Wave-Crest

Wave-Crest reconstructs gene expression trajectories from single-cell RNA sequencing (scRNA-seq) data to resolve temporal differentiation programs such as the transition from pluripotent states through mesendoderm to definitive endoderm (DE).

Key Features:

• Trajectory Reconstruction: Maps differentiation trajectories across ordered conditions, including transitions from pluripotent human embryonic stem cell-derived progenitors through mesendoderm to definitive endoderm.
• Stage-Specific Gene Identification: Identifies genes specific to particular differentiation stages in conjunction with the SCPattern statistical approach.
• Single-Cell Resolution Analysis: Analyzes single-cell RNA-seq data at single-cell resolution, demonstrated on 1776 cells from distinct progenitor states to capture heterogeneity and transitional phases.
• Application to Human Embryonic Lineage Specification: Applied to study pluripotent human embryonic stem cell differentiation toward definitive endoderm, revealing a critical time window where hypoxia enhances DE differentiation.
• Integration with Genetic Approaches: Combined with genetic validation strategies such as CRISPR/Cas9-engineered T-2A-EGFP knock-in reporters to functionally validate regulators, exemplified by KLF8.

Scientific Applications:

• Developmental Biology: Reconstruction of lineage trajectories and temporal gene expression during human embryonic lineage specification from pluripotency to definitive endoderm.
• Regulator Discovery and Validation: Identification of stage-specific regulators and pathways and functional validation using CRISPR/Cas9 T-2A-EGFP knock-in reporters, including discovery of regulators such as KLF8.
• General Single-Cell Trajectory Mapping: Mapping temporal gene expression changes in systems that require precise trajectory reconstruction from scRNA-seq data, including analysis of environmental effects such as hypoxia on differentiation.

Methodology:

Statistical reconstruction of trajectories from ordered scRNA-seq conditions and stage-specific gene identification performed in conjunction with SCPattern.