Sökning: WFRF:(Diamanti Klev 1987 ) >
Single nucleus tran...
Single nucleus transcriptomics data integration recapitulates the major cell types in human liver
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- Diamanti, Klev, 1987- (författare)
- Uppsala universitet,Medicinsk genetik och genomik,Science for Life Laboratory, SciLifeLab
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- Inda Diaz, Juan Salvador, 1984 (författare)
- Uppsala universitet,Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper,Department of Mathematical Sciences,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Raine, Amanda (författare)
- Uppsala universitet,Uppsala University,Chalmers Univ Technol & Univ Gothenburg, Dept Math Sci, Gothenburg, Sweden.
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- Pan, Gang (författare)
- Uppsala universitet,Medicinsk genetik och genomik,Science for Life Laboratory, SciLifeLab
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- Wadelius, Claes, 1955- (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik
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- Cavalli, Marco (författare)
- Uppsala universitet,Medicinsk genetik och genomik,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2020-11-28
- 2021
- Engelska.
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Ingår i: Hepatology Research. - : Wiley. - 1386-6346 .- 1872-034X. ; 51:2, s. 233-238
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Abstract
Ämnesord
Stäng
- Hepatology Research published by John Wiley & Sons Australia, Ltd on behalf of Japan Society of Hepatology Aim: The aim of this study was to explore the benefits of data integration from different platforms for single nucleus transcriptomics profiling to characterize cell populations in human liver. Methods: We generated single-nucleus RNA sequencing data from Chromium 10X Genomics and Drop-seq for a human liver sample. We utilized state of the art bioinformatics tools to undertake a rigorous quality control and to integrate the data into a common space summarizing the gene expression variation from the respective platforms, while accounting for known and unknown confounding factors. Results: Analysis of single nuclei transcriptomes from both 10X and Drop-seq allowed identification of the major liver cell types, while the integrated set obtained enough statistical power to separate a small population of inactive hepatic stellate cells that was not characterized in either of the platforms. Conclusions: Integration of droplet-based single nucleus transcriptomics data enabled identification of a small cluster of inactive hepatic stellate cells that highlights the potential of our approach. We suggest single-nucleus RNA sequencing integrative approaches could be utilized to design larger and cost-effective studies.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi -- Biomedicinsk laboratorievetenskap/teknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology -- Biomedical Laboratory Science/Technology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Gastroenterologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Gastroenterology and Hepatology (hsv//eng)
Nyckelord
- Drop-seq
- data integration
- snRNA-seq
- liver
- 10X
- 10X
- data integration
- Drop-seq
- liver
- snRNA-seq
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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