Transcriptomic analysis of pluripotent stem cells: insights into health and disease

Table 1 Transcriptomic approaches for studying stem cells

Objective	Method	Reference
DNA sequencing	NGS	[65]
mRNA expression analysis	Microarray	[58]
	RNA-seq	[93]
miRNA expression analysis	Microarray	[11]
	RNA-seq	[18]
lncRNA expression analysis	Microarray	[12, 13]
Identification of alternative splicing isoforms	Microarray	[22, 94]
	RNA-seq	[95]
Mapping of protein-DNA binding	ChIP-chip	[9, 10, 24]
	ChIP-PET	[23]
	ChIP-seq	[15]
DNA methylation profiling	BS-seq	[68]
	MethylC-seq	[68]
	DIP-seq	[16]
Mapping of long-range chromatin interactions	ChIA-PET	[17]
	3C	[29]
Identification of RNA-protein interactions	RIP-seq	[19]
	RIP and direct RNA quantification	[14]

BS-seq, bisulfite sequencing; ChIA-PET, chromatin interaction analysis with paired-end tag sequencing; ChIP-chip, chromatin immunoprecipitation on chip; ChIP-PET, chromatin immunoprecipitation with paired-end tag sequencing; ChIP-seq, chromatin immunoprecipitation and sequencing; DIP-seq, DNA immunoprecipitation and sequencing; MethylC-seq, methylcytosine sequencing; NGS, next-generation sequencing; RIP, RNA-binding protein immunoprecipitation; RIP-seq, RNA-binding protein immunoprecipitation and sequencing; RNA-seq, RNA sequencing; 3C, chromosome conformation capture.

ISSN: 1756-994X