Effects of Sample Size on Plant Single-Cell RNA Profiling.
Curr Issues Mol Biol
; 43(3): 1685-1697, 2021 Oct 20.
Article
en En
| MEDLINE
| ID: mdl-34698115
Single-cell RNA (scRNA) profiling or scRNA-sequencing (scRNA-seq) makes it possible to parallelly investigate diverse molecular features of multiple types of cells in a given plant tissue and discover cell developmental processes. In this study, we evaluated the effects of sample size (i.e., cell number) on the outcome of single-cell transcriptome analysis by sampling different numbers of cells from a pool of ~57,000 Arabidopsis thaliana root cells integrated from five published studies. Our results indicated that the most significant principal components could be achieved when 20,000-30,000 cells were sampled, a relatively high reliability of cell clustering could be achieved by using ~20,000 cells with little further improvement by using more cells, 96% of the differentially expressed genes could be successfully identified with no more than 20,000 cells, and a relatively stable pseudotime could be estimated in the subsample with 5000 cells. Finally, our results provide a general guide for optimizing sample size to be used in plant scRNA-seq studies.
Palabras clave
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
ARN de Planta
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Perfilación de la Expresión Génica
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Análisis de la Célula Individual
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Transcriptoma
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Curr Issues Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2021
Tipo del documento:
Article
País de afiliación:
China