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The spatial RNA int...
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
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- Kvastad, Linda (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Carlberg, Konstantin (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Larsson, Ludvig (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Villacampa, Eva Gracia (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Stuckey, Alexander (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Stenbeck, Linnea (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Mollbrink, Annelie (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Zamboni, Margherita (author)
- Karolinska Institutet,Karolinska Institute
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- Magnusson, Jens Peter (author)
- Karolinska Institutet,Karolinska Institute,Stanford University
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- Basmaci, Elisa (author)
- Karolinska Institutet,Karolinska Institute,Karolinska University Hospital
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- Shamikh, Alia (author)
- Karolinska Institutet,Karolinska Institute,Karolinska University Hospital
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- Prochazka, Gabriela (author)
- Karolinska Institutet,Karolinska Institute,Karolinska University Hospital
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- Schaupp, Anna-Lena (author)
- Univ Oxford, Oxford Ctr Neuroinflammat, John Radcliffe Hosp,Weatherall Inst Mol Med, Nuffield Dept Clin Neurosci,MRC Human Immunol Uni, Oxford, England.,University of Oxford
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- Borg, Åke (author)
- Lund University,Lunds universitet,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments
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- Fugger, Lars (author)
- Univ Oxford, Oxford Ctr Neuroinflammat, John Radcliffe Hosp,Weatherall Inst Mol Med, Nuffield Dept Clin Neurosci,MRC Human Immunol Uni, Oxford, England.,University of Oxford
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- Nister, Monica (author)
- Karolinska Institutet,Karolinska Institute,Karolinska University Hospital
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- Lundeberg, Joakim (author)
- KTH Royal Institute of Technology,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2021-01-08
- 2021
- English.
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In: Communications Biology. - : Springer Nature. - 2399-3642. ; 4:1
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Abstract
Subject headings
Close
- The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows. Kvastad et al. develop the spatial RNA Integrity Number (sRIN) assay that evaluates the RNA integrity at cellular resolution. This method improves the resolution of a similar method called the RNA Integrity Number (RIN), demonstrating spatial variation in the quality of RNA samples.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Kvastad, Linda
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Carlberg, Konsta ...
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Larsson, Ludvig
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Villacampa, Eva ...
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Stuckey, Alexand ...
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Stenbeck, Linnea
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show more...
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Mollbrink, Annel ...
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Zamboni, Margher ...
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Magnusson, Jens ...
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Basmaci, Elisa
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Shamikh, Alia
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Prochazka, Gabri ...
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Schaupp, Anna-Le ...
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Borg, Åke
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Fugger, Lars
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Nister, Monica
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Lundeberg, Joaki ...
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show less...
- 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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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Cell and Molecul ...
- Articles in the publication
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Communications B ...
- By the university
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Royal Institute of Technology
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Lund University
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Karolinska Institutet