Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation

GigaScience
Zhouchun ShangXun Xu

Abstract

Investigating cell fate decision and subpopulation specification in the context of the neural lineage is fundamental to understanding neurogenesis and neurodegenerative diseases. The differentiation process of neural-tube-like rosettes in vitro is representative of neural tube structures, which are composed of radially organized, columnar epithelial cells and give rise to functional neural cells. However, the underlying regulatory network of cell fate commitment during early neural differentiation remains elusive. In this study, we investigated the genome-wide transcriptome profile of single cells from six consecutive reprogramming and neural differentiation time points and identified cellular subpopulations present at each differentiation stage. Based on the inferred reconstructed trajectory and the characteristics of subpopulations contributing the most toward commitment to the central nervous system lineage at each stage during differentiation, we identified putative novel transcription factors in regulating neural differentiation. In addition, we dissected the dynamics of chromatin accessibility at the neural differentiation stages and revealed active cis-regulatory elements for transcription factors known to have a key rol...Continue Reading

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Citations

May 22, 2019·Scientific Data·Chuanyu LiuLongqi Liu
Jul 23, 2020·Proceedings of the National Academy of Sciences of the United States of America·Chia-Chen HsuHua Ye
Jan 29, 2021·World Journal of Stem Cells·Hai-Long LiuShi-Yu Feng
Apr 30, 2021·Neurochemistry International·Emily M A LewisKristen L Kroll
Dec 24, 2021·Advanced Biology·Zida LiYue Shao

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Datasets Mentioned

BETA
SRP155759

Methods Mentioned

BETA
scRNA-seq
dissect
RNA-seq
dissection
PCA

Software Mentioned

HOMER
SOAPnuke
Bowtie2
R package GenomicAlignments
ChIPseeker
hisat2
R package ,
scde
Seurat
Image J

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