Single nucleus transcriptomics data integration recapitulates the major cell types in human liver.
10X
Drop-seq
data integration
liver
snRNA-seq
Journal
Hepatology research : the official journal of the Japan Society of Hepatology
ISSN: 1386-6346
Titre abrégé: Hepatol Res
Pays: Netherlands
ID NLM: 9711801
Informations de publication
Date de publication:
Feb 2021
Feb 2021
Historique:
received:
17
08
2020
revised:
02
10
2020
accepted:
20
10
2020
pubmed:
30
10
2020
medline:
30
10
2020
entrez:
29
10
2020
Statut:
ppublish
Résumé
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. 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. 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. 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.
Types de publication
Journal Article
Langues
eng
Pagination
233-238Subventions
Organisme : AstraZeneca
Organisme : Diabetesförbundet
Organisme : Exodiab
Organisme : Science for Life Laboratory
Informations de copyright
© 2020 The Authors. Hepatology Research published by John Wiley & Sons Australia, Ltd on behalf of Japan Society of Hepatology.
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