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Spatially resolved ...
Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
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- Mirzazadeh, Reza (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Andrusivova, Zaneta (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Larsson, Ludvig (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Newton, Phillip T (author)
- Karolinska Institutet
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- Galicia, Leire Alonso (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Abalo, Xesús M (author)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Avijgan, Mahtab (author)
- Karolinska Institutet
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- Kvastad, Linda (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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- Denadai-Souza, Alexandre (author)
- Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven, Leuven, Belgium
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- Stakenborg, Nathalie (author)
- Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven, Leuven, Belgium
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- Firsova, Alexandra B. (author)
- Stockholms universitet,Science for Life Laboratory (SciLifeLab),Institutionen för molekylär biovetenskap, Wenner-Grens institut
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- Shamikh, Alia (author)
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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- Jurek, Alexandra (author)
- 10x Genomics, Stockholm, Sweden
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- Schultz, Niklas (author)
- Karolinska Institutet
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- Nistér, Monica (author)
- Karolinska Institutet
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- Samakovlis, Christos, 1962- (author)
- Stockholms universitet,Institutionen för molekylär biovetenskap, Wenner-Grens institut,Science for Life Laboratory (SciLifeLab)
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- Boeckxstaens, Guy (author)
- Department of Chronic Diseases and Metabolism, Katholieke Universiteit te Leuven, Leuven, Belgium
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- Lundeberg, Joakim (author)
- KTH,Science for Life Laboratory, SciLifeLab,Genteknologi
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(creator_code:org_t)
- 2023-01-31
- 2023
- English.
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
- Related links:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Subject headings
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- Spatially 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Annan naturvetenskap (hsv//swe)
- NATURAL SCIENCES -- Other Natural Sciences (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Mirzazadeh, Reza
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Andrusivova, Zan ...
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Larsson, Ludvig
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Newton, Phillip ...
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Galicia, Leire A ...
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Abalo, Xesús M
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show more...
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Avijgan, Mahtab
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Kvastad, Linda
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Denadai-Souza, A ...
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Stakenborg, Nath ...
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Firsova, Alexand ...
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Shamikh, Alia
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Jurek, Alexandra
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Schultz, Niklas
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Nistér, Monica
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Samakovlis, Chri ...
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Boeckxstaens, Gu ...
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Lundeberg, Joaki ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biochemistry and ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Other Natural Sc ...
- Articles in the publication
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Nature Communica ...
- By the university
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Royal Institute of Technology
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Stockholm University
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Karolinska Institutet