scTE

scTE quantifies transposable element (TE) expression and chromatin accessibility in single-cell sequencing datasets to reveal TE contributions to cellular heterogeneity and developmental regulation.

Key Features:

• Genome Indexing for Alignment: Builds genome indices that enable rapid alignment of sequencing reads specifically to genes and transposable elements (TEs).
• Single-Cell TE Expression Analysis: Quantifies TE expression at single-cell resolution from single-cell RNA-seq data to profile TE activity across individual cells.
• Dynamic Regulation Insights: Identifies dynamic regulation of specific TE types during processes such as pluripotency reprogramming, differentiation, and embryogenesis, including TEs expressed in subpopulations of embryonic stem cells.
• Expression in Somatic Cells: Detects TE expression in somatic cells, including disease-specific TEs that may be undetectable in bulk analyses.
• Application to Single-Cell ATAC-seq Data: Uses TE chromatin accessibility in single-cell ATAC-seq to discriminate between cell types.

Scientific Applications:

• Exploration of Cell Heterogeneity: Classifies dynamic TE expression patterns across single cells to investigate contributions of TEs to cellular heterogeneity.
• Developmental Biology Studies: Tracks TE expression and regulation during embryogenesis and stem cell differentiation to study developmental processes.
• Disease Research: Identifies disease-associated TEs in single cells to support investigations of molecular mechanisms in disease contexts.

Methodology:

Builds genome indices and aligns sequencing reads specifically to genes and TEs; processes single-cell sequencing data with emphasis on TE expression; integrates genome indexing and alignment techniques optimized for both gene-centric and TE-centric analyses; applies TE chromatin accessibility analysis to single-cell ATAC-seq data.