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bioRxiv · 10.1101/2025.09.03.673925

BLASE: Bulk Linkage Analysis for Single Cell Experiments - Teasing Out the Secrets of Bulk Transcriptomics with Trajectory Analysis

McCluskey, A.·Kettlewell, T.·Smith, A. M.·Kundu, R.·Gunn, D. A.·Otto, T. D.
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Abstract

1MotivationscRNA-seq experiments can capture cell process trajectories. Bulk RNA-seq is more practical, however does not have the granularity to elucidate cell-type specific trajectories. Deconvolution methods can estimate cell-types in RNA-seq data, but there is a need for methods characterising their pseudotime. ResultsWe show that our method, BLASE, can identify the progress of an RNA-seq sample through a trajectory in a scRNA-seq reference. ConclusionBLASE can be used to a) annotate scRNA-seq data from existing RNA-seq, b) identify progress of RNA-seq data through a process based on scRNA-seq data, and c) be used to correct developmental differences in RNA-seq differential expression analysis.

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McCluskey, A., Kettlewell, T., Smith, A. M., Kundu, R., Gunn, D. A., Otto, T. D.. 2025-09-07. BLASE: Bulk Linkage Analysis for Single Cell Experiments - Teasing Out the Secrets of Bulk Transcriptomics with Trajectory Analysis. https://doi.org/10.1101/2025.09.03.673925

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