Supporting data for "Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation"

Dataset type: Epigenomic, Transcriptomic, Neuroscience
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

DOI10.5524/100496

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.

Additional details

Read the peer-reviewed publication(s):

Shang, Z., Chen, D., Wang, Q., Wang, S., Deng, Q., Wu, L., … Xu, X. (2018). Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation. GigaScience. doi:10.1093/gigascience/giy117

Accessions (data included in GigaDB):

SRA: SRP155759





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
b10.NPCs_499606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007259
Alternative accession-BioSample:SAMN09722012
...
+
b10.NPCs_509606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007146
Alternative accession-BioSample:SAMN09722014
...
+
b10.NPCs_519606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007238
Alternative accession-BioSample:SAMN09722015
...
+
b10.NPCs_529606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007508
Alternative accession-BioSample:SAMN09722016
...
+
b10.NPCs_539606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007186
Alternative accession-BioSample:SAMN09722017
...
+
b10.NPCs_549606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007591
Alternative accession-BioSample:SAMN09722018
...
+
b10.NPCs_559606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007265
Alternative accession-BioSample:SAMN09722019
...
+
b10.NPCs_569606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007476
Alternative accession-BioSample:SAMN09722020
...
+
b10.NPCs_579606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007581
Alternative accession-BioSample:SAMN09722021
...
+
b10.NPCs_589606HumanhumanHomo sapiens Description:neural progenitor cells (NPCs) derived...
Alternative accession-CNSA_sample:CNS0007445
Alternative accession-BioSample:SAMN09722022
...
+
Displaying 1-10 of 547 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherTAR37.05 GB2018-08-24
scriptUNKNOWN2.06 KB2018-08-24
transcriptome sequenceTAR30.64 GB2018-08-24
scriptUNKNOWN0.35 KB2018-08-24
imageJPG98.37 KB2018-08-24
TextTEXT1.66 MB2018-08-24
imageTIF49.44 MB2018-08-24
imageTIF49.44 MB2018-08-24
imageTIF5.49 MB2018-08-24
imageTIF5.49 MB2018-08-24
Displaying 1-10 of 98 File(s).
Funding body Awardee Award ID Comments
Ministry of Science and Technology (MOST) Z Gao 2017YFA0104100 National Key R&D Program of China
China Postdoctoral Science Foundation D Chen 2017M622795 Transcriptome analysis of mesenchymal stem cells (MSCs) functional subgroups at the single-cell level
Science, Technology and Innovation Commission of Shenzhen Municipality L Wu CXB201108250094A Shenzhen Key Laboratory of Neurogenomics
Development and Reform Commission of Shenzhen Municipality Z Shang DRC-SZ [2016] 884 Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics

Protocols.io:

Date Action
September 10, 2018 Dataset publish
November 3, 2018 Manuscript Link added : 10.1093/gigascience/giy117