Single-cell technologies have revolutionized our understanding of cellular heterogeneity, enabling the simultaneous profiling of multiple molecular modalities. This review outlines best practices for the comprehensive analysis of single-cell data across different modalities, providing guidance on integrating and interpreting these diverse datasets.
scRNA-seq is the most common single-cell technique, measuring mRNA levels in individual cells. Key steps include:
Tools: Seurat, Scanpy, and Monocle.
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) identifies regions of open chromatin, indicating active regulatory elements. Essential analysis steps include:
Tools: ArchR, snapATAC, and Cicero.
Techniques like CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) and REAP-seq (RNA Expression and Protein Sequencing) measure both RNA and surface protein expression in single cells. Key steps involve:
TCR/BCR Sequencing profiles the diversity of T-cell and B-cell receptors at the single-cell level. This analysis provides insights into immune diversity and clonal expansions. Key steps include:
Tools: Scirpy, scRepertoire, and Immunarch.
Spatial Transcriptomics techniques retain spatial information about gene expression within tissues, providing context to cellular organization. Key analysis steps include:
Tools: Squidpy, SpatialExperiment, and Seurat.
The integration of multiple single-cell modalities is essential for a holistic understanding of cellular functions. Standardized workflows and continuous benchmarking are critical for maintaining data quality and reliability. Future advancements will likely focus on improving the resolution, throughput, and integration capabilities of single-cell technologies, leading to deeper insights into cellular biology and disease mechanisms.
For detailed insights, refer to the full article here. Best practices for single-cell analysis across modalities, Nature Review Genetics, L. Heumos et. al.
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