mitoSplitter

mitoSplitter demultiplexes pooled single-cell RNA-seq datasets by using mitochondrial RNA (mtRNA) variants to assign cells to their originating samples for downstream analyses.

Key Features:

• Mitochondrial RNA variants utilization: Uses diversity within mitochondrial genomes by extracting and analyzing mtRNA variants to distinguish samples in pooled scRNA-seq datasets.
• Efficiency and scalability: Processes datasets from up to 10 different samples comprising up to 60,000 cells in approximately six hours on modest computational resources.
• Batch effect mitigation: Enables multiplexed analysis of scRNA-seq samples to reduce batch effects arising from separate processing of samples.

Scientific Applications:

• Non-small cell lung cancer drug-response profiling: Applied to study responses of non-small cell lung cancer cell lines to BET (Bromodomain and extraterminal) chemical degradation using pooled scRNA-seq.
• Synthetic lethality identification: Facilitated identification of synthetic lethality between TOP2A inhibition and BET chemical degradation in cells resistant to BET inhibitors.

Methodology:

Extraction and analysis of mtRNA variants from pooled scRNA-seq data to assign cells back to their respective samples.