Nature Communications (Jan 2023)
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
- Reza Mirzazadeh,
- Zaneta Andrusivova,
- Ludvig Larsson,
- Phillip T. Newton,
- Leire Alonso Galicia,
- Xesús M. Abalo,
- Mahtab Avijgan,
- Linda Kvastad,
- Alexandre Denadai-Souza,
- Nathalie Stakenborg,
- Alexandra B. Firsova,
- Alia Shamikh,
- Aleksandra Jurek,
- Niklas Schultz,
- Monica Nistér,
- Christos Samakovlis,
- Guy Boeckxstaens,
- Joakim Lundeberg
Affiliations
- Reza Mirzazadeh
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- Zaneta Andrusivova
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- Phillip T. Newton
- Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden and Astrid Lindgren Children’s Hospital, Karolinska University Hospital
- Leire Alonso Galicia
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- Xesús M. Abalo
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- Mahtab Avijgan
- Department of Women’s and Children’s Health, Karolinska Institute, Solna, Sweden and Astrid Lindgren Children’s Hospital, Karolinska University Hospital
- Linda Kvastad
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- Alexandre Denadai-Souza
- Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven
- Nathalie Stakenborg
- Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven
- Alexandra B. Firsova
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Science for Life Laboratory
- Alia Shamikh
- Department of Oncology-Pathology, Karolinska Institutet
- Aleksandra Jurek
- 10x Genomics
- Niklas Schultz
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital
- Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Karolinska University Hospital
- Christos Samakovlis
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Science for Life Laboratory
- Guy Boeckxstaens
- Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven
- Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory
- DOI
- https://doi.org/10.1038/s41467-023-36071-5
- Journal volume & issue
-
Vol. 14,
no. 1
pp. 1 – 16
Abstract
Spatial transcriptomics relies on RNA quality, which is variable and dependent on sample handling, storage, and/or intrinsic factors. Here, authors present a genome-wide spatial gene expression profiling method called RNA Rescue Spatial Transcriptomics (RRST), designed for the analysis of moderate to low quality fresh frozen tissue samples and demonstrate its robustness on 7 different tissue types.
