Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

Author:

Mirzazadeh Reza,Andrusivova Zaneta,Larsson LudvigORCID,Newton Phillip T.ORCID,Galicia Leire Alonso,Abalo Xesús M.ORCID,Avijgan Mahtab,Kvastad LindaORCID,Denadai-Souza AlexandreORCID,Stakenborg NathalieORCID,Firsova Alexandra B.,Shamikh Alia,Jurek Aleksandra,Schultz Niklas,Nistér MonicaORCID,Samakovlis Christos,Boeckxstaens GuyORCID,Lundeberg JoakimORCID

Abstract

AbstractSpatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.

Funder

Stiftelsen för Strategisk Forskning

Barncancerfonden

Science for Life Laboratory

Publisher

Springer Science and Business Media LLC

Subject

General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary

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