Supporting data for "Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation"
Dataset type: Neuroscience, Transcriptomic, Epigenomic
Data released on September 10, 2018
Shang Z; Chen D; Wang Q; Wang S; Deng Q; Wu L; Liu C; Ding X; Wang S; Zhong J; Zhang D; Cai X; Zhu S; Yang H; Liu L; Fink JL; Chen F; Liu X; Gao Z; Xu X (2018): Supporting data for "Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation" GigaScience Database. http://dx.doi.org/10.5524/100496
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 towards commitment to the central nervous system (CNS) 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 same differentiation stages and revealed active cis-regulatory elements for transcription factors known to have a key role in neural differentiation as well as for those that we suggest are also involved. Further, communication network analysis demonstrated that cellular interactions most frequently occurred among embryo body (EB) stage and each cell subpopulation possessed a distinctive spectrum of ligands and receptors associated with neural differentiation, which could reflect the identity of each subpopulation. Our study provides a comprehensive and integrative study of the transcriptomics and epigenetics of human early neural differentiation, which paves the way for a deeper understanding of the regulatory mechanisms driving the differentiation of the neural lineage.
Keywords:
Additional details
Read the peer-reviewed publication(s):
(PubMed: 30239706)
Accessions (data generated as part of this study):
SRA:
SRP155759
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
b10.NPCs_49 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007259 Alternative accession-BioSample:SAMN09722012 ... + |
b10.NPCs_50 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007146 Alternative accession-BioSample:SAMN09722014 ... + |
b10.NPCs_51 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007238 Alternative accession-BioSample:SAMN09722015 ... + |
b10.NPCs_52 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007508 Alternative accession-BioSample:SAMN09722016 ... + |
b10.NPCs_53 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007186 Alternative accession-BioSample:SAMN09722017 ... + |
b10.NPCs_54 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007591 Alternative accession-BioSample:SAMN09722018 ... + |
b10.NPCs_55 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007265 Alternative accession-BioSample:SAMN09722019 ... + |
b10.NPCs_56 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007476 Alternative accession-BioSample:SAMN09722020 ... + |
b10.NPCs_57 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007581 Alternative accession-BioSample:SAMN09722021 ... + |
b10.NPCs_58 | 9606 | Human | human | Homo sapiens | Description:neural progenitor cells (NPCs) derived... Alternative accession-CNGB-Sample:CNS0007445 Alternative accession-BioSample:SAMN09722022 ... + |