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bioRxiv · 10.1101/2025.01.24.634814

ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow

Zhang, D.·Chu, Z.·Huo, Y.·Bai, Z.·Fan, R.·Lu, J.·Gerstein, M.
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Abstract

MotivationDespite significant advances in spatial transcriptomics, the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, which constitute most clinically available samples, remains challenging. Additionally, capturing both coding and noncoding RNAs in a spatial context poses significant challenges. We recently introduced Patho-DBiT, a technology designed to address these unmet needs. However, the marked differences between Patho-DBiT and existing spatial transcriptomics protocols necessitate specialized computational tools for comprehensive whole-transcriptome analysis in FFPE samples. ResultsHere, we present ASTRO, an automated pipeline developed to process spatial transcriptomics data. In addition to supporting standard datasets, ASTRO is optimized for whole-transcriptome analyses of FFPE samples, enabling the detection of various RNA species, including non-coding RNAs such as miRNAs. To compensate for the reduced RNA quality in FFPE tissues, ASTRO incorporates a specialized filtering step and optimizes spatial barcode calling, increasing the mapping rate. These optimizations allow ASTRO to spatially quantify coding and non-coding RNA species in the entire transcriptome and achieve robust performance in FFPE samples. AvailabilityCodes are available at GitHub (https://github.com/gersteinlab/ASTRO).

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Zhang, D., Chu, Z., Huo, Y., Bai, Z., Fan, R., Lu, J., Gerstein, M.. 2025-01-27. ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow. https://doi.org/10.1101/2025.01.24.634814

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