencing by incorporating additional data types, such as protein expression or sample multiplexing.
Mechanism: Uses oligonucleotide-labeled antibodies or tags to capture additional features alongside gene expression.
- Key Features:
- Measures surface protein expression using Antibody Capture.
- Detects specific CRISPR guide RNAs within cells.
Differentiates between pooled samples using unique oligonucleotide tags.
- Analysis Tool:
cellranger multi
7. Fixed RNA Profiling (Flex)
Goal: Conduct gene expression analysis from fixed samples.
Mechanism: Enables gene expression analysis from chemically fixed samples, preserving RNA integrity for downstream analysis.
- Key Features:
Allows gene expression analysis from fixed samples.
- Analysis Tool:
cellranger multi
The following table summarizes the key aspects of each product:
| Product | Analysis Tool |
|---|---|
| Single Cell Gene Expression | cellranger count |
| Single Cell Immune Profiling | cellranger multi |
| Single Cell ATAC | cellranger-atac |
| Single Cell Multiome ATAC + Gene Expression | cellranger-arc |
| Spatial Gene Expression | spaceranger |
| Gene Expression with Feature Barcode Technology | cellranger multi |
| Fixed RNA Profiling (Flex) | cellranger multi |